From 1e05a6a60173767a8d3250a065deb508f9be5900 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 29 Nov 2013 14:43:38 +0100 Subject: [PATCH 001/911] add FSA, PRANK & SMALT, coming from LCSB experimenters Signed-off-by: Fotis Georgatos --- .../f/FSA/FSA-1.15.8-goolf-1.4.10.eb | 33 +++++++++++++++++ .../f/FSA/FSA-1.15.8-ictce-5.3.0.eb | 33 +++++++++++++++++ .../p/PRANK/PRANK-130820-goolf-1.4.10.eb | 34 +++++++++++++++++ .../p/PRANK/PRANK-130820-ictce-5.3.0.eb | 34 +++++++++++++++++ .../s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb | 37 +++++++++++++++++++ .../s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb | 37 +++++++++++++++++++ .../s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 30 +++++++++++++++ .../s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 30 +++++++++++++++ 8 files changed, 268 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb new file mode 100644 index 0000000000..af8b162d43 --- /dev/null +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = "FSA" +version = "1.15.8" + +homepage = "http://fsa.sourceforge.net" +description = """FSA is a probabilistic multiple sequence alignment algorithm + which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["http://downloads.sourceforge.net/project/fsa/"] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('MUMmer', '3.23')] + +sanity_check_paths = { + 'files': ["bin/fsa"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb new file mode 100644 index 0000000000..ea38265ab5 --- /dev/null +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = "FSA" +version = "1.15.8" + +homepage = "http://fsa.sourceforge.net" +description = """FSA is a probabilistic multiple sequence alignment algorithm + which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["http://downloads.sourceforge.net/project/fsa/"] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('MUMmer', '3.23')] + +sanity_check_paths = { + 'files': ["bin/fsa"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb new file mode 100644 index 0000000000..c594c6b15f --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = "Tarball" + +name = "PRANK" +version = "130820" + +homepage = "http://code.google.com/p/prank-msa/" +description = """PRANK is a probabilistic multiple alignment program for DNA, codon + and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions + correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["http://prank-msa.googlecode.com/files"] +sources = ["prank.linux64.%(version)s.tgz"] + +sanity_check_paths = { + 'files': ["bin/prank", "bin/exonerate"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb new file mode 100644 index 0000000000..97c62af4ac --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = "Tarball" + +name = "PRANK" +version = "130820" + +homepage = "http://code.google.com/p/prank-msa/" +description = """PRANK is a probabilistic multiple alignment program for DNA, codon + and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions + correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["http://prank-msa.googlecode.com/files"] +sources = ["prank.linux64.%(version)s.tgz"] + +sanity_check_paths = { + 'files': ["bin/prank", "bin/exonerate"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..0beeeb58ca --- /dev/null +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = "Tarball" + +name = "SMALT" +version = "0.7.4" + +homepage = "http://www.sanger.ac.uk/resources/software/smalt/" +description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt"] +sources = [SOURCELOWER_TGZ] + +sanity_check_paths = { + 'files': ["smalt_x86_64"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': '', + 'MANPATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..45ed75c381 --- /dev/null +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = "Tarball" + +name = "SMALT" +version = "0.7.4" + +homepage = "http://www.sanger.ac.uk/resources/software/smalt/" +description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ["ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt"] +sources = [SOURCELOWER_TGZ] + +sanity_check_paths = { + 'files': ["smalt_x86_64"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': '', + 'MANPATH': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..bb9980bc8d --- /dev/null +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = "SMALT" +version = "0.7.5" + +homepage = "http://www.sanger.ac.uk/resources/software/smalt/" +description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/smalt"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb new file mode 100644 index 0000000000..7ffae18045 --- /dev/null +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = "SMALT" +version = "0.7.5" + +homepage = "http://www.sanger.ac.uk/resources/software/smalt/" +description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/smalt"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 909b8db982b707f095541936b7fa5c6a4308d7fc Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 21:41:44 +0100 Subject: [PATCH 002/911] init Infernal 1.1 Signed-off-by: Fotis Georgatos --- .../Infernal-1.1-goalf-1.1.0-no-OFED.eb | 32 ++++++++++++++++++ .../i/Infernal/Infernal-1.1-goolf-1.4.10.eb | 31 +++++++++++++++++ .../i/Infernal/Infernal-1.1-ictce-4.0.6.eb | 32 ++++++++++++++++++ .../i/Infernal/Infernal-1.1-ictce-5.3.0.eb | 33 +++++++++++++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..a627129670 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Infernal' +version = "1.1" + +homepage = 'http://infernal.janelia.org/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'fetch', 'press', 'scan', 'search', 'stat']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..42496c9448 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Infernal' +version = "1.1" + +homepage = 'http://infernal.janelia.org/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +for RNA structure and sequence similarities.""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'fetch', 'press', 'scan', 'search', 'stat']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb new file mode 100644 index 0000000000..4b60b1026c --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Infernal' +version = "1.1" + +homepage = 'http://infernal.janelia.org/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'fetch', 'press', 'scan', 'search', 'stat']], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..eaa4b42f4a --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Infernal' +version = "1.1" + +homepage = 'http://infernal.janelia.org/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', + 'fetch', 'press', 'scan', 'search', 'stat']], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From f43403794ecc13c3acd18d70a16b1a51310016bf Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 03:17:55 +0100 Subject: [PATCH 003/911] fix Infernal source_urls with templating Signed-off-by: Fotis Georgatos --- .../i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb | 5 +++-- easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb | 3 +-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb index a627129670..766222f0f1 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb index 42496c9448..b9331ab8e9 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -15,12 +15,13 @@ version = "1.1" homepage = 'http://infernal.janelia.org/' description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases -for RNA structure and sequence similarities.""" + for RNA structure and sequence similarities.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb index 4b60b1026c..e64ab0b0d9 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb index eaa4b42f4a..2aaa4dd946 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -17,12 +17,11 @@ homepage = 'http://infernal.janelia.org/' description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', -- GitLab From 5232769fa7638639e9dc82de47cb82e33f8124bd Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 03:23:10 +0100 Subject: [PATCH 004/911] adjust PRANK Signed-off-by: Fotis Georgatos --- .../p/PRANK/PRANK-130820-goolf-1.4.10.eb | 17 ++++++++++++----- .../p/PRANK/PRANK-130820-ictce-5.3.0.eb | 17 ++++++++++++----- 2 files changed, 24 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb index c594c6b15f..e1d713088e 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb @@ -10,21 +10,28 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## -easyblock = "Tarball" +easyblock = 'MakeCp' name = "PRANK" version = "130820" homepage = "http://code.google.com/p/prank-msa/" -description = """PRANK is a probabilistic multiple alignment program for DNA, codon - and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions - correctly and avoids over-estimation of the number of deletion events.""" +description = """PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True} source_urls = ["http://prank-msa.googlecode.com/files"] -sources = ["prank.linux64.%(version)s.tgz"] +sources = ['%(namelower)s.source.%(version)s.tgz'] + +# PRANK uses MAFFT as external tool to contruct guide tree +dependencies = [('MAFFT', '7.130')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] sanity_check_paths = { 'files': ["bin/prank", "bin/exonerate"], diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb index 97c62af4ac..9f531219a1 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb @@ -10,21 +10,28 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## -easyblock = "Tarball" +easyblock = 'MakeCp' name = "PRANK" version = "130820" homepage = "http://code.google.com/p/prank-msa/" -description = """PRANK is a probabilistic multiple alignment program for DNA, codon - and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions - correctly and avoids over-estimation of the number of deletion events.""" +description = """PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True} source_urls = ["http://prank-msa.googlecode.com/files"] -sources = ["prank.linux64.%(version)s.tgz"] +sources = ['%(namelower)s.source.%(version)s.tgz'] + +# PRANK uses MAFFT as external tool to contruct guide tree +dependencies = [('MAFFT', '7.130')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] sanity_check_paths = { 'files': ["bin/prank", "bin/exonerate"], -- GitLab From 772c4dce427557ecc80aa769756947bd807cafd5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 03:38:14 +0100 Subject: [PATCH 005/911] add MAFFT for PRANK, make sure it's used Signed-off-by: Fotis Georgatos --- ...MAFFT-7.130-with-extensions-ictce-5.3.0.eb | 32 +++++++++++++++++++ .../p/PRANK/PRANK-130820-goolf-1.4.10.eb | 4 +-- .../p/PRANK/PRANK-130820-ictce-5.3.0.eb | 4 +-- 3 files changed, 36 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb new file mode 100644 index 0000000000..7fd327efda --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'MAFFT' +version = '7.130' +versionsuffix = '-with-extensions' + +homepage = 'http://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb index e1d713088e..da877e2d72 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb @@ -27,14 +27,14 @@ source_urls = ["http://prank-msa.googlecode.com/files"] sources = ['%(namelower)s.source.%(version)s.tgz'] # PRANK uses MAFFT as external tool to contruct guide tree -dependencies = [('MAFFT', '7.130')] +dependencies = [('MAFFT', '7.130', '-with-extensions')] start_dir = 'src' files_to_copy = [(['prank'], 'bin')] sanity_check_paths = { - 'files': ["bin/prank", "bin/exonerate"], + 'files': ["bin/prank"], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb index 9f531219a1..a40acd6d3c 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb @@ -27,14 +27,14 @@ source_urls = ["http://prank-msa.googlecode.com/files"] sources = ['%(namelower)s.source.%(version)s.tgz'] # PRANK uses MAFFT as external tool to contruct guide tree -dependencies = [('MAFFT', '7.130')] +dependencies = [('MAFFT', '7.130', '-with-extensions')] start_dir = 'src' files_to_copy = [(['prank'], 'bin')] sanity_check_paths = { - 'files': ["bin/prank", "bin/exonerate"], + 'files': ["bin/prank"], 'dirs': [] } -- GitLab From 6488585f3ee6b39bf1fc43a055a34c0cb2e2587f Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 03:44:48 +0100 Subject: [PATCH 006/911] adjust SMALT builds Signed-off-by: Fotis Georgatos --- .../s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb | 37 ------------------- .../s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb | 37 ------------------- .../s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 2 +- .../s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 2 +- 4 files changed, 2 insertions(+), 76 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb deleted file mode 100644 index 0beeeb58ca..0000000000 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-goolf-1.4.10.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = "Tarball" - -name = "SMALT" -version = "0.7.4" - -homepage = "http://www.sanger.ac.uk/resources/software/smalt/" -description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'opt': True, 'optarch': True} - -source_urls = ["ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt"] -sources = [SOURCELOWER_TGZ] - -sanity_check_paths = { - 'files': ["smalt_x86_64"], - 'dirs': [] -} - -modextrapaths = { - 'PATH': '', - 'MANPATH': '', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb deleted file mode 100644 index 45ed75c381..0000000000 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.4-ictce-5.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = "Tarball" - -name = "SMALT" -version = "0.7.4" - -homepage = "http://www.sanger.ac.uk/resources/software/smalt/" -description = """SMALT efficiently aligns DNA sequencing reads with a reference genome.""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'opt': True, 'optarch': True} - -source_urls = ["ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt"] -sources = [SOURCELOWER_TGZ] - -sanity_check_paths = { - 'files': ["smalt_x86_64"], - 'dirs': [] -} - -modextrapaths = { - 'PATH': '', - 'MANPATH': '', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index bb9980bc8d..ac5e6d43c2 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -23,7 +23,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ["bin/smalt"], + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats', 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index 7ffae18045..b3475f56a3 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -23,7 +23,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ["bin/smalt"], + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats', 'dirs': [] } -- GitLab From 2bf00c668e717eacb6283453ef86cbc798d26cde Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 03:46:23 +0100 Subject: [PATCH 007/911] fix bug in SMALT Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index ac5e6d43c2..e04563db6e 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -23,7 +23,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats', + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats']], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index b3475f56a3..1930c64969 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -23,7 +23,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats', + 'files': ['bin/%s' % x for x in ['simread', 'smalt', 'mixreads','readstats']], 'dirs': [] } -- GitLab From dbdeb510118fb9b2516a3c640747ba884a730abf Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 24 Feb 2014 00:55:20 +0100 Subject: [PATCH 008/911] add rCUDA-4.0.1_linux_64_Ubuntu10.04.eb Signed-off-by: Fotis Georgatos --- .../rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb new file mode 100644 index 0000000000..1c4c98b0f0 --- /dev/null +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB +# Authors:: Fotis Georgatos , +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +easyblock = "Tarball" + +name = "rCUDA" +version = "4.0.1" +versionsuffix = "_linux_64_Ubuntu10.04" + +homepage = 'http://www.rcuda.net/' +description = """The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['rCUDA_%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ["framework/common/rCUDAcommIB.so", "framework/common/rCUDAcommTCP.so", + "framework/rCUDAl/libcudart.so", "util/rCUDA_util.h"], + 'dirs': [] +} + +moduleclass = 'system' -- GitLab From ee0ac46ff9ae257f194baf35407fd7aa23ae391f Mon Sep 17 00:00:00 2001 From: build Date: Fri, 28 Feb 2014 14:09:44 +0200 Subject: [PATCH 009/911] Contributing parallel version of ABINIT built with ETSF_IO to enable checkpointing --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 35 +++++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..c1d2b559d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..7e1b945d47 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + -- GitLab From 38696b3ba189737da986398f408d49fa21b57cb7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 9 Apr 2014 16:36:16 +0200 Subject: [PATCH 010/911] added FDS --- .../f/FDS/FDS-r18915-goolf-1.4.10.eb | 25 +++++++++++++++++++ .../easyconfigs/f/FDS/FDS_makefile.patch | 15 +++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS_makefile.patch diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb new file mode 100644 index 0000000000..532468b97f --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +patches = ['FDS_makefile.patch'] +modextrapaths = {'bin': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS_makefile.patch new file mode 100644 index 0000000000..d9c7c2a315 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS_makefile.patch @@ -0,0 +1,15 @@ +--- makefile (revision 18916) ++++ makefile (working copy) +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod -- GitLab From 2178f44c0af1b92efed808dd242edaa2e7e04e26 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 9 Apr 2014 16:45:43 +0200 Subject: [PATCH 011/911] use mpi and add to path, not to bin --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index 532468b97f..d49cfa69e6 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -8,7 +8,7 @@ description = """ """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] # just run make in the install dir @@ -16,7 +16,7 @@ skipsteps = ['configure', 'install'] buildininstalldir = True patches = ['FDS_makefile.patch'] -modextrapaths = {'bin': 'FDS_Source'} +modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { 'files': ['FDS_Source/fds'], -- GitLab From 570d6004b3a3dece9f0d4d2964b5a7576d211573 Mon Sep 17 00:00:00 2001 From: admin6 Date: Wed, 9 Apr 2014 16:47:00 +0200 Subject: [PATCH 012/911] added ictce easyconfig --- .../f/FDS/FDS-r18915-ictce-5.5.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb new file mode 100644 index 0000000000..ef3f6f0041 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -0,0 +1,24 @@ +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +patches = ['FDS_makefile.patch'] +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' -- GitLab From fb67f5ffa111fa9aad08dba2140ec82b93958b1d Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 10 Apr 2014 22:13:57 +0200 Subject: [PATCH 013/911] Minimac-2013.7.17-goolf-1.4.10.eb --- .../Minimac/Minimac-2013.7.17-goolf-1.4.10.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb new file mode 100644 index 0000000000..6d59aab26d --- /dev/null +++ b/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock='MakeCp' + +name = 'Minimac' +version = '2013.7.17' +versionsuffix = '-beta' + +homepage = 'http://genome.sph.umich.edu/wiki/Minimac' +description = """ Minimac is a low memory, computationally efficient implementation + of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes + and can handle very large reference panels with hundreds or thousands of haplotypes. + The name has two parts. The first, 'mini', refers to the modest amount of computational + resources it requires. The second, 'mac', is short hand for MaCH, our widely used + algorithm for genotype imputation. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# the source file doesn't include version in the name so probably you should check +# in their website if the version number and date is correct +source_urls = ['http://www.sph.umich.edu/csg/cfuchsb/'] +sources = ['%(namelower)s.src.tgz'] + +# firt move to folder libStatGen to run make +# then move to foler minimac to run make +premakeopts = ["cd libStatGen && ", "cd minimac && "] + +# in libStatGen folder run just "make" +# in minimac folder run "make opt && make openmp" +makeopts = ["", " opt && make openmp"] + +# parallel build fails +parallel = 1 + +files_to_copy = [(["minimac/bin/minimac", "minimac/bin/minimac-omp"], "bin")] + +sanity_check_paths = { + 'files': ['bin/minimac', 'bin/minimac-omp'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From cb97556ae694ad5383ade61cb277419b99eff0ab Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 19 May 2014 15:54:55 +0200 Subject: [PATCH 014/911] Add Exonerate builds, adjust FSA to include them by default Signed-off-by: Fotis Georgatos --- .../Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb | 27 +++++++++++++++++++ .../Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb | 27 +++++++++++++++++++ .../f/FSA/FSA-1.15.8-goolf-1.4.10.eb | 22 ++++++++------- .../f/FSA/FSA-1.15.8-ictce-5.3.0.eb | 22 ++++++++------- 4 files changed, 80 insertions(+), 18 deletions(-) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..8f74cb642e --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'Exonerate' +version = '2.2.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..3d15ae6c32 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'Exonerate' +version = '2.2.0' + +homepage = 'http://www.ebi.ac.uk/~guy/exonerate/' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb index af8b162d43..a9915dbdff 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 University of Luxembourg, Swiss Institute of Bioinformatics +# Authors:: Fotis Georgatos, Pablo Escobar Lopez # License:: MIT/GPL # $Id$ # @@ -13,21 +13,25 @@ name = "FSA" version = "1.15.8" -homepage = "http://fsa.sourceforge.net" -description = """FSA is a probabilistic multiple sequence alignment algorithm - which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.""" +homepage = 'http://fsa.sourceforge.net/' +description = """ FSA:Fast Statistical Alignment, is a probabilistic multiple sequence + alignment algorithm which uses a distance-based approach to aligning homologous protein, + RNA or DNA sequences.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True} -source_urls = ["http://downloads.sourceforge.net/project/fsa/"] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('MUMmer', '3.23')] +dependencies = [ + ('MUMmer', '3.23'), + ('Exonerate', '2.2.0') +] sanity_check_paths = { - 'files': ["bin/fsa"], - 'dirs': [] + 'files': ["bin/%s" % x for x in ["fsa", "gapcleaner", "map_gff_coords"]], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb index ea38265ab5..037a69fcc4 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 University of Luxembourg, Swiss Institute of Bioinformatics +# Authors:: Fotis Georgatos, Pablo Escobar Lopez # License:: MIT/GPL # $Id$ # @@ -13,21 +13,25 @@ name = "FSA" version = "1.15.8" -homepage = "http://fsa.sourceforge.net" -description = """FSA is a probabilistic multiple sequence alignment algorithm - which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.""" +homepage = 'http://fsa.sourceforge.net/' +description = """ FSA:Fast Statistical Alignment, is a probabilistic multiple sequence + alignment algorithm which uses a distance-based approach to aligning homologous protein, + RNA or DNA sequences.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True} -source_urls = ["http://downloads.sourceforge.net/project/fsa/"] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('MUMmer', '3.23')] +dependencies = [ + ('MUMmer', '3.23'), + ('Exonerate', '2.2.0') +] sanity_check_paths = { - 'files': ["bin/fsa"], - 'dirs': [] + 'files': ["bin/%s" % x for x in ["fsa", "gapcleaner", "map_gff_coords"]], + 'dirs': [], } moduleclass = 'bio' -- GitLab From 141a4e355ac7afa5fc9deb19fba5accc2449c5be Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Tue, 27 May 2014 16:55:39 +1200 Subject: [PATCH 015/911] New config file for ORCA 3.0.2 based on ORCA 3.0.0 --- .../o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb new file mode 100644 index 0000000000..dd9a1e76e6 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -0,0 +1,32 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = "3_0_2-linux_x86-64" # tweaked by EasyBuild (was: '3_0_0-linux_x86-64_openmpi_165') + +homepage = 'http://www.thch.uni-bonn.de/tc/orca/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] + +dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + \ + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ + ['orca', 'otool_cosmo'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From 5cfe6a75809aaee1d332c2d66ed5d586c911169d Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Jun 2014 02:54:37 +0200 Subject: [PATCH 016/911] amend Exonerate easyconfigs with GLib dep Signed-off-by: Fotis Georgatos --- .../easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb | 2 ++ .../easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb index 8f74cb642e..60550f5635 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('GLib', '2.34.3')] + # parallel build fails parallel = 1 diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb index 3d15ae6c32..69f1442377 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb @@ -16,6 +16,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [homepage] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('GLib', '2.34.3')] + # parallel build fails parallel = 1 -- GitLab From 7c463c7c7a9a2fdd69601fbc295a28a019059118 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 8 Jul 2014 21:02:33 +0200 Subject: [PATCH 017/911] cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb --- ...utadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..3a32415096 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.4.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3f3d46701889968992ded92b3aec54bc67fa610e Mon Sep 17 00:00:00 2001 From: Jordi Blasco Date: Wed, 23 Jul 2014 13:06:18 +1200 Subject: [PATCH 018/911] Chapel-1.9.0 Chapel-1.9.0 compiled with goolf-1.5.14 --- .../c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb new file mode 100644 index 0000000000..80c79f1859 --- /dev/null +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.9.0-goolf-1.5.14.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Jordi Blasco (NeSI) +# License:: MIT/GPL +# $Id$ +## + +name = 'Chapel' +version = '1.9.0' + +homepage = 'http://chapel.cray.com' +description = """ Chapel is an emerging parallel programming language whose design and development + is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users + while also serving as a portable parallel programming model that can be used on commodity clusters + or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale + parallel computers while matching or beating the performance and portability of current programming + models like MPI.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +unpack_options = '--strip-components=1' + +# parallel build fails +parallel = 1 + +libpath = 'lib/linux64.gnu.loc-flat.tasks-fifo.tmr-generic.mem-default.atomics-intrinsics.' +libpath += 'gmp-none.hwloc-none.re-none.wide-struct.fs-none' + +sanity_check_paths = { + 'files': ['bin/linux64/chpl', 'bin/linux64/chpldoc', '%s/libchpl.a' % libpath, '%s/main.o' % libpath], + 'dirs': [], +} + +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + +moduleclass = 'lang' -- GitLab From 0063db32993fb4a1c4418ce7019fad1d5d57b1f9 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:40:05 +0300 Subject: [PATCH 019/911] Adding ABINIT v.7.4.3 with dummy and goolf (parallel version) toolchains --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 +++++++++++++++++++ .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ++++++++++++++++ .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 ++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb create mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..a3fe29c410 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ABINIT' +version = '7.4.3' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = ['%s-%s.tar.gz' % (name.lower(), version)] +source_urls = ['http://ftp.abinit.org/'] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb new file mode 100644 index 0000000000..fb4d81965f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'ABINIT' +version = '7.4.3' +versionsuffix = '-x86_64_linux_gnu4.5' + +altversions = ['7.0.3', '7.0.4', '7.0.5'] + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 +sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] +source_urls = ['http://ftp.abinit.org/'] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] + } + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..350da2d908 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] + } + +moduleclass = 'chem' -- GitLab From 38d072b44abb10c2bde6d7309c5a4466508f3040 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 11:45:37 +0300 Subject: [PATCH 020/911] Adding Bismark --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..d749578a18 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +easyblock = "Tarball" + +name = 'Bismark' +version = '0.10.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] + + +dependencies = [ + ('Bowtie2', '2.0.2'), +] + +sanity_check_paths = { + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' -- GitLab From 845d1d8b8f8a44557e47d3220fb32db7cbba3162 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 12:38:12 +0300 Subject: [PATCH 021/911] Contributing DendroPy --- ...ndroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d3ec591256 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,37 @@ +## +#This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = "PythonPackage" + +name = 'DendroPy' +version = '3.12.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. +""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] +sources = ['%s-%s.tar.gz' % (name, version)] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From bd66b7e4bf46f52756c4199c803b5abab82f7a4e Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:09:32 +0300 Subject: [PATCH 022/911] Contributing MAT I/O Library --- .../m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..99d44c6862 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'MATIO' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s-%s.zip' % (name.lower(), version)] + + +dependencies = [('zlib','1.2.7'), +] + +moduleclass = 'lib' -- GitLab From c76f17999c613ea2a5eb6647454d1d21bd3bc3d3 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 6 Aug 2014 14:31:36 +0300 Subject: [PATCH 023/911] Contributing pBWA --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb new file mode 100644 index 0000000000..754be559e1 --- /dev/null +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "MakeCp" + +name = 'pBWA' +version = '0.5.9_1.21009' + +homepage = 'http://pbwa.sourceforge.net/' +description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s_%(version)s.zip'] +source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] + + + +dependencies = [ + ('BWA', '0.7.4'), +] + +files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], + +} + +moduleclass = 'bio' -- GitLab From f11a48a7040e02bbb5a7ab04f139f143636cd3e7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 13:46:16 +0200 Subject: [PATCH 024/911] added new cutadapt for intel --- .../cutadapt-1.5-intel2014b-Python-2.7.8.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..9be9435a32 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 3f44802c275982e41ebe2b1bd100abb7994c951a Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 23 Aug 2014 16:02:59 +0200 Subject: [PATCH 025/911] pigz easyconfigs for goolf-1.4.10 and ictce-6.2.5 --- .../p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 37 +++++++++++++++++++ .../p/pigz/pigz-2.3.1-ictce-6.2.5.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..7caa293ce4 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.3.1' + +homepage = 'http://zlib.net/pigz/' +description = """ pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple cores + to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib + and pthread libraries. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://zlib.net/pigz/'] +sources = [SOURCE_TAR_GZ] + +# README recommends zlib 1.2.6 or higher +dependencies = [('zlib', '1.2.8')] + +makeopts = ' CC=$CC' + +parallel = 1 + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ["bin/pigz", "bin/unpigz"], + 'dirs': [""], +} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..1f7d3bd2f0 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.3.1' + +homepage = 'http://zlib.net/pigz/' +description = """ pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple cores + to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib + and pthread libraries. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['http://zlib.net/pigz/'] +sources = [SOURCE_TAR_GZ] + +# README recommends zlib 1.2.6 or higher +dependencies = [('zlib', '1.2.8')] + +makeopts = ' CC=$CC' + +parallel = 1 + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ["bin/pigz", "bin/unpigz"], + 'dirs': [""], +} + +moduleclass = 'tools' + -- GitLab From 97176bfc0696547a7a6314bf0a66c41e075c77b7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 10:39:30 +0200 Subject: [PATCH 026/911] PostgreSQL with Perl binding --- .../DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 26 ++++++++++++ .../PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb | 41 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000..5caf1511aa --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'DBD-Pg' +version = '3.4.1' + +homepage = 'http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/' +description = """Perl binding for PostgreSQL""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5"), +] + + +options = {'modulename': 'DBD::Pg'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb new file mode 100644 index 0000000000..9b40199a4f --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb @@ -0,0 +1,41 @@ +name = 'PostgreSQL' +version = '9.3.5' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2014b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.7.0_60' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('Perl', '5.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 36aa12e557164986ff49d4fced15e9c03dd44d09 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Sep 2014 14:27:46 +0200 Subject: [PATCH 027/911] Typo Corrected --- ...geSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PostgreSQL/{PostgeSQL-9.3.5-intel-2014b.eb => PostgreSQL-9.3.5-intel-2014b.eb} (100%) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/p/PostgreSQL/PostgeSQL-9.3.5-intel-2014b.eb rename to easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb -- GitLab From e7c3b62cd358037b8d85cd6d4a3ced20c84540d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:24 +0200 Subject: [PATCH 028/911] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 5caf1511aa..8e07224960 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,10 +15,7 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [ - (perl, perlver), - ("PostgreSQL", "9.3.5"), -] +dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] options = {'modulename': 'DBD::Pg'} -- GitLab From c62fc4a88b50b63e1461f8b02a5d045b31cdf85a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Fri, 12 Sep 2014 10:08:34 +0200 Subject: [PATCH 029/911] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index 8e07224960..ca812f75ef 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -17,7 +17,6 @@ versionsuffix = '-%s-%s' % (perl, perlver) dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] - options = {'modulename': 'DBD::Pg'} moduleclass = 'data' -- GitLab From d0e3c5a86c5e372ac14c4d2a4f54aa22e7ad02a4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 Sep 2014 10:40:06 +0200 Subject: [PATCH 030/911] CUDA 6.5.14 --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 29 +++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb new file mode 100644 index 0000000000..2698ca5e91 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +name = 'CUDA' +version = '6.5.14' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] + +moduleclass = 'system' -- GitLab From f9e11c7393bfbf54d69dceae4a80d7987a71268c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 17:56:05 +0200 Subject: [PATCH 031/911] add easyconfig for WIEN2k v14.1 with intel/2014b --- .../w/WIEN2k/WIEN2k-14.1-intel-2014b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb new file mode 100644 index 0000000000..9a8f71d9ca --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' -- GitLab From b9c43dfe98cf7377649301ad3a894beae3a99213 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Oct 2014 18:29:47 +0200 Subject: [PATCH 032/911] add missing patch files for WIEN2k 14.1 --- .../w/WIEN2k/WIEN2k-14.1_fix-tetra.patch | 57 +++ .../w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch | 461 ++++++++++++++++++ .../WIEN2k-14.1_lapw5-main-accuracy-fix.patch | 22 + 3 files changed, 540 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch new file mode 100644 index 0000000000..ef8bc83ba2 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch @@ -0,0 +1,57 @@ +see http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11178.html +--- WIEN2k_14.orig/SRC_tetra/tetra.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_tetra/tetra.f 2014-09-19 13:30:37.671774186 +0200 +@@ -165,7 +165,7 @@ + SO=1.d0 + NSORT=1 + KLMAX=1 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + IDOS(1,1)=0 + IDOS(1,2)=0 + DOSTYP(1)='TOTAL' +@@ -220,7 +220,7 @@ + READ(4,1010) ALAT1,ALAT2,ALAT3,EFERM + READ(4,1020) MINWAV,MAXWAV,KSPIN,NSORT,kso,kLmax + if(klmax.eq.0) klmax=14 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + ! INCREASE NSORT BY ONE FOR THE INTERSTITIAL DOS (OUT) + NSORT=NSORT+1 + WRITE(6,2000) SYSTEM +@@ -240,7 +240,7 @@ + DO 107 ISORT=1,NSORT + IF(ISORT.EQ.NSORT) GOTO 107 + READ(4,1030) JATOM,NEQU,isplit,text(isort) +- WRITE(6,2030) JATOM,NEQU,isplit,text(isort) ++ WRITE(6,2030) JATOM,NEQU,isplit,text(isort) + 107 CONTINUE + nndos_save=nndos + DO 90 JCASE=1,NNDOS +@@ -364,7 +364,11 @@ + if(nst.eq.1.and.ibrsw.eq.-1) then ! for one k-point calculate the DOS with broadening + ibrsw=1 + print*,'Only 1 k-point, switching to Gauss-broadening with',br +- endif ++ if(br.lt.1.d-6) then ++ br=0.002 ++ print*,' No broadening specified, increasing broadening to',br ++ endif ++ endif + if(ibrsw.ne.-1) then + CALL broadDOS (ibrsw,br,brlor,NNDOS,1,JEND,EMIN,EMAX,NYMIN,NYMAX,DE,ebs,fc,nst,densty) + endif +@@ -523,7 +527,7 @@ + 1000 FORMAT(1X,A70,/) + 1010 FORMAT(1X,15X,3F8.5,16X,F10.5) + 1020 FORMAT(1X,I4,10X,I4,8X,I1,7X,I3,8x,i2,6x,i3) +- 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a200) ++ 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a96) + 1040 FORMAT(6X,I4) + 1041 FORMAT(5X,I5) + 1050 FORMAT(F10.5,I3,F8.5,3X,(40F8.5)) +@@ -532,3 +536,4 @@ + 2020 FORMAT(1X,I4,' < NMAT < ',I4,3X,'SPIN=',I1,3X,'NATO=',I4) + 2030 FORMAT(1X,'JATOM',I3,2X,'MULT=',I2,2x,'ISPLIT=',i2,2x,a96) + END ++ diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch new file mode 100644 index 0000000000..a17c8dbe58 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch @@ -0,0 +1,461 @@ +see http://zeus.theochem.tuwien.ac.at/pipermail/wien/2014-September/021667.html +--- x_lapw.orig 2014-10-09 15:03:02.181799391 +0200 ++++ x_lapw 2014-10-09 15:08:25.254125143 +0200 +@@ -4,28 +4,28 @@ + set running = ".running.$$.`hostname`.`date +%d%m%H%M%S`" + echo $$ >$running + onintr clear +-alias error 'echo ">>> ($name) \!* -> exit"; goto error' ++alias error 'echo ">>> ($name) \!* -> exit"; goto error' + +-set name = $0 #full name of script-file +-set bin = $name:h #default directory for WIEN-executables ++set name = $0 #full name of script-file ++set bin = $name:h #default directory for WIEN-executables + if !(-d $bin) set bin = . +-set name = $name:t ++set name = $name:t + +-set def = def #def-file +-set tmp = ( ) #tmp-files, to be deleted before exit +-set log = :log #log-file +-set t = time # +-set updn # spinpolarization switch +-set dnup = 'dn' # spinpolarization switch ++set def = def #def-file ++set tmp = ( ) #tmp-files, to be deleted before exit ++set log = :log #log-file ++set t = time # ++set updn # spinpolarization switch ++set dnup = 'dn' # spinpolarization switch + set spin=1 # for -it in lapw1 + #set ne_it=1.1 # for -it in lapw1 + set emin=-999.0 # for -emin XX in lapw2 + set emax=999.0 # for -all XX YY in lapw2 + set settol=0.00001 # tol parameter for sgroup + set wf=0 # wplot: WF to plot (0 = read from file) +-set sc # semicore-switch +-set so # spinorbit-switch +-set sodum # spinorbit-switch ++set sc # semicore-switch ++set so # spinorbit-switch ++set sodum # spinorbit-switch + #set cmplx + set cmplx1 + set cmplx2 +@@ -62,12 +62,12 @@ + unset efg # regular run in lapw2 + unset emin1 # regular run in lapw2 + unset emax1 # regular run in lapw2 +-unset command #command +-unset file #file-head +-unset deffile_only #create just def file +-unset fftstop #for dstart +-unset vresp #for lapw2 +-unset help_files #for lapw2 ++unset command #command ++unset file #file-head ++unset deffile_only #create just def file ++unset fftstop #for dstart ++unset vresp #for lapw2 ++unset help_files #for lapw2 + unset super # for dstart, creates new.clmsum + unset rxes # for tetra, uses rxes-weight file + unset rxesw # for tetra, writes rxes-weight file +@@ -88,9 +88,9 @@ + + if ( $?SCRATCH && $SCRATCH != '') then + set scratch=`echo $SCRATCH | sed -e 's/\/$//'`/ # we are afraid +- # different settings in different +- # computing centers +- #use global variable for scratch if set ++ # different settings in different ++ # computing centers ++ #use global variable for scratch if set + endif + set argv1=($argv) + +@@ -138,16 +138,16 @@ + shift; breaksw + case -it: + set iter +- shift; breaksw ++ shift; breaksw + case -noHinv: + set iter + unset readHinv +- shift; breaksw ++ shift; breaksw + case -noHinv0: + set iter + unset readHinv + set writeHinv +- shift; breaksw ++ shift; breaksw + # case -ne_it: + # shift;set ne_it=$1 + # shift; breaksw +@@ -169,36 +169,36 @@ + shift; breaksw + case -help_files: + set help_files +- shift; breaksw ++ shift; breaksw + case -vresp: + set vresp +- shift; breaksw ++ shift; breaksw + case -eece: + set eece=eece +- shift; breaksw ++ shift; breaksw + case -grr: + set grr=grr +- shift; breaksw ++ shift; breaksw + case -orb: + set orb +- shift; breaksw ++ shift; breaksw + case -nmat_only: + set nmat_only +- shift; breaksw ++ shift; breaksw + case -nohns: + set nohns +- shift; breaksw ++ shift; breaksw + case -enefile: + set enefile +- shift; breaksw ++ shift; breaksw + case -rxes: + set rxes +- shift; breaksw ++ shift; breaksw + case -rxesw: + set rxesw + shift;set rxese1 = $1 + shift;set rxese2 = $1 +- shift; breaksw ++ shift; breaksw + case -so: + set so = 'so' + set sodum = 'dum' +@@ -313,7 +313,7 @@ + endif + shift; breaksw + ## w2w stuff ## +- case -pp: # passed on to Wannier90 ++ case -pp: # passed on to Wannier90 + shift; breaksw + case -wf: + shift; set wf = $1 +@@ -338,7 +338,7 @@ + + if !($?file) then + set file = `pwd` +-set file = $file:t #tail of file-names ++set file = $file:t #tail of file-names + endif + + touch $file.struct +@@ -409,7 +409,7 @@ + #echo "`date`> ($name) $command $argv1[2-]" >> $log + echo "`date`> ($name) $argv1" >> $log + +-set def = $updn$command$sc.def ++set def = $updn$command$sc.def + #touch $def + + switch ($command) +@@ -1200,7 +1200,7 @@ + cat << theend > $def + 6,'$file.outputst', 'unknown','formatted' + 7,'$file.tmpden', 'unknown','formatted' +-10,'$file.tmp', 'unknown','unformatted' ++10,'$file.tmp', 'unknown','unformatted' + 11,'$file.vsp_st', 'unknown','formatted' + 12,'$file.vspdn_st', 'unknown','formatted' + 13,'$file.sigma', 'unknown','formatted' +@@ -1268,7 +1268,7 @@ + + case mixer_vresp: + set exe = mixer +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1283,7 +1283,7 @@ + 32,'$file.vrespbroyd2', 'unknown','unformatted',164896 + 51,'$file.vrespsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1304,7 +1304,7 @@ + 52,'$file.vrespdn', 'unknown','formatted',0 + 11,'$file.vrespsum', 'unknown','formatted',0 + theend +- endif ++ endif + breaksw + + +@@ -1318,7 +1318,7 @@ + cp $file.struct $file.struct_old + endif + set exe = $command +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1334,7 +1334,7 @@ + 32,'$file.broyd2', 'unknown','unformatted',164896 + 51,'$file.clmsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1364,7 +1364,7 @@ + echo "75,'$file.dmatdn_old','unknown','formatted',0" >> $def + echo "76,'$file.dmatud_old','unknown','formatted',0" >> $def + endif +- endif ++ endif + + if($eece == 'eece') then + echo "71,'$file.vorbup','unknown','formatted',0" >> $def +@@ -1557,16 +1557,16 @@ + if($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` +-# @ cnum+=1 ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++# @ cnum+=1 + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + unset irr + if(-f "$file.irrep$hf$so${updn}_$cnum" && $cnum>0) then +- if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" ++ if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" + head -2 "$file.irrep$hf$so${updn}_$cnum" >"$file.irrep$hf$so${updn}" + set irr + endif +@@ -1574,9 +1574,9 @@ + while($count <= $cnum) + if($?irr) then + tail -n +3 $file.irrep$hf$so${updn}_$count >>$file.irrep$hf$so${updn} +- endif ++ endif + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif +@@ -2251,10 +2251,10 @@ + 7,'$file.amn$w90updn', 'unknown','formatted', 0 + 8,'$file.mmn$w90updn', 'unknown','formatted', 0 + 9,'${scratch}$file.vector$sc$hf$soupdn', 'unknown','unformatted',9000 +- 10,'$file.nnkp', 'old', 'formatted', 0 +- 12,'$file.eig$updn', 'unknown','formatted', 0 ++ 10,'$file.nnkp', 'old', 'formatted', 0 ++ 12,'$file.eig$updn', 'unknown','formatted', 0 + 18,'$file.vsp$updn', 'old', 'formatted', 0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$soupdn', 'old', 'formatted', 0 + 51,'$file.fermi$updn' 'old', 'formatted', 0 + EOF +@@ -2296,23 +2296,23 @@ + if ($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + set count=1 + while($count <= $cnum) + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif + cat >$def <$def + 4,'$file.klist', 'old', 'formatted', 0 + 10,'${scratch}$file.vector$sc$hf$so$updn', 'old', 'unformatted',0 +- 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$so$updn', 'old', 'formatted', 0 + 51,'$file.energy$so$updn', 'unknown','formatted', 0 + EOF +@@ -2402,7 +2402,7 @@ + ### end w2w ### + + default: +-error command $command does not exist ++error command $command does not exist + breaksw + + endsw +@@ -2445,10 +2445,11 @@ + if ($gw == 'gw') then + set exe = ($exe -gw) + endif +-endif ++endif + + echo $exe >>$running + $t $bin/$exe $def ++ + if($status != 0) then + echo "error: command $bin/$exe $def failed" + if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +@@ -2468,28 +2469,28 @@ + + set lapw2test=`echo $exe | cut -c 1-5` + if("$lapw2test" == 'lapw2') then ++ if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then ++ if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx ++ endif + if(! $?in1orig & ! $?band & ! $?emin1 & ! $?emax1) then +- if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then +- if($cmplx == 'c') then ++ if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then ++ if($cmplx == 'c') then + if(! (-e $file.in1$cmplx$sc && ! -z $file.in1$cmplx$sc)) set cmplx + endif +- set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` +- set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` ++ set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` ++ set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` + if($#efold == 0 ) set efold=0.5 +- set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix +- set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` +- echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp +- tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp +- mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} +- endif ++ set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix ++ set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` ++ echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp ++ tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp ++ mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} ++ endif + endif + endif + + clear: + #cleanup +-if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +- if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx +-endif + if ($?rxesw ) then + if( -e .oldint ) mv .oldint $file.int + endif +@@ -2499,10 +2500,10 @@ + error: + rm $running + +-help: #help exit ++help: #help exit + cat << theend + +-USAGE: $0 PROGRAMNAME [flags] ++USAGE: $0 PROGRAMNAME [flags] + + PURPOSE:runs WIEN executables: afminput,aim,arrows,broadening,cif2struct, + clmaddsub,clmcopy,clminter,convham,conv2prim,dftd3,dipan,dmftproj, +@@ -2514,30 +2515,30 @@ + symmetso,telnes3,tetra,txspec,wannier90,w2w,w2waddsp,wplot,xspec + + FLAGS: +--f FILEHEAD -> FILEHEAD for path of struct & input-files +--t/-T -> suppress output of running time +--h/-H -> help +--d -> create only the def-file +--up -> runs up-spin +--dn -> runs dn-spin +--du -> runs up/dn-crossterm +--sc -> runs semicore calculation +--c -> complex calculation (no inversion symmetry present) ++-f FILEHEAD -> FILEHEAD for path of struct & input-files ++-t/-T -> suppress output of running time ++-h/-H -> help ++-d -> create only the def-file ++-up -> runs up-spin ++-dn -> runs dn-spin ++-du -> runs up/dn-crossterm ++-sc -> runs semicore calculation ++-c -> complex calculation (no inversion symmetry present) + -p -> run lapw0/1/2/hf/so/dm/optic in parallel (needs .machines or .processes file) + -scratch dir/ ->defines (and makes) $SCRATCH variable + -grr -> lapw0 for mBJ or hf (using $file.in0_grr) + -eece -> for hybrid-functionals (lapw0,lapw2,mixer,orb,sumpara) + -band -> for lapw1/2/hf bandstructures: uses *klist_band +--orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat +--it -> runs lapw1 with iterative diagonalization +--noHinv -> runs lapw1 with iterative diag. without Hinv +--noHinv0 -> runs lapw1 with iterative diag. writing new Hinv +--nohns -> runs lapw1 without HNS +--nmat_only-> runs lapw1 and yields only the matrixsize +--nmr -> runs lapw1 in NMR mode +--in1orig -> runs lapw2 but does not modify case.in1 +--emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) +--all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) ++-orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat ++-it -> runs lapw1 with iterative diagonalization ++-noHinv -> runs lapw1 with iterative diag. without Hinv ++-noHinv0 -> runs lapw1 with iterative diag. writing new Hinv ++-nohns -> runs lapw1 without HNS ++-nmat_only-> runs lapw1 and yields only the matrixsize ++-nmr -> runs lapw1 in NMR mode ++-in1orig -> runs lapw2 but does not modify case.in1 ++-emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) ++-all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) + -qtl -> runs lapw2 and calculates QTL + -alm -> runs lapw2 and calculates ALM,BLM + -almd -> runs lapw2 and calculates ALM,BLM in lapw2 for DMFT (Aichhorn) +@@ -2546,11 +2547,11 @@ + -vresp-> runs lapw2 and creates case.vrespval (for TAU/meta-GGA) + -fermi-> runs lapw2 with FERMI switch + -efg -> runs lapw2 with EFG switch +--so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. ++-so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. + -hf -> runs lapw2 with Hartree-Fock/hybrid vectors + -diaghf -> calculates only the diagonal elements of HF Hamiltonian + -nonself -> calculates hf with Ex only (no eigenvalues/vectors) +--fbz -> runs kgen and generates a full mesh in the BZ ++-fbz -> runs kgen and generates a full mesh in the BZ + -fft -> runs dstart only up to case.in0_std creation + -super-> runs dstart and creates new_super.clmsum (and not $file.clmsum) + -lcore-> runs dstart with $file.rsplcore (produces $file.clmsc) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch new file mode 100644 index 0000000000..3800834f1b --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch @@ -0,0 +1,22 @@ +http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11158.html +--- WIEN2k_14.orig/SRC_lapw5/main1.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_lapw5/main1.f 2014-09-19 13:30:37.671774186 +0200 +@@ -346,7 +346,7 @@ + if(addsub.eq.' ADD') fadd=1.d0 + if(addsub.eq.' SUB') fadd=-1.d0 + +- IF(IUNIT.EQ.'ANG ') FAK=Bohr**3 ++ IF(IUNIT.EQ.'ANG ') FAK=1.D0/Bohr**3 ! Change to avoid altering lapw5 output (fix to WIEN2k 14.1): Was 6.7551d0 in WIEN2k 13.1 (and likely in verisons < 13.1) but changed to increase accuracy + R=VNORM(VX) + RELX=R + R=VNORM(VY) +@@ -373,7 +373,7 @@ + ! + ! Correct TCharge for units + if(UseSTM)then +- if(IUNIT.EQ.'ANG ')CTarget=CTarget/FAK ++ if(IUNIT.EQ.'ANG ')CTarget=CTarget*FAK ! Change to avoid altering output + ! Array for STM (LDM) + allocate(STM(NPX,NPY)) + endif + -- GitLab From e230ec249f7d63c8eee98e0c89f82626da93a587 Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 15 Oct 2014 15:19:56 +1300 Subject: [PATCH 033/911] Changed web link and removed auto-generated comment --- easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index dd9a1e76e6..476bf7eb48 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -1,9 +1,9 @@ easyblock = "PackedBinary" name = "ORCA" -version = "3_0_2-linux_x86-64" # tweaked by EasyBuild (was: '3_0_0-linux_x86-64_openmpi_165') +version = "3_0_2-linux_x86-64" -homepage = 'http://www.thch.uni-bonn.de/tc/orca/' +homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- -- GitLab From dac4073feefbb62d8660cbd7c1a56cab16bbfbb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Oct 2014 15:00:12 +0200 Subject: [PATCH 034/911] add easyconfig for GAMESS-US --- ...MESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb new file mode 100644 index 0000000000..c2b22536d1 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb @@ -0,0 +1,18 @@ +name = 'GAMESS-US' +version = '20130501-R1' + +homepage = 'http://www.msg.ameslab.gov/gamess/' +description = """The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14-no-OFED'} +toolchainopts = {'usempi': True, 'optarch': False} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +sources = ['gamess-%(version)s.tar.gz'] +patches = ['gamess_TMP.patch'] + +maxcpus = 4 +maxnodes = 1 + +moduleclass = 'chem' -- GitLab From 7e9588508dff275b96fd1990d58659aad57cdc15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Oct 2014 15:15:52 +0200 Subject: [PATCH 035/911] add missing patch for GAMESS-US --- .../easyconfigs/g/GAMESS-US/gamess_TMP.patch | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch b/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch new file mode 100644 index 0000000000..795144d2dc --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch @@ -0,0 +1,36 @@ +--- gamess/compall.orig 2014-06-11 18:37:54.000000000 +0200 ++++ gamess/compall 2014-06-11 18:40:44.000000000 +0200 +@@ -97,7 +97,7 @@ + # Debian uses the -m flag, since its -p replies "unknown" + # Gentoo uses the -m flag, since its -p gives an unusable multiword reply + if ($TARGET == linux64) then +- set chip=(`uname -p`) ++ set chip=(`uname -m`) + if (${#chip} > 1) set chip=unknown + if ($chip == unknown) set chip=`uname -m` + if ($chip == x86_64) set extraflags='-DLINUX64 -m64' +--- gamess/comp.orig 2014-06-11 21:26:28.000000000 +0200 ++++ gamess/comp 2014-06-11 21:26:03.000000000 +0200 +@@ -1806,6 +1804,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + set EXTRAOPT="$EXTRAOPT -fno-whole-file" + breaksw + default: +--- gamess/source/zunix.c.orig 2014-06-12 08:52:56.000000000 +0200 ++++ gamess/source/zunix.c 2014-06-12 08:53:05.000000000 +0200 +@@ -443,7 +443,7 @@ + #ifdef LINUX64 + + #include +-#include ++#include + + #define FORTINT long + +[?25l[?12l[?25h[?1049h[?1h=[?12;25h[?12l[?25h[?25l"diff" [New File]~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ [?12l[?25h[?25lType :quit to exit Vim[?12l[?25h[?1l>[?1049lVim: Error reading input, exiting... +Vim: Finished. +2 files to edit -- GitLab From 7de418fa703682fea59f8862a436376052e949ac Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 27 Oct 2014 09:48:31 +0100 Subject: [PATCH 036/911] GATK-3.3-0 with message on load (modloadmsg) for convenience --- .../g/GATK/GATK-3.3-0-Java-1.7.0_21.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb new file mode 100644 index 0000000000..065919e6f3 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.3-0' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +java = 'Java' +javaver = '1.7.0_21' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 008234b4c4ff2c2acda8f3eab7c60112ff4cf64b Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 28 Oct 2014 16:29:30 +0100 Subject: [PATCH 037/911] added Java dependencies to EMBOSS easyconfigs --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb | 3 ++- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index d309d40cd6..1d00add803 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -16,7 +16,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] sources = [SOURCE_TAR_GZ] -dependencies = [('libharu', '2.2.0')] +dependencies = [('libharu', '2.2.0'), + ('Java','1.7.0_21', '', True)] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb index c355837e99..55f9ab8798 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb @@ -16,7 +16,8 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] sources = [SOURCE_TAR_GZ] -dependencies = [('libharu', '2.2.0')] +dependencies = [('libharu', '2.2.0'), + ('Java','1.7.0_21', '', True)] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index f3398b3949..2561c7e76e 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -16,7 +16,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['ftp://emboss.open-bio.org/pub/EMBOSS/'] sources = [SOURCE_TAR_GZ] -dependencies = [('libharu', '2.2.0')] +dependencies = [('libharu', '2.2.0'), + ('Java','1.7.0_21', '', True)] configopts = " --with-hpdf=$EBROOTLIBHARU " -- GitLab From b26c3aaa4fa20e86f329b08ab27162a7dc34cacc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 5 Nov 2014 15:43:05 +0100 Subject: [PATCH 038/911] ncdf4 - netcdf4 for R 3.1.1 intel2014b --- .../n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000..cdf98f1940 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.13' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2') +] + +moduleclass = 'math' -- GitLab From 98a44a2ff6ac5530414bd183076d2ab7d42a85a0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 7 Nov 2014 16:57:34 +0000 Subject: [PATCH 039/911] Just bumping the bowtie version to the most recent. Compiles fine under goolf 1.4.10 Adding an author name so that users can complain more directly --- .../b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..0240ff0e2c --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team + +name = 'Bowtie' +version = '1.1.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' -- GitLab From 6ce40a54a62e04bdd6dd4a10f9c4fdfef3672440 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 11:05:49 +0100 Subject: [PATCH 040/911] Update to NWChem 6.5 --- ...243-intel-2014b-2014-09-10-Python-2.7.8.eb | 31 +++++++++++++++++++ ...Chem-6.5.revision26243-parallelbuild.patch | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb new file mode 100644 index 0000000000..2eefc9a7f3 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -0,0 +1,31 @@ +name = 'NWChem' +version = '6.5.revision26243' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'i8': True} + +source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +verdate = '2014-09-10' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch new file mode 100644 index 0000000000..8558fe4778 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -0,0 +1,29 @@ +--- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 ++++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1394,7 +1394,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1814,7 +1814,7 @@ + endif + endif + DEFINES += -DEXT_INT +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + _CPU = $(shell uname -m ) + ifeq ($(BLAS_LIB),) + CORE_SUBDIRS_EXTRA += blas +@@ -1923,7 +1923,7 @@ + endif # end of ia32 bit + ifeq ($(_CPU),x86_64) + # +- MAKEFLAGS = -j 2 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + COPTIMIZE = -O1 + ifeq ($(NWCHEM_TARGET),CATAMOUNT) + FC=pgf90 -- GitLab From a8d699b11c25fa0f9eef01317e97c076653ef451 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Nov 2014 16:43:53 +0100 Subject: [PATCH 041/911] No vec-report, please --- ...Chem-6.5.revision26243-parallelbuild.patch | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch index 8558fe4778..c3a7a32982 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -1,5 +1,16 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 --- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 +++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1231,7 +1231,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif @@ -1394,7 +1394,7 @@ CORE_SUBDIRS_EXTRA = blas lapack CC = gcc @@ -9,6 +20,24 @@ INSTALL = @echo $@ is built CPP = gcc -E -nostdinc -undef -P FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1527,7 +1527,7 @@ + DEFINES += -DGFORTRAN + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1602,7 +1602,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII @@ -1814,7 +1814,7 @@ endif endif @@ -27,3 +56,37 @@ COPTIMIZE = -O1 ifeq ($(NWCHEM_TARGET),CATAMOUNT) FC=pgf90 +@@ -1959,19 +1959,17 @@ + ifeq ($(_IFCV15ORNEWER), Y) + FOPTIONS += -qopt-report-file=stderr + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -2086,9 +2084,9 @@ + ICCV15ORNEWER=$(shell icc -V 2>&1|egrep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}') + COPTIONS += -xHOST -ftz + ifeq ($(ICCV15ORNEWER), Y) +- COPTIONS += -qopt-report-phase:openmp -vec-report=1 ++ COPTIONS += -qopt-report-phase:openmp + else +- COPTIONS += -openmp-report=2 -vec-report=1 ++ COPTIONS += -openmp-report0 + endif + #old COPTIMIZE = -O3 -hlo -mP2OPT_hlo_level=2 + COPTIMIZE = -O3 -- GitLab From 9aafec03d3092d979d73f1d276e14adb2319db2a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 19 Nov 2014 16:05:29 +0100 Subject: [PATCH 042/911] HTSeq for intel-2014b plus version bump --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..1f11e79748 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' -- GitLab From e1554e9905795b3df9e05173cf111b5a4e429978 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 043/911] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From 72bbdc9bd8a170dabd0a835f31d962bb84a890bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 044/911] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From ffae6d949021809817926cfc0514897cea9bfcb5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 045/911] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 5cfb9de38252efd9fd5a2a37eab503368dae7d01 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 11:56:24 +0100 Subject: [PATCH 046/911] add Quip Signed-off-by: Fotis Georgatos --- .../q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb new file mode 100644 index 0000000000..47c8f4a6cc --- /dev/null +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +name = 'Quip' +version = '1.1.8' + +homepage = 'http://homes.cs.washington.edu/~dcjones/quip' +description = """Quip compresses next-generation sequencing data with extreme prejudice. + It supports input and output in the FASTQ and SAM/BAM formats, + compressing large datasets to as little as 15% of their original size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +sanity_check_paths = { + 'files': ["quip"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 6e0b86d409154f6b60649b183ce317b9b3fdfe39 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 11:58:19 +0100 Subject: [PATCH 047/911] state which toolchain Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index 47c8f4a6cc..e34b7fe112 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Copyright:: Copyright 2012-2014 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ @@ -15,7 +15,7 @@ description = """Quip compresses next-generation sequencing data with extreme pr It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'GCC', 'version': '4.8.2'} # eg. http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz sources = [SOURCELOWER_TAR_GZ] -- GitLab From c0950bb40f746b51318c0e04c4a3331a9fa71d87 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 12:11:03 +0100 Subject: [PATCH 048/911] supply working version of quip plz Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index e34b7fe112..3a9fc3b2e2 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -22,7 +22,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] sanity_check_paths = { - 'files': ["quip"], + 'files': ["bin/quip"], 'dirs': [] } -- GitLab From d4556c469fcf7acee1b7de50c7a21f1dd6025b6b Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 13:02:24 +0100 Subject: [PATCH 049/911] add ZPAQ --- .../easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb new file mode 100644 index 0000000000..2b30364a1b --- /dev/null +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'MakeCp' + +name = 'ZPAQ' +version = '6.57' + +homepage = 'http://mattmahoney.net/dc/zpaq.html' +description = """Quip compresses next-generation sequencing data with extreme prejudice. + It supports input and output in the FASTQ and SAM/BAM formats, + compressing large datasets to as little as 15% of their original size.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +# eg. http://mattmahoney.net/dc/zpaq657.zip +sources = ['%%(namelower)s%s.zip' % ''.join(version.split('.'))] +source_urls = ['http://mattmahoney.net/dc/'] + +makeopts = ' && pod2man zpaq.pod > zpaq.1' + +files_to_copy = [(["zpaq"], 'bin'), (["zpaq.1"], 'share/man')] + +sanity_check_paths = { + 'files': ["bin/zpaq", "share/man/zpaq.1"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 98297d85409e15060300e02ffc76305f2bad1feb Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 17:58:17 +0100 Subject: [PATCH 050/911] add fqzcomp --- .../f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb new file mode 100644 index 0000000000..3ca5906073 --- /dev/null +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'MakeCp' + +name = 'fqzcomp' +version = '4.6' + +homepage = 'http://sourceforge.net/projects/fqzcomp/' +description = """Fqzcomp is a basic fastq compressor, designed primarily for high performance. + Despite that it is comparable to bzip2 for compression levels.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +# eg. http://sourceforge.net/projects/fqzcomp/files/fqzcomp-4.6.tar.gz/download +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +skipsteps = ['configure'] + +files_to_copy = [(['fqz_comp'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/fqz_comp"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 5b45bf8b195803697ab6d1ca1c453d35e269a609 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 18:00:49 +0100 Subject: [PATCH 051/911] add DSRC --- .../d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb new file mode 100644 index 0000000000..f3b7c1168d --- /dev/null +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'Binary' + +name = 'DSRC' +version = '2.0rc' +versionsuffix = '-linux-64-bit' + +homepage = 'http://sun.aei.polsl.pl/dsrc' +description = """DNA Sequence Reads Compression is an application designed for compression of data files + containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few + (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression + programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://sun.aei.polsl.pl/dsrc/download/2.0rc/dsrc +sources = [name.lower()] +source_urls = [homepage + '/download/%(version)s/'] + +sanity_check_paths = { + 'files': ['dsrc'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From d607a2a3d3c2e092ab6fad9e0324650f068ceb55 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 18:11:34 +0100 Subject: [PATCH 052/911] add SCALCE --- .../s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb new file mode 100644 index 0000000000..a08d8c5af1 --- /dev/null +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'MakeCp' + +name = 'SCALCE' +version = '2.7' + +homepage = 'http://scalce.sourceforge.net/Home' +description = """SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing + to obtain better compression rate. SCALCE has been specifically designed for Illumina reads but it can + handle other technologies (that generate base pair reads) if the read length is the same throughout the file.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +# eg. http://sourceforge.net/projects/scalce/files/2.7/scalce-v2.7-src.tar.gz/download +sources = ['%(namelower)s-v%(version)s-src.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +preconfigopts = 'cd zlib-1.2.8 &&' +makeopts = '-C zlib-1.2.8 && make all' + +files_to_copy = [(['scalce'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/scalce"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 37b4af6210d416099a63770f43e58d8957f610d4 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 18:12:40 +0100 Subject: [PATCH 053/911] ZPAQ is really bio category --- easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index 2b30364a1b..0911f911da 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -32,4 +32,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'tools' +moduleclass = 'bio' -- GitLab From 6830a0e8d4938a520caa3cbb52a9f81ae2c9db67 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 19:01:10 +0100 Subject: [PATCH 054/911] add fastqz --- .../f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 38 +++++++++++++++++++ .../easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 2 +- 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb new file mode 100644 index 0000000000..42feaece95 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'MakeCp' + +name = 'fastqz' +version = '1.5' + +homepage = 'http://mattmahoney.net/dc/fastqz/' +description = """fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing machines. + It is one of the compressors described in the paper: Bonfield JK, Mahoney MV (2013) Compression of + FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +dependencies = [('ZPAQ', '6.57')] + +# eg. http://mattmahoney.net/dc/fastqz/fastqz15.cpp & http://mattmahoney.net/dc/fastqz/fapack.cpp +sources = [('fastqz15.cpp', 'cp %s %(builddir)s/fastqz.cpp'), ('fapack.cpp', 'cp %s %(builddir)s')] +source_urls = [homepage] + +premakeopts = 'g++ -O3 -msse2 -s -lpthread fastqz.cpp $EBROOTZPAQ/include/libzpaq.cpp -o fastqz' +premakeopts += '&& g++ -O3 -s fapack.cpp -o fapack && /bin/true ' + +files_to_copy = [(['fastqz', 'fapack'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/fastqz", "bin/fapack"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index 0911f911da..feed550444 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -25,7 +25,7 @@ source_urls = ['http://mattmahoney.net/dc/'] makeopts = ' && pod2man zpaq.pod > zpaq.1' -files_to_copy = [(["zpaq"], 'bin'), (["zpaq.1"], 'share/man')] +files_to_copy = [(["zpaq"], 'bin'), (["zpaq.1"], 'share/man'), (["libzpaq.h", "libzpaq.cpp"], 'include')] sanity_check_paths = { 'files': ["bin/zpaq", "share/man/zpaq.1"], -- GitLab From d40818d8966ed3e67b3b94e0ef3ef451bfb25c55 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 10 Dec 2014 19:06:46 +0100 Subject: [PATCH 055/911] fix tiny little bugs, left & right --- easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 3 +-- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 3 ++- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index f3b7c1168d..8c4a091d7f 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -1,11 +1,10 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Copyright:: Copyright 2012-2014 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ -# ## easyblock = 'Binary' diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 42feaece95..5946229fc3 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -22,7 +22,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} dependencies = [('ZPAQ', '6.57')] # eg. http://mattmahoney.net/dc/fastqz/fastqz15.cpp & http://mattmahoney.net/dc/fastqz/fapack.cpp -sources = [('fastqz15.cpp', 'cp %s %(builddir)s/fastqz.cpp'), ('fapack.cpp', 'cp %s %(builddir)s')] +minver = ''.join(version.split('.')) +sources = [('fastqz%s.cpp' % minver, 'cp %s %(builddir)s/fastqz.cpp'), ('fapack.cpp', 'cp %s %(builddir)s')] source_urls = [homepage] premakeopts = 'g++ -O3 -msse2 -s -lpthread fastqz.cpp $EBROOTZPAQ/include/libzpaq.cpp -o fastqz' diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index 3a9fc3b2e2..c3812cfb0a 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'tools' +moduleclass = 'bio' -- GitLab From b85d1c25f711fd686a68e0b949c4ddc96a3ab93e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:03:42 +0100 Subject: [PATCH 056/911] Update DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb --- .../d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb index ca812f75ef..facf14e7e4 100644 --- a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -15,7 +15,10 @@ perl = 'Perl' perlver = '5.20.0' versionsuffix = '-%s-%s' % (perl, perlver) -dependencies = [(perl, perlver), ("PostgreSQL", "9.3.5")] +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5") +] options = {'modulename': 'DBD::Pg'} -- GitLab From 4d7b48d4445c3f6bdfe814b192939a7ea471c927 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:28 +0100 Subject: [PATCH 057/911] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 9b40199a4f..33c2f00038 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,7 +16,10 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [ + ('openssl-devel', + 'libssl-dev') +] java = 'Java' javaver = '1.7.0_60' @@ -25,6 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From cbf893e6a96a5c2c5e5031fe46e3e1f857ff221f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:05:47 +0100 Subject: [PATCH 058/911] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 33c2f00038..0adb8caf54 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -28,7 +28,7 @@ dependencies = [ (java, javaver, '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), -# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons ] builddependencies = [ -- GitLab From 60481d2dbba84675f5352ce5129dfc6319e19d7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 11 Dec 2014 10:09:08 +0100 Subject: [PATCH 059/911] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 0adb8caf54..b5c98f2a72 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -16,10 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [ - ('openssl-devel', - 'libssl-dev') -] +osdependencies = [('openssl-devel', 'libssl-dev')] java = 'Java' javaver = '1.7.0_60' -- GitLab From 5b9fe63969e0e408b0a565bb501ab826f7f1a455 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 11 Dec 2014 17:06:10 +0100 Subject: [PATCH 060/911] added gtest --- .../g/gtest/gtest-1.6.0-intel-2014b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb new file mode 100644 index 0000000000..7e01fd3fc1 --- /dev/null +++ b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb @@ -0,0 +1,24 @@ +easyblock = "MakeCp" + +name = 'gtest' +version = '1.6.0' + +homepage = 'https://code.google.com/p/googletest/' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_ZIP] +source_urls = ['https://googletest.googlecode.com/files'] + +with_configure = True + + +files_to_copy = ['lib', 'include'] + +sanity_check_paths={ + 'files': ['lib/libgtest.la', 'lib/libgtest_main.la'], + 'dirs': ['include'], +} + +moduleclass = 'devel' -- GitLab From f1e903f9e87acbcc338bff1f99dc0c79a15a66b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 16 Dec 2014 09:20:04 +0100 Subject: [PATCH 061/911] Update PostgreSQL-9.3.5-intel-2014b.eb --- .../easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index b5c98f2a72..f0f5501b84 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'PostgreSQL' version = '9.3.5' -- GitLab From 609a9692c777716c44e719b32376fd8e3d3403a5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 17 Dec 2014 03:28:44 +0100 Subject: [PATCH 062/911] add wherever: easyblock = 'ConfigureMake' Signed-off-by: Fotis Georgatos --- .../easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb | 2 ++ .../easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb | 2 ++ .../easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb | 2 ++ easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb | 2 ++ easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb | 2 ++ .../m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb | 2 ++ easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 2 ++ 11 files changed, 22 insertions(+) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb index 60550f5635..2bc0ea310e 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-goolf-1.4.10.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'Exonerate' version = '2.2.0' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb index 69f1442377..36527565d8 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.2.0-ictce-5.3.0.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'Exonerate' version = '2.2.0' diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb index a9915dbdff..a3b3378d12 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = "FSA" version = "1.15.8" diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb index 037a69fcc4..04a32282f2 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = "FSA" version = "1.15.8" diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb index 766222f0f1..fa3f5214e9 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = 'Infernal' version = "1.1" diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb index b9331ab8e9..47503953c4 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = 'Infernal' version = "1.1" diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb index e64ab0b0d9..bb45fb46c0 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = 'Infernal' version = "1.1" diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb index 2aaa4dd946..5f9369ccab 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = 'Infernal' version = "1.1" diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb index 7fd327efda..6bf747d607 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb @@ -3,6 +3,8 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'ConfigureMake' + name = 'MAFFT' version = '7.130' versionsuffix = '-with-extensions' diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index e04563db6e..19e446bc55 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = "SMALT" version = "0.7.5" diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index 1930c64969..ea469d6b78 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = "SMALT" version = "0.7.5" -- GitLab From 7003265903b25767ff4d133ea36905dae918d6d4 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 17 Dec 2014 03:40:22 +0100 Subject: [PATCH 063/911] fix headers and trim whitespace Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb | 4 ++-- .../i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb | 4 ++-- easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb | 4 ++-- easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb | 3 ++- .../easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb | 4 ++-- 12 files changed, 22 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb index a3b3378d12..0f49be8035 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-goolf-1.4.10.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 University of Luxembourg, Swiss Institute of Bioinformatics -# Authors:: Fotis Georgatos, Pablo Escobar Lopez +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA, Swiss Institute of Bioinformatics +# Authors:: Fotis Georgatos , Pablo Escobar Lopez # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb index 04a32282f2..27159a0ac8 100644 --- a/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/FSA/FSA-1.15.8-ictce-5.3.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 University of Luxembourg, Swiss Institute of Bioinformatics -# Authors:: Fotis Georgatos, Pablo Escobar Lopez +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA, Swiss Institute of Bioinformatics +# Authors:: Fotis Georgatos , Pablo Escobar Lopez # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb index fa3f5214e9..67c9b4b47c 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goalf-1.1.0-no-OFED.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Cedric Laczny , Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb index 47503953c4..33a8943618 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Cedric Laczny , Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb index bb45fb46c0..aa9857ce93 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-4.0.6.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Cedric Laczny , Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb index 5f9369ccab..10d6e8c986 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Cedric Laczny , Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb index b6c3429f3e..051737c067 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb @@ -17,7 +17,8 @@ version = '1.1rc1' homepage = 'http://infernal.janelia.org/' description = """Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases -for RNA structure and sequence similarities.""" + for RNA structure and sequence similarities.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb index 705db63559..d47730c4ff 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb @@ -19,7 +19,6 @@ homepage = 'http://infernal.janelia.org/' description = """Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb index da877e2d72..59d3a92f69 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-goolf-1.4.10.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb index a40acd6d3c..cc4ff83fdd 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-130820-ictce-5.3.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb index 19e446bc55..a2509710ab 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-goolf-1.4.10.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # diff --git a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb index ea469d6b78..97b9385894 100644 --- a/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SMALT/SMALT-0.7.5-ictce-5.3.0.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine -# Authors:: Fotis Georgatos +# Copyright:: Copyright 2012-2014 Uni.Lu/NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # -- GitLab From 7bcb5ac31cf03ffd1559e4f91a163ec59e7c0109 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 17 Dec 2014 15:31:27 +0100 Subject: [PATCH 064/911] Autoconf dep removed --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index e3c5f86d83..ae2c3c32ff 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -24,7 +24,6 @@ sources = ['ocaml-%(version)s.tar.gz'] sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] -builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " -- GitLab From 9ceb44f85bbff02da35f35b5769e759b6f5e09db Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 17 Dec 2014 17:48:12 +0100 Subject: [PATCH 065/911] latest picard easyconfig --- easybuild/easyconfigs/p/picard/picard-1.119.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-1.119.eb diff --git a/easybuild/easyconfigs/p/picard/picard-1.119.eb b/easybuild/easyconfigs/p/picard/picard-1.119.eb new file mode 100644 index 0000000000..cb362554cd --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.119.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.119' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_10')] + +moduleclass = 'bio' -- GitLab From c2a700e5233018acf847e37f8045680d74ea4283 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Thu, 18 Dec 2014 11:22:18 +1300 Subject: [PATCH 066/911] adding suitesparse eb file for goolf 1.5.14 --- ...eSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..0a08f2a7fe --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb @@ -0,0 +1,17 @@ +name = 'SuiteSparse' +version = '4.2.1' + +homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" +toolchain = {'name': 'goolf', 'version': '1.5.14'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} + +source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_ver)] + +moduleclass = 'numlib' -- GitLab From 75860b4c51c93d301268a87a078ec920e67a929f Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Fri, 19 Dec 2014 10:30:32 +1300 Subject: [PATCH 067/911] deleting file that does not belong here --- ...eSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb deleted file mode 100644 index 0a08f2a7fe..0000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.5.14-ParMETIS-4.0.3.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'SuiteSparse' -version = '4.2.1' - -homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) -toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} - -source_urls = ['http://www.cise.ufl.edu/research/sparse/SuiteSparse/'] -sources = [SOURCE_TAR_GZ] - -parmetis = 'ParMETIS' -parmetis_ver = '4.0.3' -versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) -dependencies = [(parmetis, parmetis_ver)] - -moduleclass = 'numlib' -- GitLab From b5c8060b45cb6a89ee08b847f73f0efc590931eb Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Mon, 22 Dec 2014 14:37:34 +1300 Subject: [PATCH 068/911] configs for AFNI and PyQt, adding R config for goolf-1.5.14' --- .../easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 275 ++++++++++++++++++ 1 file changed, 275 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..c06ef496d4 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -0,0 +1,275 @@ +name = 'R' +version = '3.1.2' +bioc_version = '3.0' #2.14' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +#toolchain = {'name': 'iomkl', 'version': '6.5.4'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'precise': True, 'opt': True} # 'openmp' is enabled in R by default +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +#preconfigopts = 'BLAS_LIBS="$LIBBLAS_MT" LAPACK_LIBS="$LIBLAPACK_MT"' # use multi-thread BLAS/LAPACK +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' # use multi-thread BLAS/LAPACK + +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.2'), # or 6.3 + ('ncurses', '5.9'), + ('libpng', '1.6.10'), # for plotting # or 1.6.12 + ('libxml2', '2.9.1'), # for XML + ('SQLite', '3.8.4.3'), # for RSQLite + ('GEOS', '3.3.5'), # for rgeos, which is for spacetime + ('cURL', '7.29.0'), # for RCurl +# ('netCDF-parallel', '4.2'), # for pbdNCDF4 + ('Java', '1.8.0_5', '', True), # Java bindings are built if Java is found, might as well provide it +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + + ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', + 'R.h', 'Rinterface.h', 'Rinternals.h', + 'Rmath.h', 'Rversion.h', 'S.h']] + + ['lib64/R/modules/%s' % x for x in ['internet.so', 'lapack.so', 'vfonts.so']] + + ['lib64/R/lib/libR.so'], + 'dirs': [] +} + + +def ext_options_extra(**kw): + options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib', # alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + } + for (name, value) in kw.items(): + options[name] = value + return options + +ext_options = ext_options_extra() + +if "easybuild R extension patching is still broken": + snow_options = ext_options_extra( + source_tmpl = '%(name)s_%(version)s-hpcpatched.tar.gz', source_urls = []) +else: + snow_options = ext_options_extra( + patches = ['snowfixedmpi.patch']) + +bioconductor_options = ext_options_extra( + source_urls = ['http://www.bioconductor.org/packages/%s/bioc/src/contrib/' % bioc_version]) + + +# Left out from original ictce easyconfig: translations & tcltk (extensions), libjpeg-turbo (dep) + +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', ext_options), + ('snow', '0.3-13', snow_options), + ('snowfall', '1.84-6', ext_options), + ('iterators', '1.0.7', ext_options), + ('codetools', '0.2-9', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMPI', '0.2', ext_options), + ('doParallel', '1.0.8', ext_options), + ('rJava', '0.9-6', ext_options), + ('irace', '1.05', ext_options), + ('lattice', '0.20-29', ext_options), + ('RColorBrewer', '1.0-5', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.1-4', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.3', ext_options), + ('RcppEigen', '0.3.2.2.0', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('MASS', '7.3-35', ext_options), + ('class', '7.3-11', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-8', ext_options), + ('car', '2.0-21', ext_options), + ('colorspace', '1.2-4', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('robustbase', '0.92-1', ext_options), + ('sp', '1.0-16', ext_options), + ('vcd', '1.3-2', ext_options), + ('rpart', '4.1-8', ext_options), + ('randomForest', '4.6-10', ext_options), + ('mice', '2.22', ext_options), + ('nlme', '3.1-118', ext_options), + ('nloptr', '1.0.4', ext_options), + ('minqa', '1.2.4', ext_options), + ('lme4', '1.1-7', ext_options), + ('ape', '3.1-4', ext_options), + ('mgcv', '1.8-3', ext_options), + ('logistf', '1.21', ext_options), + ('bitops', '1.0-6', ext_options), + ('RCurl', '1.95-4.3', ext_options), # For rtracklayer + ('boot', '1.3-13', ext_options), + ('foreign', '0.8-61', ext_options), + ('survival', '2.37-7', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-1', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-13', ext_options), + ('zoo', '1.7-11', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-1', ext_options), + ('mvtnorm', '1.0-1', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('coda', '0.16-1', ext_options), + ('pscl', '1.4.6', ext_options), + ('sandwich', '2.3-2', ext_options), + ('sfsmisc', '1.0-26', ext_options), + ('spatial', '7.3-8', ext_options), + ('VGAM', '0.9-5', ext_options), + ('waveslim', '1.7.3', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-32', ext_options), + ('neuRosim', '0.2-10', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.6.1', ext_options), + ('R.oo', '1.18.0', ext_options), + ('Rniftilib', '0.0-32', ext_options), + ('igraph', '0.7.1', ext_options), + ('gbm', '2.1', ext_options), + ('stringr', '0.6.2', ext_options), + ('plyr', '1.8.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('reshape2', '1.4', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.1-2', ext_options), + ('cluster', '1.15.3', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('Hmisc', '3.14-5', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.4', ext_options), + ('fastcluster', '1.1.13', ext_options), + ('digest', '0.6.4', ext_options), + ('gtable', '0.1.2', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.0', ext_options), + ('maptools', '0.8-30', ext_options), + ('intervals', '0.15.0', ext_options), + ('xts', '0.9-7', ext_options), + ('rgeos', '0.3-8', ext_options), + ('spacetime', '1.1-1', ext_options), + ('FNN', '1.1', ext_options), + ('gstat', '1.0-19', ext_options), + ('deldir', '0.1-6', ext_options), + ('LearnBayes', '2.15', ext_options), + ('abind', '1.4-0', ext_options), + ('spdep', '0.5-77', ext_options), + ('splancs', '2.01-36', ext_options), + ('DCluster', '0.2-6', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-0', ext_options), + ('goftest', '1.0-2', ext_options), + ('spatstat', '1.39-1', ext_options), + + ('getopt', '1.20.0', ext_options), + ('optparse', '1.2.0', ext_options), # for QIIME + ('permute', '0.8-3', ext_options), + ('vegan', '2.2-0', ext_options), # for QIIME + + ('spam', '1.0-1', ext_options), + ('RandomFields', '3.0.35', ext_options), # 3.0.44 requires Tcl etc. + ('geoR', '1.7-4.1', ext_options), + ('geoRglm', '0.9-4', ext_options), + ('R2WinBUGS', '2.1-19', ext_options), + ('R2OpenBUGS', '3.2-2.2', ext_options), + ('akima', '0.5-11', ext_options), + ('rjags', '3-14', ext_options), + ('R2jags', '0.04-03', ext_options), + ('DBI', '0.3.1', ext_options), + ('xtable', '1.7-4', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('lpSolve', '5.6.10', ext_options), + ('glmmML', '1.0', ext_options), + ('survey', '3.30-3', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('crs', '0.15-23', ext_options), + ('dclone', '2.0-0', ext_options), + + ('caTools', '1.17.1', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('gplots', '2.14.2', ext_options), + ('gsalib', '2.0', ext_options), + ('inline', '0.3.13', ext_options), + ('RcppArmadillo', '0.4.500.0', ext_options), + + ('XML', '3.98-1.1', ext_options), + ('spgrass6', '0.8-6', ext_options), + + ('checkmate', '1.5.0', ext_options), + ('BBmisc', '1.8', ext_options), + ('fail', '1.2', ext_options), + ('brew', '1.0-6', ext_options), + ('base64enc', '0.1-2', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('BatchJobs', '1.5', ext_options), + + ('BiocInstaller', '1.16.1', bioconductor_options), + ('BiocGenerics', '0.12.1', bioconductor_options), + ('Biobase', '2.26.0', bioconductor_options), + ('S4Vectors', '0.4.0', bioconductor_options), + ('IRanges', '2.0.0', bioconductor_options), + ('XVector', '0.6.0', bioconductor_options), + ('zlibbioc', '1.12.0', bioconductor_options), + ('Biostrings', '2.34.0', bioconductor_options), + ('GenomeInfoDb', '1.2.3', bioconductor_options), + ('AnnotationDbi', '1.28.1', bioconductor_options), + ('GenomicRanges', '1.18.1', bioconductor_options), + ('Rsamtools', '1.18.2', bioconductor_options), + ('BiocParallel', '1.0.0', bioconductor_options), + ('GenomicAlignments', '1.2.1', bioconductor_options), + ('rtracklayer', '1.26.2', bioconductor_options), + ('BSgenome', '1.34.0', bioconductor_options), + ('graph', '1.44.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('DESeq2', '1.6.2', bioconductor_options), + ('ShortRead', '1.24.0', bioconductor_options), + + ('rlecuyer', '0.3-3', ext_options), + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.1-9', ext_options), + ('pbdBASE', '0.2-3', ext_options), # with icc: Rtools/tools.c(41): error: incorrect use of va_start + ('pbdDMAT', '0.2-3', ext_options), # depends on pdbBASE + #('pbdNCDF4', '0.1-4', ext_options), # add parallel netCDF as a dependency if this gets added + + #('BH', '1.54.0-5', ext_options), # Boost headers for rstan + #('rstan', '2.4', ext_options_extra(source_urls = ['http://rstan.org/repo/src/contrib/'])), +] + +moduleclass = 'lang' -- GitLab From 9474643f13bb40f1c95e0ffe761076ce7b1d398b Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Mon, 22 Dec 2014 14:42:52 +1300 Subject: [PATCH 069/911] adding config for SIP too --- .../s/SIP/SIP-4.16.4-goolf-1.5.14.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..5b0fc8c465 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMakePythonPackage' +name = 'SIP' +version = '4.16.4' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """ +SIP is a tool that makes it very easy to create Python bindings for C and C++ +libraries. It was originally developed to create PyQt, the Python bindings +for the Qt toolkit, but can be used to create bindings for any C or C++ library. +""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.4'] + +dependencies = [('Python', '2.7.6')] + +configopts = " configure.py" + -- GitLab From 628557f8279cd72c1b40dbbe933e8dcf90199a7c Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Mon, 22 Dec 2014 15:00:33 +1300 Subject: [PATCH 070/911] adding more configs --- .../AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb | 33 +++++++++++++++++++ .../PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb | 25 ++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb new file mode 100644 index 0000000000..d90c936191 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland + + +name = 'AFNI' +version = 'linux_openmp_64' +# see VersionDate in caps3 output + +easyblock = 'PackedBinary' + +homepage = 'http://afni.nimh.nih.gov' +description = """Free software for analysis and display of FMRI data """ + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [('http://afni.nimh.nih.gov/pub/dist/tgz/')] +sources = ['%(version)s.tgz'] + +dependencies = [ + ('R', '3.1.2'), + ('PyQt', 'x11-gpl-4.11.3'), +] + +osdependencies = [ + ('libXp','tcsh') +] + +sanity_check_paths = { + 'files': ['afni'], + 'dirs': [], +} + diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..6c3e97606d --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMakePythonPackage' +name = 'PyQt' +version = 'x11-gpl-4.11.3' + + + + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """ +PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework +and runs on all platforms supported by Qt including Windows, MacOS/X and Linux. +PyQt5 supports Qt v5. PyQt4 supports Qt v4 and will build against Qt v5. +The bindings are implemented as a set of Python modules and contain over 620 classes. +""" +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3'] + +dependencies = [('Python', '2.7.6'), + ('SIP','4.16.4'), + ('Qt','4.8.5')] + +configopts = " configure-ng.py --confirm-license" + -- GitLab From 1f06c2c43c152b2170605a2af9a5d159535e45a2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 6 Jan 2015 17:15:25 +0100 Subject: [PATCH 071/911] added newer cutadapt versions. Updated download url --- .../cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ .../cutadapt-1.5-foss-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ .../cutadapt-1.6-foss-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ .../cutadapt-1.7-foss-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ .../cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 5 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..cf67752ee4 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.4.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..f9435f3efa --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..b165a51c0c --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.6' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..fbe7a035d3 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.7' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..a5093a2f21 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.7.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 9c43f96b16714dec9f4ad2548ad82d2cc1bfbd26 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 11 Jan 2015 11:32:31 +0100 Subject: [PATCH 072/911] init gompi-1.6.10 w. OpenMPI/1.8.4-GCC-4.8.4 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb | 25 ++++++++++++ .../h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb | 23 +++++++++++ .../n/numactl/numactl-2.0.9-GCC-4.8.4.eb | 24 ++++++++++++ .../o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 38 +++++++++++++++++++ 4 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb b/easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb new file mode 100644 index 0000000000..a2dd8f90be --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.6.20' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.4' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.8.4' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb new file mode 100644 index 0000000000..2d5251f89c --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.10.0" + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +dependencies = [('numactl', '2.0.9')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb new file mode 100644 index 0000000000..631c25771b --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.9' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. +It does this by supplying a NUMA memory policy to the operating system before running your program. +The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +sources = [SOURCE_TAR_GZ] +source_urls = ["ftp://oss.sgi.com/www/projects/libnuma/download/"] + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +skipsteps = ['configure'] +installopts = "PREFIX=%(installdir)s libdir='${prefix}/lib'" + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb new file mode 100644 index 0000000000..bf74f56b70 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = "1.8.4" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.0')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 4343d72938ddb933f53febcbf66ff1d9d687702f Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 11 Jan 2015 12:15:51 +0100 Subject: [PATCH 073/911] init fftw, openblas, scalapack w. gompi/1.6.20 Signed-off-by: Fotis Georgatos --- .../f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb | 34 ++++++++++++ easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb | 37 +++++++++++++ .../OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 52 +++++++++++++++++++ ...mpi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 29 +++++++++++ 4 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb new file mode 100644 index 0000000000..002bd8dda5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.6.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb new file mode 100644 index 0000000000..635ab13824 --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.6.20' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.8.4' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + ('GCC', '4.8.4'), + ('OpenMPI', '1.8.4', '', comp), # part of gompi-1.6.20 + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..c678bbcc6e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' + diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..3931fb0ef3 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,29 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '1.6.20'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +comp_name = 'GCC' +comp_version = '4.8.4' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, comp)] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From e28c188800d346499afe855af45cbdf29c66ed62 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 11 Jan 2015 12:23:24 +0100 Subject: [PATCH 074/911] add HPL/2.1 for goolf/1.6.20 Signed-off-by: Fotis Georgatos --- .../easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb new file mode 100644 index 0000000000..c245a1d304 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.6.20'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From fbe18fa83394133ca1a1601ec15a01396a4a7280 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:04 +0100 Subject: [PATCH 075/911] All deps for gnuplot 5 with intel-2015a --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 29 +++++++++++++++++ .../e/expat/expat-2.1.0-intel-2015a.eb | 15 +++++++++ .../fontconfig-2.11.1-intel-2015a.eb | 22 +++++++++++++ .../f/freetype/freetype-2.5.5-intel-2015a.eb | 21 +++++++++++++ .../libjpeg-turbo-1.4.0-intel-2015a.eb | 24 ++++++++++++++ .../l/libpng/libpng-1.6.16-intel-2015a.eb | 19 ++++++++++++ .../n/NASM/NASM-2.11.06-intel-2015a.eb | 31 +++++++++++++++++++ .../p/pixman/pixman-0.32.6-intel-2015a.eb | 20 ++++++++++++ 8 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb new file mode 100644 index 0000000000..e43e75307f --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. +Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, +PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('freetype', '2.5.5'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb new file mode 100644 index 0000000000..0eb1188648 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb new file mode 100644 index 0000000000..a8f2612b6a --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb new file mode 100644 index 0000000000..3f93bd6070 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb new file mode 100644 index 0000000000..639a4e904b --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb new file mode 100644 index 0000000000..23292508e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb new file mode 100644 index 0000000000..88003caecd --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb new file mode 100644 index 0000000000..480001289a --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 2bdc74f8dacb175fddf22ea06495f54ece3236fc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 13:03:28 +0100 Subject: [PATCH 076/911] Gnuplot 5 for intel-2014b and intel-2015a --- .../g/gnuplot/gnuplot-5.0.0-intel-2014b.eb | 35 +++++++++++++++++++ .../g/gnuplot/gnuplot-5.0.0-intel-2015a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb new file mode 100644 index 0000000000..e30d4a22d3 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb new file mode 100644 index 0000000000..8f7d80279e --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' -- GitLab From 441dd17e18b9dffa536fe73cd3aa5ee70db3642e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:18:56 +0100 Subject: [PATCH 077/911] Added autoconf for intel 2015a --- .../a/Autoconf/Autoconf-2.69-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb new file mode 100644 index 0000000000..a3c280daab --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From d24528dc73eec74272050e5dcf06876c35a902a5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:19:13 +0100 Subject: [PATCH 078/911] Updated cairo to work around pthread detection issues --- .../c/cairo/cairo-1.12.18-intel-2015a.eb | 6 ++++++ .../c/cairo/cairo-1.12.18-pthread-check.patch | 17 +++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index e43e75307f..d051b99544 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,6 +23,12 @@ dependencies = [ ('bzip2', '1.0.6'), ] +builddependencies = [('autoconf', '2.69')] + +patches = ['cairo-1.12.18-pthread-check.patch'] + +preconfigopts = " autoconf configure.ac > configure && " + # disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC configopts = "--enable-symbol-lookup=no" diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch new file mode 100644 index 0000000000..20821e7211 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -0,0 +1,17 @@ +# Make sure the configure script doesn't fail over a 'no version information available' warning +# by wpoely86@gmail.com +diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.cairo.m4 +--- cairo-1.12.18.orig/build/aclocal.cairo.m4 2013-03-15 21:29:27.000000000 +0100 ++++ cairo-1.12.18/build/aclocal.cairo.m4 2015-01-14 14:08:01.000000000 +0100 +@@ -101,9 +101,9 @@ + $1 + AC_LINK_IFELSE( + [AC_LANG_SOURCE([$_compile_program])], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=yes], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` + cairo_cc_flag=no]) + + if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 9701985a5c4b5e603263bed5d39ff6bfa557dc5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 14:20:55 +0100 Subject: [PATCH 079/911] Fix typo in cairo --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index d051b99544..c3b27fffcb 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('autoconf', '2.69')] +builddependencies = [('Autoconf', '2.69')] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 22feb6bfe7fafec7f5e1dbf667ea9aff4ef0e70e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 14 Jan 2015 16:52:23 +0100 Subject: [PATCH 080/911] Stupid stupid stupid error in patch --- .../easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch index 20821e7211..9019afb946 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -8,10 +8,10 @@ diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.c AC_LINK_IFELSE( [AC_LANG_SOURCE([$_compile_program])], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=yes], - [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` -+ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err && grep -v 'no version information available' ` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` cairo_cc_flag=no]) if test "x$cairo_cc_stderr" != "x"; then -- GitLab From 0eecf91045d577231c83b4bc0fab1091d2835633 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 10:54:48 +0100 Subject: [PATCH 081/911] fix style issues in AFNI easyconfig, remove incomplete/out-of-sync R 3.1.2 easyconfig --- ...-linux_openmp_64-goolf-1.5.14-20141023.eb} | 16 +- .../easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 275 ------------------ 2 files changed, 8 insertions(+), 283 deletions(-) rename easybuild/easyconfigs/a/AFNI/{AFNI-linux_openmp_64-goolf-1.5.14.eb => AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb} (72%) delete mode 100644 easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb similarity index 72% rename from easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb rename to easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb index d90c936191..108fd2aeb2 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb @@ -1,33 +1,33 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Bart Verleye # Center for eResearch, Auckland - +easyblock = 'PackedBinary' name = 'AFNI' version = 'linux_openmp_64' -# see VersionDate in caps3 output - -easyblock = 'PackedBinary' +versionsuffix = '-20141023' homepage = 'http://afni.nimh.nih.gov' description = """Free software for analysis and display of FMRI data """ toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = [('http://afni.nimh.nih.gov/pub/dist/tgz/')] +source_urls = ['http://afni.nimh.nih.gov/pub/dist/tgz/'] sources = ['%(version)s.tgz'] +checksums = [''] dependencies = [ ('R', '3.1.2'), ('PyQt', 'x11-gpl-4.11.3'), + ('tcsh', '6.18.01'), + ('libXp', '1.0.2'), ] -osdependencies = [ - ('libXp','tcsh') -] +modextrapaths = {'PATH': ['']} sanity_check_paths = { 'files': ['afni'], 'dirs': [], } +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb deleted file mode 100644 index c06ef496d4..0000000000 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ /dev/null @@ -1,275 +0,0 @@ -name = 'R' -version = '3.1.2' -bioc_version = '3.0' #2.14' - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -#toolchain = {'name': 'iomkl', 'version': '6.5.4'} -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'precise': True, 'opt': True} # 'openmp' is enabled in R by default -sources = [SOURCE_TAR_GZ] -source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] - -#preconfigopts = 'BLAS_LIBS="$LIBBLAS_MT" LAPACK_LIBS="$LIBLAPACK_MT"' # use multi-thread BLAS/LAPACK -preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' # use multi-thread BLAS/LAPACK - -configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below -configopts += " --with-recommended-packages=no" - -dependencies = [ - ('libreadline', '6.2'), # or 6.3 - ('ncurses', '5.9'), - ('libpng', '1.6.10'), # for plotting # or 1.6.12 - ('libxml2', '2.9.1'), # for XML - ('SQLite', '3.8.4.3'), # for RSQLite - ('GEOS', '3.3.5'), # for rgeos, which is for spacetime - ('cURL', '7.29.0'), # for RCurl -# ('netCDF-parallel', '4.2'), # for pbdNCDF4 - ('Java', '1.8.0_5', '', True), # Java bindings are built if Java is found, might as well provide it -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['R', 'Rscript']] + - ['lib64/R/include/%s' % x for x in ['Rconfig.h', 'Rdefines.h', 'Rembedded.h', - 'R.h', 'Rinterface.h', 'Rinternals.h', - 'Rmath.h', 'Rversion.h', 'S.h']] + - ['lib64/R/modules/%s' % x for x in ['internet.so', 'lapack.so', 'vfonts.so']] + - ['lib64/R/lib/libR.so'], - 'dirs': [] -} - - -def ext_options_extra(**kw): - options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib', # alternative for current packages - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', - } - for (name, value) in kw.items(): - options[name] = value - return options - -ext_options = ext_options_extra() - -if "easybuild R extension patching is still broken": - snow_options = ext_options_extra( - source_tmpl = '%(name)s_%(version)s-hpcpatched.tar.gz', source_urls = []) -else: - snow_options = ext_options_extra( - patches = ['snowfixedmpi.patch']) - -bioconductor_options = ext_options_extra( - source_urls = ['http://www.bioconductor.org/packages/%s/bioc/src/contrib/' % bioc_version]) - - -# Left out from original ictce easyconfig: translations & tcltk (extensions), libjpeg-turbo (dep) - -exts_list = [ - # default libraries, only here to sanity check their presence - 'base', - 'compiler', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'parallel', - 'splines', - 'stats', - 'stats4', - 'tools', - 'utils', - - # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', ext_options), - ('snow', '0.3-13', snow_options), - ('snowfall', '1.84-6', ext_options), - ('iterators', '1.0.7', ext_options), - ('codetools', '0.2-9', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMPI', '0.2', ext_options), - ('doParallel', '1.0.8', ext_options), - ('rJava', '0.9-6', ext_options), - ('irace', '1.05', ext_options), - ('lattice', '0.20-29', ext_options), - ('RColorBrewer', '1.0-5', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-4', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.3', ext_options), - ('RcppEigen', '0.3.2.2.0', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('MASS', '7.3-35', ext_options), - ('class', '7.3-11', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-8', ext_options), - ('car', '2.0-21', ext_options), - ('colorspace', '1.2-4', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('robustbase', '0.92-1', ext_options), - ('sp', '1.0-16', ext_options), - ('vcd', '1.3-2', ext_options), - ('rpart', '4.1-8', ext_options), - ('randomForest', '4.6-10', ext_options), - ('mice', '2.22', ext_options), - ('nlme', '3.1-118', ext_options), - ('nloptr', '1.0.4', ext_options), - ('minqa', '1.2.4', ext_options), - ('lme4', '1.1-7', ext_options), - ('ape', '3.1-4', ext_options), - ('mgcv', '1.8-3', ext_options), - ('logistf', '1.21', ext_options), - ('bitops', '1.0-6', ext_options), - ('RCurl', '1.95-4.3', ext_options), # For rtracklayer - ('boot', '1.3-13', ext_options), - ('foreign', '0.8-61', ext_options), - ('survival', '2.37-7', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-1', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-13', ext_options), - ('zoo', '1.7-11', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), - ('mvtnorm', '1.0-1', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('coda', '0.16-1', ext_options), - ('pscl', '1.4.6', ext_options), - ('sandwich', '2.3-2', ext_options), - ('sfsmisc', '1.0-26', ext_options), - ('spatial', '7.3-8', ext_options), - ('VGAM', '0.9-5', ext_options), - ('waveslim', '1.7.3', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-32', ext_options), - ('neuRosim', '0.2-10', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.6.1', ext_options), - ('R.oo', '1.18.0', ext_options), - ('Rniftilib', '0.0-32', ext_options), - ('igraph', '0.7.1', ext_options), - ('gbm', '2.1', ext_options), - ('stringr', '0.6.2', ext_options), - ('plyr', '1.8.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('reshape2', '1.4', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.1-2', ext_options), - ('cluster', '1.15.3', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('Hmisc', '3.14-5', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('fastcluster', '1.1.13', ext_options), - ('digest', '0.6.4', ext_options), - ('gtable', '0.1.2', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.0', ext_options), - ('maptools', '0.8-30', ext_options), - ('intervals', '0.15.0', ext_options), - ('xts', '0.9-7', ext_options), - ('rgeos', '0.3-8', ext_options), - ('spacetime', '1.1-1', ext_options), - ('FNN', '1.1', ext_options), - ('gstat', '1.0-19', ext_options), - ('deldir', '0.1-6', ext_options), - ('LearnBayes', '2.15', ext_options), - ('abind', '1.4-0', ext_options), - ('spdep', '0.5-77', ext_options), - ('splancs', '2.01-36', ext_options), - ('DCluster', '0.2-6', ext_options), - ('tensor', '1.5', ext_options), - ('polyclip', '1.3-0', ext_options), - ('goftest', '1.0-2', ext_options), - ('spatstat', '1.39-1', ext_options), - - ('getopt', '1.20.0', ext_options), - ('optparse', '1.2.0', ext_options), # for QIIME - ('permute', '0.8-3', ext_options), - ('vegan', '2.2-0', ext_options), # for QIIME - - ('spam', '1.0-1', ext_options), - ('RandomFields', '3.0.35', ext_options), # 3.0.44 requires Tcl etc. - ('geoR', '1.7-4.1', ext_options), - ('geoRglm', '0.9-4', ext_options), - ('R2WinBUGS', '2.1-19', ext_options), - ('R2OpenBUGS', '3.2-2.2', ext_options), - ('akima', '0.5-11', ext_options), - ('rjags', '3-14', ext_options), - ('R2jags', '0.04-03', ext_options), - ('DBI', '0.3.1', ext_options), - ('xtable', '1.7-4', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('locfit', '1.5-9.1', ext_options), - ('lpSolve', '5.6.10', ext_options), - ('glmmML', '1.0', ext_options), - ('survey', '3.30-3', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('crs', '0.15-23', ext_options), - ('dclone', '2.0-0', ext_options), - - ('caTools', '1.17.1', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('gplots', '2.14.2', ext_options), - ('gsalib', '2.0', ext_options), - ('inline', '0.3.13', ext_options), - ('RcppArmadillo', '0.4.500.0', ext_options), - - ('XML', '3.98-1.1', ext_options), - ('spgrass6', '0.8-6', ext_options), - - ('checkmate', '1.5.0', ext_options), - ('BBmisc', '1.8', ext_options), - ('fail', '1.2', ext_options), - ('brew', '1.0-6', ext_options), - ('base64enc', '0.1-2', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('BatchJobs', '1.5', ext_options), - - ('BiocInstaller', '1.16.1', bioconductor_options), - ('BiocGenerics', '0.12.1', bioconductor_options), - ('Biobase', '2.26.0', bioconductor_options), - ('S4Vectors', '0.4.0', bioconductor_options), - ('IRanges', '2.0.0', bioconductor_options), - ('XVector', '0.6.0', bioconductor_options), - ('zlibbioc', '1.12.0', bioconductor_options), - ('Biostrings', '2.34.0', bioconductor_options), - ('GenomeInfoDb', '1.2.3', bioconductor_options), - ('AnnotationDbi', '1.28.1', bioconductor_options), - ('GenomicRanges', '1.18.1', bioconductor_options), - ('Rsamtools', '1.18.2', bioconductor_options), - ('BiocParallel', '1.0.0', bioconductor_options), - ('GenomicAlignments', '1.2.1', bioconductor_options), - ('rtracklayer', '1.26.2', bioconductor_options), - ('BSgenome', '1.34.0', bioconductor_options), - ('graph', '1.44.0', bioconductor_options), - ('annotate', '1.44.0', bioconductor_options), - ('genefilter', '1.48.1', bioconductor_options), - ('geneplotter', '1.44.0', bioconductor_options), - ('DESeq', '1.18.0', bioconductor_options), - ('DESeq2', '1.6.2', bioconductor_options), - ('ShortRead', '1.24.0', bioconductor_options), - - ('rlecuyer', '0.3-3', ext_options), - ('pbdMPI', '0.2-5', ext_options), - ('pbdSLAP', '0.1-9', ext_options), - ('pbdBASE', '0.2-3', ext_options), # with icc: Rtools/tools.c(41): error: incorrect use of va_start - ('pbdDMAT', '0.2-3', ext_options), # depends on pdbBASE - #('pbdNCDF4', '0.1-4', ext_options), # add parallel netCDF as a dependency if this gets added - - #('BH', '1.54.0-5', ext_options), # Boost headers for rstan - #('rstan', '2.4', ext_options_extra(source_urls = ['http://rstan.org/repo/src/contrib/'])), -] - -moduleclass = 'lang' -- GitLab From ae21d7547d6b4bf22f47adc0f7020a1c9e7069dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 11:20:46 +0100 Subject: [PATCH 082/911] style cleanup in PyQt and SIP easyconfigs, ad checksum in AFNI easyconfigs --- ...I-linux_openmp_64-goolf-1.5.14-20141023.eb | 4 +-- .../PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb | 29 +++++++++++++++++++ .../PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb | 25 ---------------- .../SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb | 25 ++++++++++++++++ .../s/SIP/SIP-4.16.4-goolf-1.5.14.eb | 20 ------------- 5 files changed, 56 insertions(+), 47 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb delete mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb delete mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb index 108fd2aeb2..b6787ef029 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb @@ -14,11 +14,11 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = ['http://afni.nimh.nih.gov/pub/dist/tgz/'] sources = ['%(version)s.tgz'] -checksums = [''] +checksums = ['8800092268d8bfc05611515b0795dae2'] dependencies = [ ('R', '3.1.2'), - ('PyQt', 'x11-gpl-4.11.3'), + ('PyQt', '4.11.3', '-Python-2.7.6'), ('tcsh', '6.18.01'), ('libXp', '1.0.2'), ] diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb new file mode 100644 index 0000000000..3bddca7274 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.3' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-x11-gpl-%(version)s'] + +python = 'Python' +pyver = '2.7.6' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.4', versionsuffix), + ('Qt', '4.8.5'), +] + +configopts = " configure-ng.py --confirm-license" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb deleted file mode 100644 index 6c3e97606d..0000000000 --- a/easybuild/easyconfigs/p/PyQt/PyQt-x11-gpl-4.11.3-goolf-1.5.14.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMakePythonPackage' -name = 'PyQt' -version = 'x11-gpl-4.11.3' - - - - -homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' -description = """ -PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework -and runs on all platforms supported by Qt including Windows, MacOS/X and Linux. -PyQt5 supports Qt v5. PyQt4 supports Qt v4 and will build against Qt v5. -The bindings are implemented as a set of Python modules and contain over 620 classes. -""" -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3'] - -dependencies = [('Python', '2.7.6'), - ('SIP','4.16.4'), - ('Qt','4.8.5')] - -configopts = " configure-ng.py --confirm-license" - diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb new file mode 100644 index 0000000000..09fa92b8cd --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.4' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.6' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb deleted file mode 100644 index 5b0fc8c465..0000000000 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'ConfigureMakePythonPackage' -name = 'SIP' -version = '4.16.4' - -homepage = 'http://www.riverbankcomputing.com/software/sip/' -description = """ -SIP is a tool that makes it very easy to create Python bindings for C and C++ -libraries. It was originally developed to create PyQt, the Python bindings -for the Qt toolkit, but can be used to create bindings for any C or C++ library. -""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.4'] - -dependencies = [('Python', '2.7.6')] - -configopts = " configure.py" - -- GitLab From ef2ea2ac734fe6cddd250168a6f92b82bb6fd343 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 11:31:21 +0100 Subject: [PATCH 083/911] change Python version to 2.7.9 in PyQt/SIP easyconfigs --- .../a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb | 2 +- ...Python-2.7.6.eb => PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb} | 2 +- ...-Python-2.7.6.eb => SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PyQt/{PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb => PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb} (98%) rename easybuild/easyconfigs/s/SIP/{SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb => SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb} (97%) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb index b6787ef029..83a0bf5863 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb @@ -18,7 +18,7 @@ checksums = ['8800092268d8bfc05611515b0795dae2'] dependencies = [ ('R', '3.1.2'), - ('PyQt', '4.11.3', '-Python-2.7.6'), + ('PyQt', '4.11.3', '-Python-2.7.9'), ('tcsh', '6.18.01'), ('libXp', '1.0.2'), ] diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb rename to easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 3bddca7274..634473d36d 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -15,7 +15,7 @@ sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-x11-gpl-%(version)s'] python = 'Python' -pyver = '2.7.6' +pyver = '2.7.9' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb similarity index 97% rename from easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb rename to easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 09fa92b8cd..20ee0d6828 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] python = 'Python' -pyver = '2.7.6' +pyver = '2.7.9' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -- GitLab From 8f4db313d50b573d5c8ebd9c344944a9a3591e6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 11:36:58 +0100 Subject: [PATCH 084/911] bump Qt version in PyQt to 4.8.6 --- .../easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 634473d36d..3a7c99d3b4 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -21,7 +21,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), ('SIP', '4.16.4', versionsuffix), - ('Qt', '4.8.5'), + ('Qt', '4.8.6'), ] configopts = " configure-ng.py --confirm-license" -- GitLab From 7859e2ee4c870dea9f48c4a8ed6faaabb1a1b372 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 12:16:48 +0100 Subject: [PATCH 085/911] add easyconfig for libXp 1.0.2 with goolf/1.5.14 --- .../inputproto/inputproto-2.3-goolf-1.5.14.eb | 19 ++++ .../k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb | 19 ++++ .../l/libX11/libX11-1.6.1-goolf-1.5.14.eb | 37 ++++++++ .../l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 25 +++++ .../l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb | 25 +++++ .../l/libXext/libXext-1.3.2-goolf-1.5.14.eb | 34 +++++++ .../l/libXp/libXp-1.0.2-goolf-1.5.14.eb | 30 ++++++ .../libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb | 35 +++++++ .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 95 +++++++++++++++++++ .../printproto-1.0.5-goolf-1.5.14.eb | 19 ++++ ...xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb | 27 ++++++ .../xextproto/xextproto-7.2.1-goolf-1.5.14.eb | 25 +++++ .../x/xproto/xproto-7.0.26-goolf-1.5.14.eb | 24 +++++ .../x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb | 26 +++++ 14 files changed, 440 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..56a7e864e0 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb new file mode 100644 index 0000000000..9d5719533c --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..1f3f05b34f --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +pythonversion = '-Python-2.7.8' +builddependencies = [ + ('xextproto', '7.2.1'), + ('xcb-proto', '1.7', pythonversion), + ('kbproto', '1.0.6'), + ('inputproto', '2.3'), + ('xproto', '7.0.26'), +] + +dependencies = [ + ('libxcb', '1.8', pythonversion), + ('xtrans', '1.3.4'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb new file mode 100644 index 0000000000..e1924b4781 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.26'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..c63e8fb713 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.26'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..730c692843 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libX11', '1.6.1'), + ('libXdmcp', '1.1.1'), +] + +builddependencies = [ + ('xproto','7.0.26'), + ('xextproto', '7.2.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..2b397002a4 --- /dev/null +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXp' +version = '1.0.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.2.1'), + ('printproto', '1.0.5'), +] + +dependencies = [ + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXau', '1.0.8'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb new file mode 100644 index 0000000000..543b30f4e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.8' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, + latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libxcb-no-pthread-stubs.patch'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [ + (python, pyver), + ('xcb-proto', '1.7', versionsuffix), +] + +preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " + +sanity_check_paths = { + 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb new file mode 100644 index 0000000000..df184b1c3e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -0,0 +1,95 @@ +name = 'Python' +version = '2.7.8' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb new file mode 100644 index 0000000000..b92c1df92c --- /dev/null +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'printproto' +version = '1.0.5' + +homepage = 'http://xorg.freedesktop.org/' +description = """X.org PrintProto protocol headers.""" + +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sanity_check_paths = { + 'files': ['include/X11/extensions/Print.h', 'include/X11/extensions/Printstr.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb new file mode 100644 index 0000000000..401760336f --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.7' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, + latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..6b4cef16fe --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb new file mode 100644 index 0000000000..a5635671e9 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.26' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..f6435d5d2b --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', + 'Xtranssock.c', 'Xtransutil.c' + ] + ], + 'dirs' : [] +} + +moduleclass = 'devel' -- GitLab From 7bdf12ff5adf13e2131dbd6c61b21c4ef2163d0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jan 2015 12:40:37 +0100 Subject: [PATCH 086/911] add easyconfig for libXp 1.0.2 with intel/2015a --- .../inputproto/inputproto-2.3-intel-2015a.eb | 19 ++++++++++ .../k/kbproto/kbproto-1.0.6-intel-2015a.eb | 19 ++++++++++ .../l/libX11/libX11-1.6.1-intel-2015a.eb | 37 +++++++++++++++++++ .../l/libXau/libXau-1.0.8-intel-2015a.eb | 25 +++++++++++++ .../l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb | 25 +++++++++++++ .../l/libXext/libXext-1.3.2-intel-2015a.eb | 34 +++++++++++++++++ .../l/libXp/libXp-1.0.2-intel-2015a.eb | 30 +++++++++++++++ .../libxcb-1.8-intel-2015a-Python-2.7.8.eb | 35 ++++++++++++++++++ .../printproto-1.0.5-intel-2015a.eb | 19 ++++++++++ .../xcb-proto-1.7-intel-2015a-Python-2.7.8.eb | 27 ++++++++++++++ .../xextproto/xextproto-7.2.1-intel-2015a.eb | 25 +++++++++++++ .../x/xproto/xproto-7.0.26-intel-2015a.eb | 24 ++++++++++++ .../x/xtrans/xtrans-1.3.4-intel-2015a.eb | 26 +++++++++++++ 13 files changed, 345 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb new file mode 100644 index 0000000000..0437a042db --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb new file mode 100644 index 0000000000..2d16cb0b13 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb new file mode 100644 index 0000000000..70b695c73d --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +pythonversion = '-Python-2.7.8' +builddependencies = [ + ('xextproto', '7.2.1'), + ('xcb-proto', '1.7', pythonversion), + ('kbproto', '1.0.6'), + ('inputproto', '2.3'), + ('xproto', '7.0.26'), +] + +dependencies = [ + ('libxcb', '1.8', pythonversion), + ('xtrans', '1.3.4'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb new file mode 100644 index 0000000000..5deb59be94 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.26'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb new file mode 100644 index 0000000000..f1b75921a7 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.26'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb new file mode 100644 index 0000000000..b57d363d51 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libX11', '1.6.1'), + ('libXdmcp', '1.1.1'), +] + +builddependencies = [ + ('xproto','7.0.26'), + ('xextproto', '7.2.1'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', + 'Xdbe.h', 'XEVI.h', 'Xext.h', 'Xge.h', 'XLbx.h', 'XShm.h', 'xtestext1.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb new file mode 100644 index 0000000000..469ffffd9b --- /dev/null +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXp' +version = '1.0.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.2.1'), + ('printproto', '1.0.5'), +] + +dependencies = [ + ('libX11', '1.6.1'), + ('libXext', '1.3.2'), + ('libXau', '1.0.8'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb new file mode 100644 index 0000000000..3343368288 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.8' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, + latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libxcb-no-pthread-stubs.patch'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [ + (python, pyver), + ('xcb-proto', '1.7', versionsuffix), +] + +preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " + +sanity_check_paths = { + 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb new file mode 100644 index 0000000000..0e5bfb142c --- /dev/null +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'printproto' +version = '1.0.5' + +homepage = 'http://xorg.freedesktop.org/' +description = """X.org PrintProto protocol headers.""" + +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['include/X11/extensions/Print.h', 'include/X11/extensions/Printstr.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb new file mode 100644 index 0000000000..1a9784f1e8 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.7' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, + latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015a'} + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb new file mode 100644 index 0000000000..e1651c87e5 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb new file mode 100644 index 0000000000..5c1117654b --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.26' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb new file mode 100644 index 0000000000..dc21e51c71 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', + 'Xtranssock.c', 'Xtransutil.c' + ] + ], + 'dirs' : [] +} + +moduleclass = 'devel' -- GitLab From f03619b2b01ad1fb34ff6c5393ade18112004d85 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 23 Jan 2015 09:02:13 +0100 Subject: [PATCH 087/911] drop comp variable Signed-off-by: Fotis Georgatos --- ...APACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 3931fb0ef3..7c911189b3 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -11,17 +11,13 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] -comp_name = 'GCC' -comp_version = '4.8.4' -comp = (comp_name, comp_version) - blaslib = 'OpenBLAS' blasver = '0.2.13' blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, comp)] +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.8.4'))] ## parallel build tends to fail, so disabling it parallel = 1 -- GitLab From d7bb89816cbf876d700f1ef516097edccdf6be52 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 23 Jan 2015 09:27:35 +0100 Subject: [PATCH 088/911] bump in favor of numactl-2.0.10 Signed-off-by: Fotis Georgatos --- .../a/Autoconf/Autoconf-2.69-GCC-4.8.4.eb | 26 +++++++++++++++ .../a/Automake/Automake-1.15-GCC-4.8.4.eb | 33 +++++++++++++++++++ .../h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb | 2 +- .../l/libtool/libtool-2.4.2-GCC-4.8.4.eb | 15 +++++++++ .../easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb | 23 +++++++++++++ .../n/numactl/numactl-2.0.10-GCC-4.8.4.eb | 31 +++++++++++++++++ 6 files changed, 129 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.4.eb new file mode 100644 index 0000000000..2dc3403799 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.4.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb new file mode 100644 index 0000000000..bf119a1eaf --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-4.8.4.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb index 2d5251f89c..48456705b1 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb @@ -13,7 +13,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.4'} -dependencies = [('numactl', '2.0.9')] +dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb new file mode 100644 index 0000000000..82d1212976 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb new file mode 100644 index 0000000000..90c7eb9017 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.8.4.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb new file mode 100644 index 0000000000..4e761b0ac5 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Automake', '1.15'), + ('libtool', '2.4.2'), +] + +preconfigopts = './autogen.sh && ' + + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' -- GitLab From 8506833708dcc67a2d5732ce95ad8f286e56e457 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jan 2015 14:46:06 +0100 Subject: [PATCH 089/911] fix remarks --- .../a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.14-goolf-1.5.14.eb | 33 +++++++++++++++++++ .../k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb | 2 +- .../l/libX11/libX11-1.6.1-goolf-1.5.14.eb | 2 +- .../libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb | 5 +++ .../printproto-1.0.5-goolf-1.5.14.eb | 6 ++-- ...xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb | 4 +-- 7 files changed, 70 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb new file mode 100644 index 0000000000..3ca1111122 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure + software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual + user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating + system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb new file mode 100644 index 0000000000..64606d8726 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.14" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb index 9d5719533c..1b4c06dfef 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X.org KBProto protocol headers.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] +source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb index 1f3f05b34f..09434cd3d2 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb @@ -9,7 +9,7 @@ description = """X11 client-side library""" toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.8' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb index 543b30f4e9..17ee8c1cb5 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb @@ -14,6 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69'), +] + python = 'Python' pyver = '2.7.8' versionsuffix = '-%s-%s' % (python, pyver) diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb index b92c1df92c..c81ebb4993 100644 --- a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-goolf-1.5.14.eb @@ -6,11 +6,11 @@ version = '1.0.5' homepage = 'http://xorg.freedesktop.org/' description = """X.org PrintProto protocol headers.""" -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] -sources = [SOURCELOWER_TAR_GZ] - toolchain = {'name': 'goolf', 'version': '1.5.14'} +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + sanity_check_paths = { 'files': ['include/X11/extensions/Print.h', 'include/X11/extensions/Printstr.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb index 401760336f..2c38355a2b 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb @@ -7,11 +7,11 @@ homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" +toolchain = {'name': 'goolf', 'version': '1.5.14'} + source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'goolf', 'version': '1.5.14'} - python = 'Python' pyver = '2.7.8' versionsuffix = '-%s-%s' % (python, pyver) -- GitLab From af8ce19b2ce0ae261e1b96624d8495cb939c5db7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jan 2015 16:55:04 +0100 Subject: [PATCH 090/911] add libtool build dep in libxcb easyconfig --- .../l/libtool/libtool-2.4.5-goolf-1.5.14.eb | 15 +++++++++++++++ .../libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb | 1 + 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb new file mode 100644 index 0000000000..28e63562d7 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.5' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb index 17ee8c1cb5..91991fe021 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb @@ -17,6 +17,7 @@ patches = ['libxcb-no-pthread-stubs.patch'] builddependencies = [ ('Automake', '1.14'), ('Autoconf', '2.69'), + ('libtool', '2.4.5'), ] python = 'Python' -- GitLab From 468a0e1e41c25ec1e10664a3598d3bf3ac086091 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jan 2015 17:00:54 +0100 Subject: [PATCH 091/911] add M4 as build dep for libtool --- .../l/libtool/libtool-2.4.5-goolf-1.5.14.eb | 2 ++ .../m/M4/M4-1.4.17-goolf-1.5.14.eb | 23 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb index 28e63562d7..89de693e51 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb @@ -12,4 +12,6 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +builddependencies = [('M4', '1.14.17')] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb new file mode 100644 index 0000000000..39d957f556 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From e2dc1907d6ec6ee1a3cfa7e7f5baaf430242496f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jan 2015 17:03:13 +0100 Subject: [PATCH 092/911] fix typo --- easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb index 89de693e51..c98f951ee7 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb @@ -12,6 +12,6 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] -builddependencies = [('M4', '1.14.17')] +builddependencies = [('M4', '1.4.17')] moduleclass = 'lib' -- GitLab From b29994cb3b0017d479e823fb19c464cfbd441a13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jan 2015 17:08:13 +0100 Subject: [PATCH 093/911] add M4 as build dep for libxcb --- .../easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb index 91991fe021..497d6bc032 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb @@ -15,6 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] builddependencies = [ + ('M4', '1.4.17'), ('Automake', '1.14'), ('Autoconf', '2.69'), ('libtool', '2.4.5'), -- GitLab From c233fad4010f9995bdc248ce2eb64c419c0bce60 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Tue, 27 Jan 2015 13:25:36 +1300 Subject: [PATCH 094/911] not sure what i --- .../r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb new file mode 100644 index 0000000000..3b2244afd0 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb @@ -0,0 +1,19 @@ +name = 'Rosetta' +version = '3.5' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s%(version)s_bundles.tgz'] + +modextravars = { + 'ROSETTA3_DB': '$root/rosetta_database' +} + +builddependencies = [('SCons', '2.3.0', '-Python-2.7.3')] + +moduleclass = 'bio' -- GitLab From 1241a05b1f7d379ae60edd928721c4b40399dae1 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Tue, 27 Jan 2015 13:25:59 +1300 Subject: [PATCH 095/911] deleting file --- .../r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb deleted file mode 100644 index 3b2244afd0..0000000000 --- a/easybuild/easyconfigs/r/Rosetta/Rosetta-3.5-ictce-5.4.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'Rosetta' -version = '3.5' - -homepage = 'https://www.rosettacommons.org' -description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, -multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and -nucleic acids.""" -toolchain = {'name': 'ictce', 'version': '5.4.0'} -toolchainopts = {'usempi': True} - -sources = ['%(namelower)s%(version)s_bundles.tgz'] - -modextravars = { - 'ROSETTA3_DB': '$root/rosetta_database' -} - -builddependencies = [('SCons', '2.3.0', '-Python-2.7.3')] - -moduleclass = 'bio' -- GitLab From 1aa81e9a343e6eb30b89d9fbe5d3635901159343 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 27 Jan 2015 09:36:26 +0100 Subject: [PATCH 096/911] Added intel easyconfig for libX11 and dependencies --- .../inputproto-2.3.1-intel-2015a.eb | 19 +++++++++ .../k/kbproto/kbproto-1.0.6-intel-2015a.eb | 19 +++++++++ .../libX11-1.6.2-intel-2015a-Python-2.7.9.eb | 37 ++++++++++++++++++ .../l/libXau/libXau-1.0.8-intel-2015a.eb | 25 ++++++++++++ .../libpthread-stubs-0.3-intel-2015a.eb | 20 ++++++++++ ...ibxcb-1.11-intel-2015a-Python-2.7.9.eb.swp | Bin 0 -> 12288 bytes .../libxcb-1.11-intel-2015a-Python-2.7.9.eb | 34 ++++++++++++++++ ...xcb-proto-1.11-intel-2015a-Python-2.7.9.eb | 27 +++++++++++++ .../xextproto/xextproto-7.3.0-intel-2015a.eb | 25 ++++++++++++ .../x/xproto/xproto-7.0.27-intel-2015a.eb | 24 ++++++++++++ .../x/xtrans/xtrans-1.3.5-intel-2015a.eb | 26 ++++++++++++ 11 files changed, 256 insertions(+) create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb new file mode 100644 index 0000000000..21d5d376d5 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb new file mode 100644 index 0000000000..2d16cb0b13 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..3f72262d57 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.2' +versionsuffix = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +dependencies = [ + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb new file mode 100644 index 0000000000..03dfe7dd92 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb new file mode 100644 index 0000000000..3665102104 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.3' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files' : ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [] , +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp b/easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp new file mode 100644 index 0000000000000000000000000000000000000000..7015b4fd640e56b6c355bdc5cf312959de633dcd GIT binary patch literal 12288 zcmeI2L5n0c6vwlI7j;$i;Kf6>WvE%`s_O1#cE$x2cUTr-hm~tfLD{=rJo+W}1L(m8@#fKk2L-SC4g9C7#$`nY^|nhw|2wId)Jxtk$-vNWHhTY^ z1G<|{2+E6u{B-ld(fxA#^uZn>&1iIWXJ>aObe&g9%Tt>wvyeI+pEEFDIi8lRF4D?0 z+PhqdW+il5Fwb(garxPVxnOQHYosdD(BekV<-$F*wyiU(%9Wh0`K+(faW)>OQhTA& z$!NU8(swt$G&-GRyV>iRn4Po0*cAypsRSB7Pxmg8E0ggkg!tOv5`FolJ5Oq~F|J4; z5{LvMfk+?{hy)^mNFWmU2Lj$+AfLegRNpt~>kEIY`^Q*C0+B!@5D7#Akw7F62}A;s zKqL?eL;{h(V@QA%g#7RfA@*4;9>4#e{r~^#3xxav{Rn*veFJ?3Z9@;9C*(WmOXv&e zBj_#YO=t+c3jJ}Bkl&%7q3@xup?lCADj*Ksf_{6BkWZmkp!-Ua>S{vBT|!ZkLe?(1Mo$u{xoQfLBdawT zwu5rJTyzPq$#mF`4sZOsGDz1_i<(tzFr;{}HL_#7rWdYntvbW1;)Ch`n8B6Iiq?fI ztFGQ?-uV$bwdsmBEcGkIE3pe=hvD8c#b?c%Q+|)(i)P*>+!YjgbycR+`whDF< zNF{TrgiB~34DNlt@RrM1LbvFe&P|PPsp-j}^}tPKjg!7xd;xxozGyM5Ptaeg50Pfl@;16QNSFw1FulmSZiuO zq&Qzxtl`ednN--&Y%mxABo36c9>lRMSdQTE_%D}qKUGXG8XOUNUFz23_VNDp%Tzkb zXf3Q_TvS5)_Lv>xDA2iJzQJ8wV1TQbQs^?iy`4i+no8K<4YbdJhArrMgn=RTJt2Wu dc)}dv4+tS`HoY=@8LazlGJR8v1GW?i`4iXzsN4Vm literal 0 HcmV?d00001 diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7d20038412 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('xcb-proto', '1.11', versionsuffix), + ('libXau', '1.0.8'), + ('libpthread-stubs', '0.3'), +] + +sanity_check_paths = { + 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", + "-randr", "-record", "-render", "-res", "-screensaver", + "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", + "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..38f0fd5a88 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb new file mode 100644 index 0000000000..ee0ab26f86 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb new file mode 100644 index 0000000000..4093d23e90 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.27' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', + 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', + 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', + 'XWDFile.h', 'Xwinsock.h']], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb new file mode 100644 index 0000000000..ef00169dc4 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +sanity_check_paths = { + 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', + 'Xtranssock.c', 'Xtransutil.c' + ] + ], + 'dirs' : [] +} + +moduleclass = 'devel' -- GitLab From 7b49fdce5c8eebd5e0612cdd0f672145a9cedc87 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 27 Jan 2015 09:42:56 +0100 Subject: [PATCH 097/911] Removed accidentally added swp file --- ....libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp | Bin 12288 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp diff --git a/easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp b/easybuild/easyconfigs/l/libxcb/.libxcb-1.11-intel-2015a-Python-2.7.9.eb.swp deleted file mode 100644 index 7015b4fd640e56b6c355bdc5cf312959de633dcd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI2L5n0c6vwlI7j;$i;Kf6>WvE%`s_O1#cE$x2cUTr-hm~tfLD{=rJo+W}1L(m8@#fKk2L-SC4g9C7#$`nY^|nhw|2wId)Jxtk$-vNWHhTY^ z1G<|{2+E6u{B-ld(fxA#^uZn>&1iIWXJ>aObe&g9%Tt>wvyeI+pEEFDIi8lRF4D?0 z+PhqdW+il5Fwb(garxPVxnOQHYosdD(BekV<-$F*wyiU(%9Wh0`K+(faW)>OQhTA& z$!NU8(swt$G&-GRyV>iRn4Po0*cAypsRSB7Pxmg8E0ggkg!tOv5`FolJ5Oq~F|J4; z5{LvMfk+?{hy)^mNFWmU2Lj$+AfLegRNpt~>kEIY`^Q*C0+B!@5D7#Akw7F62}A;s zKqL?eL;{h(V@QA%g#7RfA@*4;9>4#e{r~^#3xxav{Rn*veFJ?3Z9@;9C*(WmOXv&e zBj_#YO=t+c3jJ}Bkl&%7q3@xup?lCADj*Ksf_{6BkWZmkp!-Ua>S{vBT|!ZkLe?(1Mo$u{xoQfLBdawT zwu5rJTyzPq$#mF`4sZOsGDz1_i<(tzFr;{}HL_#7rWdYntvbW1;)Ch`n8B6Iiq?fI ztFGQ?-uV$bwdsmBEcGkIE3pe=hvD8c#b?c%Q+|)(i)P*>+!YjgbycR+`whDF< zNF{TrgiB~34DNlt@RrM1LbvFe&P|PPsp-j}^}tPKjg!7xd;xxozGyM5Ptaeg50Pfl@;16QNSFw1FulmSZiuO zq&Qzxtl`ednN--&Y%mxABo36c9>lRMSdQTE_%D}qKUGXG8XOUNUFz23_VNDp%Tzkb zXf3Q_TvS5)_Lv>xDA2iJzQJ8wV1TQbQs^?iy`4i+no8K<4YbdJhArrMgn=RTJt2Wu dc)}dv4+tS`HoY=@8LazlGJR8v1GW?i`4iXzsN4Vm -- GitLab From f4c8416d21a83206b93adef5d30cc93331af8243 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:38:11 +0000 Subject: [PATCH 098/911] Building an older version of Cufflinks for users that like the older format --- .../Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 42 +++++++++++++++++ .../c/Cufflinks/cufflinks-1.3.0-ldflags.patch | 45 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..2eca2eb6ac --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Cufflinks' +version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch new file mode 100644 index 0000000000..9c2bd9e9a2 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch @@ -0,0 +1,45 @@ +diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure +--- cufflinks-1.3.0/configure 2012-01-02 13:36:44.000000000 +0000 ++++ cufflinks-1.3.0_patched/configure 2015-01-27 18:32:24.810282390 +0000 +@@ -6386,7 +6386,8 @@ + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++user_LDFLAGS="$LDFLAGS" ++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + + # Checks for structures/functions that can be used to determine system memory + echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5 +diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in +--- cufflinks-1.3.0/src/Makefile.in 2012-01-02 13:36:43.000000000 +0000 ++++ cufflinks-1.3.0_patched/src/Makefile.in 2015-01-27 18:20:02.944386541 +0000 +@@ -438,24 +438,24 @@ + # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@ + cufflinks_SOURCES = cufflinks.cpp + cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) ++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) + cuffcompare_SOURCES = cuffcompare.cpp + cuffcompare_LDADD = libgc.a + gffread_SOURCES = gffread.cpp + gffread_LDADD = libgc.a + cuffdiff_SOURCES = cuffdiff.cpp + cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + gtf_to_sam_SOURCES = gtf_to_sam.cpp + gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + #cuffcluster_SOURCES = cuffcluster.cpp + #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) + #cuffcluster_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + compress_gtf_SOURCES = compress_gtf.cpp + compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + all: all-am + + .SUFFIXES: -- GitLab From 6f4ac9178ba8ad044f765c67cdc1b215b03cb18f Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 18:46:15 +0000 Subject: [PATCH 099/911] removing a bad comment --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 2eca2eb6ac..60d2ee4a72 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -11,7 +11,7 @@ ## name = 'Cufflinks' -version = "1.3.0" # tweaked by EasyBuild (was: '2.0.2') +version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -- GitLab From e3c1dfff1ac6377bd2b62621f09447573345a574 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:05:51 +0000 Subject: [PATCH 100/911] new R version --- .../easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 388 ++++++++++++++++++ 1 file changed, 388 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb new file mode 100644 index 0000000000..16a52c2e37 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -0,0 +1,388 @@ +name = 'R' +version = '3.1.2' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-0', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.6', ext_options), + ('bootstrap', '2014.4', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.13', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-19', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', 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('DynDoc', '1.44.0', bioconductor_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '0.7.7', ext_options), + ('mixOmics', '5.0-3', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.2.1', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), +] + +moduleclass = 'lang' -- GitLab From 55c4a267adec324bb0ba120fcc5c08921e0481a6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:18:33 +0000 Subject: [PATCH 101/911] some style changes --- .../c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 7 +++++-- ...nks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} | 0 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Cufflinks/{cufflinks-1.3.0-ldflags.patch => cufflinks-1.x-ldflags.patch} (100%) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index 60d2ee4a72..d03c8b241d 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} +toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -29,7 +29,10 @@ dependencies = [ ('zlib', '1.2.7'), ] -patches = ['Cufflinks_GCC-4.7.patch', 'cufflinks-1.3.0-ldflags.patch'] +patches = [ + 'Cufflinks_GCC-4.7.patch', + 'cufflinks-1.x-ldflags.patch' +] configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch similarity index 100% rename from easybuild/easyconfigs/c/Cufflinks/cufflinks-1.3.0-ldflags.patch rename to easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch -- GitLab From 6bf1b6cd4d227abefce167ec9eaf533d5ad0098c Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 27 Jan 2015 20:21:24 +0000 Subject: [PATCH 102/911] whoops, inverted wrong line --- .../easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb index d03c8b241d..96199f4bf2 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ version = "1.3.0" homepage = 'http://cufflinks.cbcb.umd.edu/' description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" -toolchainopts = {'optarch': True, 'pic': True} toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] @@ -34,8 +34,8 @@ patches = [ 'cufflinks-1.x-ldflags.patch' ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From f3daf828b6dab722749c2395d73c14e65c8c5e6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Jan 2015 22:51:31 +0100 Subject: [PATCH 103/911] include zlib as a dependency in all Tcl easyconfigs --- .../t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-foss-2014b.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-gmvapich2-1.7.12.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-gmvolf-1.7.12.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-goalf-1.1.0-no-OFED.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-ictce-4.0.10.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-ictce-4.0.6.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb | 4 ++++ .../t/Tcl/Tcl-8.5.12-intel-2014b.eb | 4 ++++ .../t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb | 4 ++++ .../t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb | 4 ++++ .../t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb | 4 ++++ .../t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb | 4 ++++ .../t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb | 4 ++++ .../t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb | 4 ++++ .../t/Tcl/Tcl-8.6.2-intel-2014b.eb | 4 ++++ .../z/zlib/zlib-1.2.5-ictce-5.3.0.eb | 1 - .../z/zlib/zlib-1.2.5-ictce-5.5.0.eb | 24 +++++++++++++++++++ .../z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb | 22 +++++++++++++++++ .../z/zlib/zlib-1.2.7-goolfc-1.3.12.eb | 22 +++++++++++++++++ 23 files changed, 144 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb index 726260bf2a..c8585dbd41 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.3.5-ictce-5.5.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.5'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb index 56aa85437a..25a490d28f 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'foss', 'version': '2014b'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvapich2-1.7.12.eb index 0b513c298d..ebb7aaad40 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvapich2-1.7.12.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvapich2-1.7.12.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'gmvapich2', 'version': '1.7.12'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvolf-1.7.12.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvolf-1.7.12.eb index 9743808746..636a05dbcc 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-gmvolf-1.7.12.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'gmvolf', 'version': '1.7.12'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goalf-1.1.0-no-OFED.eb index 798d6318ab..f0adbd439b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goalf-1.1.0-no-OFED.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb index 03ee12ce9e..7c9d9e8066 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolf-1.4.10.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb index cbf87195ac..8b61aeff73 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-goolfc-1.3.12.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolfc', 'version': '1.3.12'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.10.eb index 6cb79b440c..fa762e96dc 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.10.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.6.eb index d5ce26d001..51a0291ac2 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-4.0.6.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb index 202d36aca9..19f101522b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.3.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb index e9377fec2a..35f9095bc8 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-ictce-5.5.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb index 6cf99c0db3..c54aec7e60 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb index b3c4b0b321..3e317dec24 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-goolf-1.4.10.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb index c792463dcf..5e237ee834 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.14-ictce-5.3.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb index c6470074d5..7f7f55c666 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb index 8acb552d5d..f46eebeee8 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.16-ictce-5.5.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb index 656a267905..39ddf4b3a8 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-goolf-1.4.10.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb index 71cf86f3ac..1392ae5cc8 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.7'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb index 193e0aaf1c..7a5ef170a5 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.2-intel-2014b.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb index 62745d552f..4bf4930349 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb @@ -8,7 +8,6 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..9a7769b77c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.5' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb new file mode 100644 index 0000000000..bf8527b938 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-gmvapich2-1.7.12.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, +not covered by any patents -- lossless data-compression library for use on virtually any +computer hardware and operating system.""" + +toolchain = {'name': 'gmvapich2', 'version': '1.7.12'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ["include/zconf.h", "include/zlib.h", "lib/libz.a", "lib/libz.so"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb new file mode 100644 index 0000000000..48c06464a8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goolfc-1.3.12.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, +not covered by any patents -- lossless data-compression library for use on virtually any +computer hardware and operating system.""" + +toolchain = {'name': 'goolfc', 'version': '1.3.12'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 54b055749d5f3b4259c01b52ec21943e0d20fed1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:31:04 +0100 Subject: [PATCH 104/911] binutils 2.25 for GCC 4.9.2 --- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb new file mode 100644 index 0000000000..e44a4bc4f7 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [ + ('zlib', '1.2.8'), +] + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 088c20eb5e6a8756cf380d5ead691f3be15e8f3e Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:32:22 +0100 Subject: [PATCH 105/911] fosss-2015.01: with zlib & binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 39 ++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2015.01.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb new file mode 100644 index 0000000000..7266051e56 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.9.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 9991a4e9bd90acedd99b0146f84c94d87cdcbd5c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:38:12 +0100 Subject: [PATCH 106/911] New gompi with zlib & binutils --- easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 24 +++++++++++++++++++ .../easyconfigs/g/gompi/gompi-2015.01.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.01.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb new file mode 100644 index 0000000000..f50cd40115 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.9.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.2' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb new file mode 100644 index 0000000000..e59112cb7f --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -0,0 +1,24 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015.01' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.9.2' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), +] + +moduleclass = 'toolchain' -- GitLab From cd2a6f815f46bf2983e3a11795f5def1d3e7033c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:38:33 +0100 Subject: [PATCH 107/911] New goolf & foss with zlib & binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 2 +- easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 39 ++++++++++++++++++++ 2 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 7266051e56..411ab43736 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -18,7 +18,7 @@ blasver = '0.2.13' blas = '%s-%s' % (blaslib, blasver) blassuff = '-LAPACK-3.5.0' -# toolchain used to build goolf dependencies +# toolchain used to build foss dependencies comp_mpi_tc_name = 'gompi' comp_mpi_tc_ver = "%s" % version comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb new file mode 100644 index 0000000000..0f2aea75a4 --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.9.0' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.9.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('zlib', '1.2.8', '', comp), + ('binutils', '2.25', '', comp), + ('OpenMPI', '1.8.4', '', comp), + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 6c8f97284b062e5dcb9ab7b6e1a327bef6114255 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:39:59 +0100 Subject: [PATCH 108/911] New FFTW easyconfigs for new gompi's --- .../f/FFTW/FFTW-3.3.4-gompi-2015.01.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb new file mode 100644 index 0000000000..080b817838 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 2132b1deeb371d18baa424cac1d498990d31bad9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:44:22 +0100 Subject: [PATCH 109/911] New scalapack easyconfigs --- ...ompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ ...pi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..e0aff023b0 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..962d8049d0 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 8c06ce5366b6903de62cbd3af0af18cf0bc0a1e9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 14:44:54 +0100 Subject: [PATCH 110/911] New FFTW easyconfigs --- .../f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb | 34 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.4-gompi-2015.01.eb | 2 +- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb new file mode 100644 index 0000000000..080b817838 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb index 080b817838..bcb190c092 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '1.9.0'} +toolchain = {'name': 'gompi', 'version': '2015.01'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0c4f936088ed782fc5a6793fd03b87deb6cc6ee6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 28 Jan 2015 15:11:27 +0100 Subject: [PATCH 111/911] Added HPL for new foss & goolf --- .../easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb | 18 ++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb new file mode 100644 index 0000000000..6e2eb261d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2015.01'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb new file mode 100644 index 0000000000..e9fc6dc2e2 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.9.0'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 46bc2daebf79665ed7407d1a94b2116026e854e7 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 28 Jan 2015 17:04:54 +0100 Subject: [PATCH 112/911] Added Oracle Java easyconfig --- easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb new file mode 100644 index 0000000000..0ab768fe89 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_31' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From f1759eb0ffb687c1b6694cdad94c36c01f17f98d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Thu, 29 Jan 2015 10:47:49 +1300 Subject: [PATCH 113/911] Cleaned up version suffixes --- ...65.eb => ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb} | 11 +++++++---- ...64.eb => ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb} | 5 ++++- ...65.eb => ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb} | 5 ++++- 3 files changed, 15 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64_openmpi_165.eb => ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb} (85%) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_2-linux_x86-64.eb => ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb} (91%) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_2-linux_x86-64_openmpi_165.eb => ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb} (91%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb similarity index 85% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb index cab4bf21a6..f4147dd3b8 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb @@ -1,20 +1,23 @@ easyblock = "PackedBinary" name = "ORCA" -version = '3_0_0-linux_x86-64_openmpi_165' +version = '3_0_0-linux_x86-64' + +openmpiversion = '1.6.5' +versionsuffix = '-OpenMPI-%s' % openmpiversion homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry - with specific emphasis on spectroscopic properties of open-shell molecules. + with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- - and multireference correlated ab initio methods. + and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb index 7942dc6b14..c63048d89b 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.6.5.eb @@ -3,6 +3,9 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_2-linux_x86-64' +openmpiversion = '1.6.5' +versionsuffix = '-OpenMPI-%s' % openmpiversion + homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -14,7 +17,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', '1.8.1', '-GCC-4.8.3')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb similarity index 91% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64_openmpi_165.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index 0103993c7a..5a28bbce0d 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -3,6 +3,9 @@ easyblock = "PackedBinary" name = "ORCA" version = '3_0_2-linux_x86-64' +openmpiversion = '1.8.1' +versionsuffix = '-OpenMPI-%s' % openmpiversion + homepage = 'http://cec.mpg.de/forum/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. @@ -14,7 +17,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] -dependencies = [('OpenMPI', '1.6.5', '-GCC-4.7.2')] +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.8.3')] sanity_check_paths = { 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', -- GitLab From 4b02c46e3f9c0556a749006b6d6952d1514188e3 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 29 Jan 2015 13:56:50 +0100 Subject: [PATCH 114/911] modify as per #1242 feedback --- easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index 8c4a091d7f..8be9aa164d 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -22,8 +22,9 @@ description = """DNA Sequence Reads Compression is an application designed for c toolchain = {'name': 'dummy', 'version': 'dummy'} # fi. http://sun.aei.polsl.pl/dsrc/download/2.0rc/dsrc -sources = [name.lower()] +sources = ['%(namelower)s'] source_urls = [homepage + '/download/%(version)s/'] +checksums = [('md5', 'bdc40a96e33411cd4cdbe2b58ae285b7')] sanity_check_paths = { 'files': ['dsrc'], -- GitLab From 2d572c2117caf53ed624cbefc90ae04e6fa6a09a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 29 Jan 2015 14:03:50 +0100 Subject: [PATCH 115/911] not makeopts, rather buildopts --- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 4 ++-- easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 5946229fc3..9726d8c156 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -26,8 +26,8 @@ minver = ''.join(version.split('.')) sources = [('fastqz%s.cpp' % minver, 'cp %s %(builddir)s/fastqz.cpp'), ('fapack.cpp', 'cp %s %(builddir)s')] source_urls = [homepage] -premakeopts = 'g++ -O3 -msse2 -s -lpthread fastqz.cpp $EBROOTZPAQ/include/libzpaq.cpp -o fastqz' -premakeopts += '&& g++ -O3 -s fapack.cpp -o fapack && /bin/true ' +prebuildopts = 'g++ -O3 -msse2 -s -lpthread fastqz.cpp $EBROOTZPAQ/include/libzpaq.cpp -o fastqz' +prebuildopts += '&& g++ -O3 -s fapack.cpp -o fapack && /bin/true ' files_to_copy = [(['fastqz', 'fapack'], 'bin')] diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb index a08d8c5af1..5724bab7ac 100644 --- a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -24,7 +24,7 @@ sources = ['%(namelower)s-v%(version)s-src.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] preconfigopts = 'cd zlib-1.2.8 &&' -makeopts = '-C zlib-1.2.8 && make all' +buildopts = '-C zlib-1.2.8 && make all' files_to_copy = [(['scalce'], 'bin')] diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index feed550444..3ab5b6fbdc 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = ['%%(namelower)s%s.zip' % ''.join(version.split('.'))] source_urls = ['http://mattmahoney.net/dc/'] -makeopts = ' && pod2man zpaq.pod > zpaq.1' +buildopts = ' && pod2man zpaq.pod > zpaq.1' files_to_copy = [(["zpaq"], 'bin'), (["zpaq.1"], 'share/man'), (["libzpaq.h", "libzpaq.cpp"], 'include')] -- GitLab From 076d8971e8f5043c0b611168a9c389b51373a6aa Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Jan 2015 14:13:25 +0100 Subject: [PATCH 116/911] Drop preconfigopts from zlib We don't know why it's there and it seems to be messing up the `zlib.map` inclusion. --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb index 1b3b05c520..73e6b29017 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From f9b6c48f134bdfebb0a0ccf06fbb915a0d5fff8a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 29 Jan 2015 14:42:01 +0100 Subject: [PATCH 117/911] Drop the `-shared` flag passed when building zlib For some unknown reason, we pass the -shared flag to CC when building GCC. This overwrites some stuff in the configure script which we don't want to override. The zlib.map is not being used when build the so file. --- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.7-foss-2014b.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2014b.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015a.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.4.10.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.14.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.3.0.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.5.0.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.1.2.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014b.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015a.eb | 2 -- easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb | 2 -- 21 files changed, 42 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb index 2e18c3c221..8eedf49cf6 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb index 3ea3c48ed3..1bcd57dece 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb index d2f50aacb7..4a778d2bba 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb index 62745d552f..46d721cc9d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb @@ -15,8 +15,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-foss-2014b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-foss-2014b.eb index 3368016589..9909f13d52 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-foss-2014b.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-foss-2014b.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb index a100b33695..2135132db6 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb index bdb56c788c..719603c67b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb index 1b3b05c520..73e6b29017 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2014b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2014b.eb index 7ceb9c2b65..0e2477a576 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2014b.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2014b.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015a.eb index 2011a3f3b4..5ee64f138f 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015a.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015a.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.4.10.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.4.10.eb index 6cd26f940d..31d9f79f39 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.4.10.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.14.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.14.eb index 8b2ff4d3a0..5aab00b506 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.14.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb index 4fe89ed538..6426ff8246 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-4.1.13.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.3.0.eb index caf2dc0994..4fdee82cf9 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.3.0.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.5.0.eb index f62e4705f9..90d83e616d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.5.0.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb index 4f273b2129..0e7907365c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb index 434f52a5c9..b685cd0ccc 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.3.5.eb @@ -17,8 +17,6 @@ source_urls = [ ('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download') ] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.1.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.1.2.eb index 67693b864b..1e7e916a55 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.1.2.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014b.eb index f986af06f4..fafed06166 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014b.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014b.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015a.eb index 81a7fb149f..13f8b375ac 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015a.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015a.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb index 3a10e30ffe..8f93afc07c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From ebfea94815bc0b6f7c2b75b5751be9b3fdc4b4f9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 29 Jan 2015 14:53:25 +0100 Subject: [PATCH 118/911] convert easyconfig from hackish MakeCp to less such CmdCp --- .../easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 9726d8c156..b750d29bed 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -7,7 +7,7 @@ # $Id$ ## -easyblock = 'MakeCp' +easyblock = 'CmdCp' name = 'fastqz' version = '1.5' @@ -18,16 +18,21 @@ description = """fastqz is a compressor for FASTQ files. FASTQ is the output of FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchainopts = {'opt': True, 'optarch': True} dependencies = [('ZPAQ', '6.57')] # eg. http://mattmahoney.net/dc/fastqz/fastqz15.cpp & http://mattmahoney.net/dc/fastqz/fapack.cpp minver = ''.join(version.split('.')) -sources = [('fastqz%s.cpp' % minver, 'cp %s %(builddir)s/fastqz.cpp'), ('fapack.cpp', 'cp %s %(builddir)s')] +sources = ['fastqz%s.cpp' % minver, 'fapack.cpp'] source_urls = [homepage] -prebuildopts = 'g++ -O3 -msse2 -s -lpthread fastqz.cpp $EBROOTZPAQ/include/libzpaq.cpp -o fastqz' -prebuildopts += '&& g++ -O3 -s fapack.cpp -o fapack && /bin/true ' +skipsteps = ['source'] + +cmds_map = [ + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o fastqz'), + ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') +] files_to_copy = [(['fastqz', 'fapack'], 'bin')] -- GitLab From 6eabe54406309d9299f3bde9d046400f316688c1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 29 Jan 2015 15:00:30 +0100 Subject: [PATCH 119/911] fix DSRC & fqzcomp minor issues, as asked --- easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 2 +- easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index 8be9aa164d..e0cb4f9a7d 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # fi. http://sun.aei.polsl.pl/dsrc/download/2.0rc/dsrc sources = ['%(namelower)s'] -source_urls = [homepage + '/download/%(version)s/'] +source_urls = ['http://sun.aei.polsl.pl/dsrc/download/%(version)s/'] checksums = [('md5', 'bdc40a96e33411cd4cdbe2b58ae285b7')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb index 3ca5906073..867cc250e1 100644 --- a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -22,8 +22,6 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -skipsteps = ['configure'] - files_to_copy = [(['fqz_comp'], 'bin')] sanity_check_paths = { -- GitLab From 194a90159c492562e72d399f924a1ec437062565 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 29 Jan 2015 15:06:54 +0100 Subject: [PATCH 120/911] make Quip compatible w. eb/2.0 --- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index c3812cfb0a..01169de210 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -7,6 +7,8 @@ # $Id$ ## +easyblock = 'ConfigureMake' + name = 'Quip' version = '1.1.8' -- GitLab From 997f1baf47f0ce8120d6d442d130ca08269b752d Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:34:46 +0000 Subject: [PATCH 121/911] a foss-2015a version of Cufflinks-2.2.1 --- .../Boost-1.55.0-foss-2015a-Python-2.7.9.eb | 25 ++++++++++++++++ .../c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 29 +++++++++++++++++++ .../e/Eigen/Eigen-3.2.3-foss-2015a.eb | 14 +++++++++ .../s/SAMtools/SAMtools-0.1.19-foss-2015a.eb | 21 ++++++++++++++ 4 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..88a81a73e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb new file mode 100644 index 0000000000..7ae5cdce38 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.9'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000..a2767dc205 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb new file mode 100644 index 0000000000..c7a055062e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' -- GitLab From 9d7b3d81fb4b342881becb00d0f9f779523b0864 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 14:38:28 +0000 Subject: [PATCH 122/911] switching order of config and preconfig --- easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb index 7ae5cdce38..d0372e6f70 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -18,8 +18,8 @@ dependencies = [ ('zlib', '1.2.8'), ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' sanity_check_paths = { 'files': ['bin/cufflinks'], -- GitLab From f244f84c3a1c56eabb84c3b1e2d20b2cac1fb31b Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 29 Jan 2015 17:57:12 +0000 Subject: [PATCH 123/911] this is a dep of the gmp extension --- .../easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb new file mode 100644 index 0000000000..c7f00d04ae --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '5.1.3' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 2e6998f16884b1d817c7244f7ed310efb022c024 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Fri, 30 Jan 2015 16:57:34 +1300 Subject: [PATCH 124/911] adding bsoft --- .../easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb new file mode 100644 index 0000000000..666dd772d0 --- /dev/null +++ b/easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb @@ -0,0 +1,28 @@ +easyblock = 'CmdCp' + +name = 'bsoft' +version = '1.8.8' + +homepage = 'http://lsbr.niams.nih.gov/bsoft/' +description = """Bsoft is a collection of programs and a platform for development of software +for image and molecular processing in structural biology. Problems in structural biology +are approached with a highly modular design, allowing fast development of new algorithms +without the burden of issues such as file I/O. It provides an easily accessible interface, +a resource that can be and has been used in other packages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': True} + +source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] +sources = ['%(name)s1_8_8.tar'] + +cmds_map = [('./bmake', 'omp fftw=$EBROOTFFTW')] + +files_to_copy = [('bin')] + +sanity_check_paths = { + 'files': [''], + 'dirs': ['bin'], +} + +moduleclass = 'bio' -- GitLab From dcf2f5f54872047b97d301ee74013a9adf1fafa5 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 09:38:37 +0100 Subject: [PATCH 125/911] Added foss easyconfig for Boost --- .../Boost-1.57.0-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1c2ebd212d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.57.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From a8553aed07cf06f6af9fcf4405fbbea669a2d6d7 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 09:39:38 +0100 Subject: [PATCH 126/911] Added foss easyconfig for GSL --- .../easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb new file mode 100644 index 0000000000..b20d7731f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.16' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From e2d1111e149a904a8d6454f63ef1b17d04bf4d07 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 09:47:03 +0100 Subject: [PATCH 127/911] Added foss easyconfig for expat --- .../easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb new file mode 100644 index 0000000000..1381b2b8cd --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From 05d224d4e9345756c7191dfe6cda535319fb1534 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 09:52:07 +0100 Subject: [PATCH 128/911] Added foss easyconfig for libxml2 --- .../l/libxml2/libxml2-2.9.2-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb new file mode 100644 index 0000000000..12454bc9c4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' -- GitLab From cb82dc83e3b7083b4c5dc8e47529a7df68306bd3 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 10:01:03 +0100 Subject: [PATCH 129/911] Added foss easyconfig for GMP --- .../easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb new file mode 100644 index 0000000000..c7f00d04ae --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '5.1.3' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 3fb1251870e878bc7cb8d521f65378b7e18a1669 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 10:17:25 +0100 Subject: [PATCH 130/911] Added foss easyconfig for latest GMP --- .../g/GMP/GMP-6.0.0a-foss-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb new file mode 100644 index 0000000000..2b5b650040 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0a' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 356bb45f656a6adac65444adaa59e45684d0b7a8 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 10:21:06 +0100 Subject: [PATCH 131/911] Added foss easyconfig for MPFR --- .../m/MPFR/MPFR-3.1.2-foss-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a.eb new file mode 100644 index 0000000000..4224e2bf0a --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.2' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '5.1.3')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' -- GitLab From 5b5fd4a043662a9b238bdce8fb0b58cbb00c43bb Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 10:23:09 +0100 Subject: [PATCH 132/911] Added foss easyconfig for MPC --- .../easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb new file mode 100644 index 0000000000..6024ebbee4 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.0.2' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.multiprecision.org/mpc/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GMP', '5.1.3'), + ('MPFR', '3.1.2')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.so', 'include/mpc.h'], + 'dirs': [] + } + +moduleclass = 'math' -- GitLab From c3212fb694a0705ba58f647dbd5543c2729f70b3 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 15:40:09 +0100 Subject: [PATCH 133/911] Added GCC easyconfig for expat --- .../easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..e10b56409e --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' -- GitLab From 2e964144fac6826c8b5e3c5db6ac9b4f8c4cb32b Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 15:41:10 +0100 Subject: [PATCH 134/911] Added GCC easyconfig for gettext --- .../g/gettext/gettext-0.19.4-GCC-4.9.2.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..7e8ff4e184 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 0194c0bf5cf26ffbd5902cc9ca32a981d7557068 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 15:51:11 +0100 Subject: [PATCH 135/911] Added GCC easyconfig for latest git 1.8.x --- .../g/git/git-1.8.5.6-GCC-4.9.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb new file mode 100644 index 0000000000..e8677ef233 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# Authors:: Dmitri Gribenko +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'git' +version = '1.8.5.6' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz +sources = ['v%s.tar.gz' % version] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = 'make configure && ' + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), +] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--enable-pthreads='-lpthread'" + +moduleclass = 'tools' -- GitLab From 67a63f66e366455cd4bf4df14cb0c81297d97eae Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 15:56:37 +0100 Subject: [PATCH 136/911] Added GCC easyconfig for git 2.x --- .../easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb new file mode 100644 index 0000000000..bcd6e205c6 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# Authors:: Dmitri Gribenko +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.2.2' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz +sources = ['v%s.tar.gz' % version] +source_urls = ['https://github.com/git/git/archive'] + +preconfigopts = 'make configure && ' + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), +] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--enable-pthreads='-lpthread'" + +moduleclass = 'tools' -- GitLab From 543f60b2d261760cd1fd24fa4dc2bb14ccdbbab6 Mon Sep 17 00:00:00 2001 From: gjbex Date: Fri, 30 Jan 2015 16:16:07 +0100 Subject: [PATCH 137/911] Added foss easyconfig for Mercurial 3.x --- ...Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb new file mode 100644 index 0000000000..f9e0be44b5 --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '3.2.4' + +homepage = 'http://mercurial.selenic.com/' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://mercurial.selenic.com/release/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/hg'], + 'dirs': ['lib/python%s/site-packages/mercurial' % pythonshortversion], +} + +moduleclass = 'tools' -- GitLab From eaa32794a2c70a15b76b614df5b66df88fb1b0e3 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 30 Jan 2015 16:16:47 +0000 Subject: [PATCH 138/911] adding R dependencies for 2015a --- .../libjpeg-turbo-1.4.0-foss-2015a.eb | 24 ++++++++++++++ .../l/libpng/libpng-1.6.16-foss-2015a.eb | 19 ++++++++++++ .../n/NASM/NASM-2.11.06-foss-2015a.eb | 31 +++++++++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb new file mode 100644 index 0000000000..57eea7cba0 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015a.eb new file mode 100644 index 0000000000..e0dd323091 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb new file mode 100644 index 0000000000..a9ff827237 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-foss-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 72ed3845015990581d1221e31def071690642196 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 30 Jan 2015 16:17:18 +0000 Subject: [PATCH 139/911] version bump for BiocParallel and adding GMP as dep --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index 16a52c2e37..0e010cb5cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('GMP', '5.1.3'), ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -220,7 +221,7 @@ exts_list = [ ('Biostrings', '2.34.1', bioconductor_options), ('GenomicRanges', '1.18.4', bioconductor_options), ('Rsamtools', '1.18.2', bioconductor_options), - ('BiocParallel', '1.0.0', bioconductor_options), + ('BiocParallel', '1.0.1', bioconductor_options), ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), -- GitLab From 4faed4c4494e6aed8ef2b76215d2cbae514fb792 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Mon, 2 Feb 2015 11:49:34 +1300 Subject: [PATCH 140/911] dirty hack, but it works --- .../easyconfigs/b/{ => bsoft}/bsoft-1.8.8-goolf-1.5.14.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/b/{ => bsoft}/bsoft-1.8.8-goolf-1.5.14.eb (91%) diff --git a/easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb similarity index 91% rename from easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb rename to easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb index 666dd772d0..fb170b88ed 100644 --- a/easybuild/easyconfigs/b/bsoft-1.8.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -easyblock = 'CmdCp' +easyblock = 'MakeCp' name = 'bsoft' version = '1.8.8' @@ -16,8 +16,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] sources = ['%(name)s1_8_8.tar'] -cmds_map = [('./bmake', 'omp fftw=$EBROOTFFTW')] - +prebuildopts = [("./bmake omp fftw=$EBROOTFFTW #")] files_to_copy = [('bin')] sanity_check_paths = { -- GitLab From 60c00164f456a766ef063e8ae085dd537233ebbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Feb 2015 05:28:58 +0100 Subject: [PATCH 141/911] switch to CmdCp in bsoft easyconfig + style fixes --- .../easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb index fb170b88ed..5bba690060 100644 --- a/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/bsoft/bsoft-1.8.8-goolf-1.5.14.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'CmdCp' name = 'bsoft' version = '1.8.8' @@ -14,14 +14,14 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'openmp': True} source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] -sources = ['%(name)s1_8_8.tar'] +sources = ['%%(name)s%s.tar' % '_'.join(version.split('.'))] -prebuildopts = [("./bmake omp fftw=$EBROOTFFTW #")] -files_to_copy = [('bin')] +cmds_map = [('.*', "./bmake omp fftw=$EBROOTFFTW")] +files_to_copy = ['bin'] sanity_check_paths = { - 'files': [''], - 'dirs': ['bin'], + 'files': ['bin/brun', 'bin/bshow', 'bin/bview'], + 'dirs': [], } moduleclass = 'bio' -- GitLab From a70f6a73452951f1f8764251cd795534387f0453 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Feb 2015 06:30:32 +0100 Subject: [PATCH 142/911] fix zlib dep versions in Tcl easyconfigs --- easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb | 2 +- easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb | 2 +- easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb index 25a490d28f..32fe48b93c 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-foss-2014b.eb @@ -13,7 +13,7 @@ source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb index c54aec7e60..ca1465be0b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.12-intel-2014b.eb @@ -13,7 +13,7 @@ source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb index 7f7f55c666..78a978f384 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb @@ -13,7 +13,7 @@ source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ - ('zlib', '1.2.7'), + ('zlib', '1.2.5'), ] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' -- GitLab From 7389d94f608bf42a2eb65ee333dfa390ec389cef Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Tue, 3 Feb 2015 14:58:17 +1300 Subject: [PATCH 143/911] updated version for Eigen --- .../e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb new file mode 100644 index 0000000000..38b0fe9f28 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Eigen' +version = '3.2.2' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' -- GitLab From 63390225a972d544d52168c0604fa8f678737fcb Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Tue, 3 Feb 2015 15:09:53 +1300 Subject: [PATCH 144/911] upgrading ULF --- .../UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb new file mode 100644 index 0000000000..dfe8b9eccf --- /dev/null +++ b/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'UFL' +version = '1.5.0' + +homepage = 'https://launchpad.net/ufl' +description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations +of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions +for weak forms in a notation close to mathematical notation.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +majorversion = "%s.x" % ".".join(version.split('.')[:-1]) +source_urls = ['https://bitbucket.org/fenics-project/ufl/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] + } + +moduleclass = 'cae' -- GitLab From fef8592006a7d89cc3c464c688bd64d1168233fe Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Tue, 3 Feb 2015 15:25:16 +1300 Subject: [PATCH 145/911] Update UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb --- .../u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb index dfe8b9eccf..e6e912f041 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.5.0-goolf-1.5.14-Python-2.7.8.eb @@ -4,9 +4,11 @@ name = 'UFL' version = '1.5.0' homepage = 'https://launchpad.net/ufl' -description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations -of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions -for weak forms in a notation close to mathematical notation.""" +description = """The Unified Form Language (UFL) is a domain specific language + for declaration of finite element discretizations of variational forms. + More precisely, it defines a flexible interface for choosing finite element + spaces and defining expressions for weak forms in a notation close to + mathematical notation.""" toolchain = {'name': 'goolf', 'version': '1.5.14'} @@ -23,8 +25,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], - 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] - } + 'files': ['bin/%s' % x for x in ["form2ufl", "ufl2py", "ufl-analyse", "ufl-convert", "ufl-version"]], + 'dirs': ['lib/python%s/site-packages/ufl' % pythonshortversion] +} moduleclass = 'cae' -- GitLab From cb72e773d51856979c831d9db1028820e8c5bf46 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 08:49:58 +0100 Subject: [PATCH 146/911] Added intel easyconfig for FFTW --- .../f/FFTW/FFTW-3.3.4-intel-2015a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb new file mode 100644 index 0000000000..ce8a9b16ca --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 637e3228cd649088160ee6a0fd40567507c5ba8c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 09:15:00 +0100 Subject: [PATCH 147/911] Added foss easyconfig for PCRE --- .../p/PCRE/PCRE-8.36-foss-2015a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb new file mode 100644 index 0000000000..d43a790e2f --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.36' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +configopts = "--with-pic --disable-cpp" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' -- GitLab From c4874fee095c749e5e7d5a20ba3d8da01c85c0cc Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:22:39 +0100 Subject: [PATCH 148/911] Added foss easyconfig for Octave --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb new file mode 100644 index 0000000000..150b37eaf0 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -0,0 +1,26 @@ +name = 'Octave' +version = '3.8.2' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/octave/'] + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +configopts = ['--with-blas="-lopenblas"'] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +moduleclass = 'math' + -- GitLab From 204e617d08eb2ce87f52052652f2163ef5a1c4a5 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:53:14 +0100 Subject: [PATCH 149/911] Added GCC easyconfig for XZ --- .../easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..5a6ed9b122 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.0' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 54343d8faebbeaeb61054461be98e36e4bbe25d9 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:55:26 +0100 Subject: [PATCH 150/911] Fixed style issues as per request --- .../easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 150b37eaf0..25b2a7b0a9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -9,11 +9,6 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/octave/'] -sanity_check_paths = { - 'files': ['bin/octave'], - 'dirs': [] -} - configopts = ['--with-blas="-lopenblas"'] dependencies = [ @@ -22,5 +17,9 @@ dependencies = [ ('libreadline', '6.3'), ] -moduleclass = 'math' +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} +moduleclass = 'math' -- GitLab From 277d7e0dbf695d7c9b417e342661f9e95ebf4a6d Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 13:55:56 +0100 Subject: [PATCH 151/911] Fixed style issues as per request --- easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index d43a790e2f..dd7d330b7c 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -12,9 +12,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' -- GitLab From f448096adc29c302039c50a5c4b556614e3ef04f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Feb 2015 14:10:41 +0100 Subject: [PATCH 152/911] Add usefull comment about binutils --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 411ab43736..dfce67f25b 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -26,6 +26,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # compiler toolchain depencies # we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain # because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ comp, ('zlib', '1.2.8', '', comp), -- GitLab From a5778bf7ba50e3c04f4c101dc1ccd5ca1585aefa Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 14:24:11 +0100 Subject: [PATCH 153/911] Fixed BLAS library flags style issue --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 25b2a7b0a9..ca0386a404 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/octave/'] -configopts = ['--with-blas="-lopenblas"'] +configopts = ['--with-blas="${LIBBLAS}"'] dependencies = [ ('PCRE', '8.36'), -- GitLab From 18138b2bb26393b4bce19e839835d04d92520f20 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 14:28:24 +0100 Subject: [PATCH 154/911] Added GCC easyconfig for Coreutils --- .../c/Coreutils/Coreutils-8.23-GCC-4.9.2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.23-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.23-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.23-GCC-4.9.2.eb new file mode 100644 index 0000000000..da397d5d5e --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.23-GCC-4.9.2.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "8.23" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the + GNU operating system. These are the core utilities which are expected to exist on every operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From f19fa0f1641dff338b1dff465fa0d4974f393b17 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 14:54:24 +0100 Subject: [PATCH 155/911] Added GCC easyconfig for mc --- .../easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb new file mode 100644 index 0000000000..ef4c9cf3a2 --- /dev/null +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'mc' +version = '4.8.13' + +homepage = 'https://www.midnight-commander.org/' +description = """mc-4.6.1: User-friendly file manager and visual shell""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/MidnightCommander/mc/archive/'] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/mc'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 7ee9bcd55131b71386aea71d086be71cd0e21276 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 14:57:21 +0100 Subject: [PATCH 156/911] Fixed style issues as per request --- easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb index 6024ebbee4..d5449c24a4 100644 --- a/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb +++ b/easybuild/easyconfigs/m/MPC/MPC-1.0.2-foss-2015a.eb @@ -17,14 +17,16 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['http://www.multiprecision.org/mpc/download/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('GMP', '5.1.3'), - ('MPFR', '3.1.2')] +dependencies = [ + ('GMP', '5.1.3'), + ('MPFR', '3.1.2'), +] runtest = 'check' sanity_check_paths = { 'files': ['lib/libmpc.so', 'include/mpc.h'], - 'dirs': [] - } + 'dirs': [], +} moduleclass = 'math' -- GitLab From 5f37d6f259c244941c2c388fd4a543bf077052f7 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 15:28:41 +0100 Subject: [PATCH 157/911] Fixed some more style issues --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index ca0386a404..e311f5fe2d 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -6,10 +6,10 @@ description = """GNU Octave is a high-level interpreted language, primarily inte toolchain = {'name': 'foss', 'version': '2015a'} -sources = [SOURCELOWER_TAR_GZ] +sources = [GNU_SOURCE] source_urls = ['http://ftpmirror.gnu.org/octave/'] -configopts = ['--with-blas="${LIBBLAS}"'] +configopts = '--with-blas="${LIBBLAS}"' dependencies = [ ('PCRE', '8.36'), -- GitLab From 0f0aee950c720a5ce5f56465558d802399288438 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 16:22:20 +0100 Subject: [PATCH 158/911] Fixed style issue as per request --- easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb index e8677ef233..7360f033fe 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.5.6-GCC-4.9.2.eb @@ -19,6 +19,7 @@ version = '1.8.5.6' homepage = 'http://git-scm.com/' description = """Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.""" + toolchain = {'name': 'GCC', 'version': '4.9.2'} # eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -- GitLab From c3511d9aed4e00f613a2a01d503c7b1ef3c8dd7c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 16:22:59 +0100 Subject: [PATCH 159/911] Fixed style issue as per request --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index bcd6e205c6..cb7b6916f1 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -19,6 +19,7 @@ version = '2.2.2' homepage = 'http://git-scm.com/' description = """Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.""" + toolchain = {'name': 'GCC', 'version': '4.9.2'} # eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -- GitLab From 6800080372310175336978cb3a636611752ccb6c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 16:23:36 +0100 Subject: [PATCH 160/911] Fixed style issue as per request --- .../m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb index f9e0be44b5..047324c714 100644 --- a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb @@ -7,6 +7,7 @@ homepage = 'http://mercurial.selenic.com/' description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. """ + toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ['http://mercurial.selenic.com/release/'] -- GitLab From 16875304f45994aa81959b2cc8ed83540816062a Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 16:33:22 +0100 Subject: [PATCH 161/911] Added GCC easyconfig for GLib --- .../g/GLib/GLib-2.42.1-GCC-4.9.2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..abd733597e --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.42.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.4'), +] +builddependencies = [('Python', '2.7.9')] + +moduleclass = 'vis' -- GitLab From 30a952abae6a03b1836f4cdeb2120814cdfa3395 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 17:08:51 +0100 Subject: [PATCH 162/911] Added GCC easyconfig for GLib, libffi, S_Lang --- .../g/GLib/GLib-2.42.1-GCC-4.9.2.eb | 2 +- .../l/libffi/libffi-3.2.1-GCC-4.9.2.eb | 23 +++++++++++++++++++ .../s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb | 22 ++++++++++++++++++ 3 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb index abd733597e..78ac531e4f 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb @@ -16,6 +16,6 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ] -builddependencies = [('Python', '2.7.9')] +builddependencies = [('Python', '2.7.9', '', ('foss', '2015a'))] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..b980f40d3e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb b/easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..697f40c689 --- /dev/null +++ b/easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'S_Lang' +version = '2.3.0' + +homepage = 'http://www.jedsoft.org/slang/' +description = """S-Lang is a multi-platform programmer's library designed to allow + a developer to create robust multi-platform software. It provides facilities + required by interactive applications such as display/screen management, keyboard + input, keymaps, and so on.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['slang-%(version)s.tar.gz'] +source_urls = ['http://www.jedsoft.org/releases/slang/'] + +sanity_check_paths = { + 'files': ['include/slang.h', 'bin/slsh', 'lib/libslang.so'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From f3beb86c8fcb65f45d9f994e49cb123eb9bb8f47 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 17:13:04 +0100 Subject: [PATCH 163/911] Finished mc --- easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index ef4c9cf3a2..a8c6ce238b 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -23,6 +23,11 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['%(version)s.tar.gz'] source_urls = ['https://github.com/MidnightCommander/mc/archive/'] +dependencies = [ + ('GLib', '2.42.1'), + ('S_Lang', '2.3.0'), +] + preconfigopts = './autogen.sh && ' sanity_check_paths = { -- GitLab From c23974e96bd2d795aaf6b21318e79cfbfe0985ba Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 17:24:38 +0100 Subject: [PATCH 164/911] Added GCC easyconfig for libevent --- .../l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb new file mode 100644 index 0000000000..35bf28ab3b --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.0.22' + +homepage = 'http://libevent.org/' +description = """The libevent API provides a mechanism to execute a callback function when a specific + event occurs on a file descriptor or after a timeout has been reached. + Furthermore, libevent also support callbacks due to signals or regular timeouts.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['https://github.com/downloads/libevent/libevent/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +source_urls = ['https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-2.0/'] + +moduleclass = 'lib' -- GitLab From 6aa2b514c275e1b6f08c3258188cda3977c77db2 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Feb 2015 17:28:46 +0100 Subject: [PATCH 165/911] Added GCC easyconfig for tmux --- .../easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb new file mode 100644 index 0000000000..ba34aab87a --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '1.9a' + +homepage = 'http://tmux.sourceforge.net/' +description = """tmux is a terminal multiplexer. It lets you switch easily +between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True} + +#http://sourceforge.net/projects/tmux/files/tmux/tmux-1.9/tmux-1.9a.tar.gz/download +sources = [SOURCE_TAR_GZ] +source_urls = ['http://downloads.sourceforge.net/%(name)s/'] + +dependencies = [ + ('libevent', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': ['bin'] +} + +moduleclass = 'tools' -- GitLab From 222cdfd7da765c4a54921b5dce61cbb13b9ab9de Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Feb 2015 16:34:19 +0000 Subject: [PATCH 166/911] removing gmp and gl dependencies --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index 0e010cb5cc..fc8a268e2c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -20,7 +20,6 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it - ('GMP', '5.1.3'), ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -280,9 +279,6 @@ exts_list = [ ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), ('partitions', '1.9-15', ext_options), - ('rgl', '0.95.1201', ext_options), - ('phangorn', '1.99-11', ext_options), - ('phytools', '0.4-31', ext_options), ('vegan', '2.2-0', ext_options), ('picante', '1.6-2', ext_options), ('quantreg', '5.05', ext_options), @@ -372,7 +368,6 @@ exts_list = [ ('genoset', '1.20.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '0.7.7', ext_options), - ('mixOmics', '5.0-3', ext_options), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), ('openxlsx', '2.2.1', ext_options), @@ -387,3 +382,4 @@ exts_list = [ ] moduleclass = 'lang' + -- GitLab From cd5927e2754be0c76e53813b7e3b857336334a24 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Feb 2015 19:52:01 +0000 Subject: [PATCH 167/911] remove gmp extension --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index fc8a268e2c..d5984e2bae 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -269,7 +269,6 @@ exts_list = [ ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '1.9-8', ext_options), - ('gmp', '0.5-12', ext_options), ('labdsv', '1.6-1', ext_options), ('MatrixModels', '0.3-1.1', ext_options), ('stabs', '0.5-0', ext_options), -- GitLab From c360434e3c5a7cc489ee5a4cbe74a81b8e3460e6 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Feb 2015 19:53:54 +0000 Subject: [PATCH 168/911] removing GMP EB --- .../easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb deleted file mode 100644 index c7f00d04ae..0000000000 --- a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-foss-2015a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GMP' -version = '5.1.3' - -homepage = 'http://gmplib.org/' -description = """GMP is a free library for arbitrary precision arithmetic, -operating on signed integers, rational numbers, and floating point numbers. """ - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] - -# enable C++ interface -configopts = '--enable-cxx' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], - 'dirs': [], -} - -moduleclass = 'math' -- GitLab From 073c6bbe684e3065dc81c5628fe7f0a463b3bd7c Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 08:32:43 +0100 Subject: [PATCH 169/911] Added GCC easyconfig for mawk --- .../m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb new file mode 100644 index 0000000000..1c23e63925 --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20141206' + +homepage = 'http://invisible-island.net/mawk/mawk.html' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/mawk'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': ["bin"] +} + +moduleclass = 'tools' -- GitLab From e8ae9f719bf32a2369c01b27c571b77aabc839a0 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:03:12 +0100 Subject: [PATCH 170/911] Added intel easyconfig for libxml2 --- .../l/libxml2/libxml2-2.9.2-intel-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb new file mode 100644 index 0000000000..84a2d133c6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' -- GitLab From e157f4712464694e7b28a32998703339ed2bb815 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:03:36 +0100 Subject: [PATCH 171/911] Added intel easyconfig for libxslt --- .../l/libxslt/libxslt-1.1.28-intel-2015a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015a.eb new file mode 100644 index 0000000000..31f8acfbc8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' -- GitLab From 6729a30ed28896f3657cb9a2ebe628de5cb229eb Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:05:12 +0100 Subject: [PATCH 172/911] Added foss easyconfig for libxslt --- .../l/libxslt/libxslt-1.1.28-foss-2015a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2015a.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2015a.eb new file mode 100644 index 0000000000..c643283ea5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.28' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' -- GitLab From c46a7c5fd41abee7d22676d04fa3933eeab037b2 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:13:14 +0100 Subject: [PATCH 173/911] Renamed S_Lang to S-Lang --- .../S-Lang-2030-GCC-4.9.2.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb => S-Lang/S-Lang-2030-GCC-4.9.2.eb} (97%) diff --git a/easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb b/easybuild/easyconfigs/s/S-Lang/S-Lang-2030-GCC-4.9.2.eb similarity index 97% rename from easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb rename to easybuild/easyconfigs/s/S-Lang/S-Lang-2030-GCC-4.9.2.eb index 697f40c689..d5d02f5692 100644 --- a/easybuild/easyconfigs/s/S_Lang/S_Lang-2.3.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/s/S-Lang/S-Lang-2030-GCC-4.9.2.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'S_Lang' +name = 'S-Lang' version = '2.3.0' homepage = 'http://www.jedsoft.org/slang/' -- GitLab From 90e9ce9cb252171d4596f885f569c473508b9494 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:30:13 +0100 Subject: [PATCH 174/911] Fixed dependency for S-Lang rename --- easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index a8c6ce238b..c3b1a15562 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -25,7 +25,7 @@ source_urls = ['https://github.com/MidnightCommander/mc/archive/'] dependencies = [ ('GLib', '2.42.1'), - ('S_Lang', '2.3.0'), + ('S-Lang', '2.3.0'), ] preconfigopts = './autogen.sh && ' -- GitLab From 2c984337e09add925ad4eac05d6a23859efaf5b7 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:41:52 +0100 Subject: [PATCH 175/911] Added intel easyconfig for Xerces C++ --- .../Xerces-C++-3.1.1-intel-2015a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb new file mode 100644 index 0000000000..3deed28bad --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb @@ -0,0 +1,19 @@ +name = 'Xerces-C++' +version = '3.1.1' + +homepage = 'http://xerces.apache.org/xerces-c/' +description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/3/sources/' +] + + +dependencies = [ + ('cURL', '7.40.0'), +] + +moduleclass = 'lib' -- GitLab From 6bd8301b5afcb108bd69fa3c483d2e8069b26301 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:46:19 +0100 Subject: [PATCH 176/911] Added foss easyconfig for cURL --- .../c/cURL/cURL-7.40.0-foss-2015a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb new file mode 100644 index 0000000000..a8c7d1b972 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.40.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' -- GitLab From c289a2e64a2283f5b793a3f29a79ee0555fc1900 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:50:06 +0100 Subject: [PATCH 177/911] Added foss easyconfig for Xerces C++ --- .../Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb new file mode 100644 index 0000000000..d8a60cefb4 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.1' + +homepage = 'http://xerces.apache.org/xerces-c/' +description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/3/sources/' +] + + +dependencies = [ + ('cURL', '7.40.0'), +] + +moduleclass = 'lib' -- GitLab From ccd13ac7bccf618242acf9a0febcfad396dfbb76 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:57:37 +0100 Subject: [PATCH 178/911] Added intel easyconfig for XQilla --- .../x/XQilla/XQilla-2.3.0-intel-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb new file mode 100644 index 0000000000..b169cb5840 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.0' + +homepage = 'http://xqilla.sourceforge.net/HomePage' +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C∞ library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +dependencies = [ + ('Xerces-C++', '3.1.1'), +] + +moduleclass = 'lib' -- GitLab From a461142bb905092ee42f8d3ab5f9d1fe328ccb9b Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 09:59:59 +0100 Subject: [PATCH 179/911] Added foss easyconfig for XQilla --- .../x/XQilla/XQilla-2.3.0-foss-2015a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb new file mode 100644 index 0000000000..aa79e51474 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.0' + +homepage = 'http://xqilla.sourceforge.net/HomePage' +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C∞ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/xqilla/%s' % version, +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +dependencies = [ + ('Xerces-C++', '3.1.1'), +] + +moduleclass = 'lib' -- GitLab From a323bb4dff57c7e633fe6fb6cbea03adfe4cc156 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 10:28:07 +0100 Subject: [PATCH 180/911] Added missing easyblock directive --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb index 3deed28bad..458d80e62e 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Xerces-C++' version = '3.1.1' -- GitLab From e13ea007186459d14df6500550a0d302164abb3a Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:02:47 +0100 Subject: [PATCH 181/911] Added GCC easybuild for Emacs --- .../e/Emacs/Emacs-24.4-GCC-4.9.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb b/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..70d51139b0 --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '24.4' + +homepage = 'http://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor—and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language + with extensions to support text editing.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('ncurses', '5.9'), +] + +configopts = '--with-gif=no --with-tiff=no --with-x-toolkit=no --with-xpm=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 28b8df7dbcffa026033b33c9560526af67f82734 Mon Sep 17 00:00:00 2001 From: gjbex Date: Wed, 4 Feb 2015 14:07:04 +0100 Subject: [PATCH 182/911] Added GCC easyconfig for Doxygen --- .../d/Doxygen/Doxygen-1.8.9.1-GCC-4.9.2.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.9.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.9.1-GCC-4.9.2.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.9.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..1cb88eb2d0 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.9.1-GCC-4.9.2.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.9.1' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.3'), +] + +moduleclass = 'devel' -- GitLab From 44be1367a0e6d75236eae6be15cd0c976bb07fa3 Mon Sep 17 00:00:00 2001 From: Geert Jan BEX Date: Wed, 4 Feb 2015 15:10:54 +0100 Subject: [PATCH 183/911] Fixed style issue as per request --- easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb b/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb index 70d51139b0..ceb01e01dd 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-24.4-GCC-4.9.2.eb @@ -9,7 +9,6 @@ description = """GNU Emacs is an extensible, customizable text editor—and more with extensions to support text editing.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} -toolchainopts = {} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -- GitLab From 5eb860c0ee5d4c1f097c3d7df320003cc9e89a3d Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 4 Feb 2015 14:48:54 -0500 Subject: [PATCH 184/911] bumping versions that have disappeared from Bioconductor and removing partitions(gmp) and vegan(tcl/tk) for deps --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index d5984e2bae..62367a74a4 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -220,7 +220,7 @@ exts_list = [ ('Biostrings', '2.34.1', bioconductor_options), ('GenomicRanges', '1.18.4', bioconductor_options), ('Rsamtools', '1.18.2', bioconductor_options), - ('BiocParallel', '1.0.1', bioconductor_options), + ('BiocParallel', '1.0.2', bioconductor_options), ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), @@ -277,8 +277,6 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('partitions', '1.9-15', ext_options), - ('vegan', '2.2-0', ext_options), ('picante', '1.6-2', ext_options), ('quantreg', '5.05', ext_options), ('RcppEigen', '0.3.2.3.0', ext_options), @@ -315,7 +313,7 @@ exts_list = [ ('limma', '3.22.4', bioconductor_options), ('RBGL', '1.42.0', bioconductor_options), ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.1', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), ('KEGG.db', '3.0.0', bioconductor_options), ('annaffy', '1.38.0', bioconductor_options), ('gcrma', '2.38.0', bioconductor_options), -- GitLab From 70d2b775d52c9544fb588771005f66334eec8228 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Thu, 5 Feb 2015 16:30:35 +1300 Subject: [PATCH 185/911] Update Eigen-3.2.2-goolf-1.5.14.eb Using BITBUCKET_SOURCE. --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb index 38b0fe9f28..024205f8b6 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.2-goolf-1.5.14.eb @@ -20,7 +20,7 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] moduleclass = 'math' -- GitLab From 3726f433eab8eb42c11e0197eec3be83e778e0db Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Thu, 5 Feb 2015 16:35:18 +1300 Subject: [PATCH 186/911] adding python file --- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 160 ++++++++++++++++++ 1 file changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb new file mode 100644 index 0000000000..33fd2ef2d0 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -0,0 +1,160 @@ +name = 'Python' +version = '2.7.8' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.2' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), # for bz2 package +# ('zlib', '1.2.8'), # use version selected by libxslt below + ('libreadline', '6.2'), + ('ncurses', '5.9'), + ('LLVM', '3.2'), # for Numba + ('SQLite', '3.8.4.3'), # for IPython and general use + ('libxslt', '1.1.28'), # for lxml. brings in libxml2 and zlib dependencies. + ('CUDA', '6.0.37','', True), # for pycuda, duh. +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + + ('libjpeg-turbo','1.3.0'), # For matplotlib and Pillow + ('libpng','1.6.10'), # For matplotlib and Pillow + ('freetype', '2.5.3'), # For matplotlib and Pillow + +] + +# order is important! +exts_list = [ + ('setuptools', '5.7', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('ipython', '2.2.0', { + 'modulename': 'IPython', + 'source_urls': ['http://pypi.python.org/packages/source/i/ipython/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('virtualenv', '1.11.6', { + 'source_urls': ['http://pypi.python.org/packages/source/v/virtualenv/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('line_profiler', '1.0b3', { + 'source_urls': ['http://pypi.python.org/packages/source/l/line_profiler/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % ('1.8.1' if numpyversion.startswith('1.8') else numpyversion), + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + + + ('networkx', '1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], + 'modulename': 'Bio', + }), + ('biopython', '1.64', { + 'source_urls': ['https://pypi.python.org/packages/source/b/biopython/'], + 'modulename': 'Bio', + }), + + ('Pillow', '2.5.3', { + 'source_tmpl': SOURCE_ZIP, #'%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow/'], + 'modulename': 'PIL', + }), + ('matplotlib', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + }), + ('skimage', '0.10.1', { + 'source_tmpl': 'scikit-image-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/s/scikit-image/'], + }), + + ('lxml', '3.3.5', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], + }), + ('pycuda', '2014.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycuda/'], + }), + #('pyopencl', '2014.1', { + # 'source_urls': ['https://pypi.python.org/packages/source/p/puopencl/'], + #}), + ('pysam', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pysam/'], + }), + ('pytz', '2014.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + }), + + ('mpi4py', '1.3.1', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['http://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('llvmpy', '0.12.7', { +# 'source_urls': ['https://pypi.python.org/packages/source/l/llvmpy/'], + 'source_urls': ['https://github.com/llvmpy/llvmpy/archive/'], # since pypi tarball is incomplete + 'source_tmpl': '%(version)s.zip', + }), + ('numba', '0.13.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), + ('numexpr', '2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr/'], + }), + ('Bottleneck', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Bottleneck/'], + }), + ('pandas', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + }), + +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +moduleclass = 'lang' -- GitLab From dccb1001bed919679ef8df274e2bf14d76601745 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Feb 2015 07:50:23 +0100 Subject: [PATCH 187/911] add unit test to check that all extra_options keys are defined in EasyConfig instance --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d339976033..0dac782165 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -266,6 +266,10 @@ def template_easyconfig_test(self, spec): msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) self.assertTrue(os.path.isfile(ext_patch_full), msg) + # check whether all extra_options defined for used easyblock are defined + for key in app.extra_options(): + self.assertTrue(key in app.cfg) + app.close_log() os.remove(app.logfile) -- GitLab From 5d031e47103d8c6b5324cbddbe4191bb67771a25 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 09:49:39 +0100 Subject: [PATCH 188/911] Fixed style issue as per request --- easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index cb7b6916f1..48bda49ebe 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -22,12 +22,15 @@ to handle everything from small to very large projects with speed and efficiency toolchain = {'name': 'GCC', 'version': '4.9.2'} -# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -sources = ['v%s.tar.gz' % version] +sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] preconfigopts = 'make configure && ' +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--enable-pthreads='-lpthread'" + dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), @@ -39,8 +42,4 @@ sanity_check_paths = { 'dirs': [], } -# Work around git build system bug. If LIBS contains -lpthread, then configure -# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--enable-pthreads='-lpthread'" - moduleclass = 'tools' -- GitLab From b302372f3548f83ff7fb8ca7dc5707ffef6b773e Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 09:51:34 +0100 Subject: [PATCH 189/911] Rename Mercurial easyconfig to match toolchain used --- ...Python-2.7.9.eb => Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/Mercurial/{Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb => Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb} (100%) diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2014a-Python-2.7.9.eb rename to easybuild/easyconfigs/m/Mercurial/Mercurial-3.2.4-foss-2015a-Python-2.7.9.eb -- GitLab From b1dd33f0ebe8e1c06b33d271111d42ab726b8b63 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 11:49:05 +0100 Subject: [PATCH 190/911] Removed outdated source_urls directive --- easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index 35bf28ab3b..d2e3142b03 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -10,7 +10,6 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} -source_urls = ['https://github.com/downloads/libevent/libevent/'] sources = ['%(name)s-%(version)s-stable.tar.gz'] source_urls = ['https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-2.0/'] -- GitLab From 1abded66e1078846a4d5ed71b04337bc2ecc287a Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 11:50:32 +0100 Subject: [PATCH 191/911] Fixed style issue as per request --- easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index d2e3142b03..78c88db863 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -11,6 +11,6 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['%(name)s-%(version)s-stable.tar.gz'] -source_urls = ['https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-2.0/'] +source_urls = ['https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%version_major_minor)s/'] moduleclass = 'lib' -- GitLab From 1a367fd3ebbd22bfb9bbd84f7b4a6129845e2870 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 11:53:22 +0100 Subject: [PATCH 192/911] Fixed style issue as per request --- easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb index 1c23e63925..dd90e4fccd 100644 --- a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb @@ -13,7 +13,7 @@ source_urls = ['ftp://invisible-island.net/mawk'] sanity_check_paths = { 'files': ['bin/mawk'], - 'dirs': ["bin"] + 'dirs': [] } moduleclass = 'tools' -- GitLab From 3ac301ee23d3a4a44324b4c92bb1dce0bdd6a4f6 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 12:02:00 +0100 Subject: [PATCH 193/911] Added GCC easyconfig for libtool --- .../l/libtool/libtool-2.4.5-GCC-4.9.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb new file mode 100644 index 0000000000..fad1572815 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.5' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +moduleclass = 'lib' -- GitLab From bf8d0bcd830f7f190072c4cb2f1827d911663ffa Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 12:02:57 +0100 Subject: [PATCH 194/911] Fixed build depedencies --- easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index c3b1a15562..b567b31978 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -28,6 +28,11 @@ dependencies = [ ('S-Lang', '2.3.0'), ] +builddependencies = [ + ('Automake', '2.15'), + ('libtool', '2.4.5'), +] + preconfigopts = './autogen.sh && ' sanity_check_paths = { -- GitLab From 6096794da6b922dc52f78f25714a08dbd689cd46 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 12:10:28 +0100 Subject: [PATCH 195/911] Fixed style issues as per request --- easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index ba34aab87a..99ee62947e 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -10,9 +10,8 @@ between several programs in one terminal, detach them (they keep running in the toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'optarch': True} -#http://sourceforge.net/projects/tmux/files/tmux/tmux-1.9/tmux-1.9a.tar.gz/download sources = [SOURCE_TAR_GZ] -source_urls = ['http://downloads.sourceforge.net/%(name)s/'] +source_urls = [SOURCEFORGE_SOURCE] dependencies = [ ('libevent', '2.0.22'), @@ -20,7 +19,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/tmux'], - 'dirs': ['bin'] + 'dirs': [] } moduleclass = 'tools' -- GitLab From 556ebe6c4d6223948d6406e2fa637d4e45eb440d Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 12:12:54 +0100 Subject: [PATCH 196/911] Renamed easyconfig to be consistent with version --- .../{S-Lang-2030-GCC-4.9.2.eb => S-Lang-2.3.0-GCC-4.9.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/S-Lang/{S-Lang-2030-GCC-4.9.2.eb => S-Lang-2.3.0-GCC-4.9.2.eb} (100%) diff --git a/easybuild/easyconfigs/s/S-Lang/S-Lang-2030-GCC-4.9.2.eb b/easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/s/S-Lang/S-Lang-2030-GCC-4.9.2.eb rename to easybuild/easyconfigs/s/S-Lang/S-Lang-2.3.0-GCC-4.9.2.eb -- GitLab From 60577ab80bcdc8d98897b1eccda47f53b50d65f5 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 12:16:14 +0100 Subject: [PATCH 197/911] Added GCC easyconfig for gettext --- .../g/gettext/gettext-0.19.4-GCC-4.9.2.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..7e8ff4e184 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-GCC-4.9.2.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' -- GitLab From 34ba372ece6302b36e3bb14d7b5cab6f62967960 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 13:16:58 +0100 Subject: [PATCH 198/911] Added foss easyconfig for libxml2 --- .../l/libxml2/libxml2-2.9.2-foss-2015a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb new file mode 100644 index 0000000000..12454bc9c4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' -- GitLab From af962ef8479aadd4e982ed7eea01652e72918681 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 13:18:07 +0100 Subject: [PATCH 199/911] Fixed style issue as per request --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb index 458d80e62e..9437987e64 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb @@ -13,7 +13,6 @@ source_urls = [ 'http://apache.belnet.be/xerces/c/3/sources/' ] - dependencies = [ ('cURL', '7.40.0'), ] -- GitLab From f471fabf6b1869e37bac44f3dce08ceff7db23d2 Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 13:18:39 +0100 Subject: [PATCH 200/911] Fixed style issue as per request --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb index d8a60cefb4..443076c83e 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb @@ -13,7 +13,6 @@ source_urls = [ 'http://apache.belnet.be/xerces/c/3/sources/' ] - dependencies = [ ('cURL', '7.40.0'), ] -- GitLab From 0a8d3f7afe0e24d80f7024cdda4e52d8f527764c Mon Sep 17 00:00:00 2001 From: gjbex Date: Thu, 5 Feb 2015 13:46:55 +0100 Subject: [PATCH 201/911] Fixed build dependency on non-existing Automake version :) --- easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index b567b31978..893cc852b8 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -29,7 +29,7 @@ dependencies = [ ] builddependencies = [ - ('Automake', '2.15'), + ('Automake', '1.15'), ('libtool', '2.4.5'), ] -- GitLab From fe51176decea7fbd38557d4793c681419da7f132 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 5 Feb 2015 14:57:05 +0100 Subject: [PATCH 202/911] Added gompi toolchain 1.5.16 (GCC 4.8.3, OpenMPI 1.6.5) --- .../b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb | 16 ++++++++ easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb | 25 +++++++++++ .../h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb | 19 +++++++++ .../libreadline-6.2-gompi-1.5.16.eb | 28 +++++++++++++ .../n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 16 ++++++++ .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 41 +++++++++++++++++++ .../p/Python/Python-2.7.9-gompi-1.5.16.eb | 24 +++++++++++ .../z/zlib/zlib-1.2.8-gompi-1.5.16.eb | 24 +++++++++++ 8 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb new file mode 100644 index 0000000000..8546b30e25 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb @@ -0,0 +1,16 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb new file mode 100644 index 0000000000..9bc8981a24 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.5.16' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.3' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.6.5' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb new file mode 100644 index 0000000000..dd1343eaa7 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.8.1" + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb new file mode 100644 index 0000000000..91974bd874 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb new file mode 100644 index 0000000000..c1d5e51e55 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -0,0 +1,16 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb new file mode 100644 index 0000000000..1d1348fcbb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.6.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +configopts += '--with-hwloc=$EBROOTHWLOC ' + +dependencies = [('hwloc', '1.8.1')] + +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb new file mode 100644 index 0000000000..51bc309e32 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb @@ -0,0 +1,24 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb new file mode 100644 index 0000000000..82920e5897 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From fa42638bff3578bf089bee3917d5fd5d4709ad1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 5 Feb 2015 15:28:55 +0100 Subject: [PATCH 203/911] libreadline changed to 6.3, empty lines removed --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb | 1 - ...6.2-gompi-1.5.16.eb => libreadline-6.3-gompi-1.5.16.eb} | 3 +-- .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb | 1 - easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 7 +------ .../easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb | 3 +-- 5 files changed, 3 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/l/libreadline/{libreadline-6.2-gompi-1.5.16.eb => libreadline-6.3-gompi-1.5.16.eb} (98%) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb index 8546b30e25..db84860379 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb @@ -13,4 +13,3 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://www.bzip.org/%(version)s/'] moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb similarity index 98% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb index 91974bd874..f0ee343099 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-gompi-1.5.16.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libreadline' -version = '6.2' +version = '6.3' homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' description = """The GNU Readline library provides a set of functions for use by applications that @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index c1d5e51e55..9f6619baca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -13,4 +13,3 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 1d1348fcbb..fe19ab4c9f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -20,12 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev','libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb index 51bc309e32..4bcf8efac0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TGZ] dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), - ('libreadline', '6.2'), + ('libreadline', '6.3'), ('ncurses', '5.9'), # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] @@ -21,4 +21,3 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev')] moduleclass = 'lang' - -- GitLab From 82423ebdf88a9f6546d2a6373228377daf9593e1 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 5 Feb 2015 09:37:17 -0500 Subject: [PATCH 204/911] more extensions removed for tk/tcl deps --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index 62367a74a4..e60a4bb6fd 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -277,7 +277,6 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('picante', '1.6-2', ext_options), ('quantreg', '5.05', ext_options), ('RcppEigen', '0.3.2.3.0', ext_options), ('polspline', '1.1.9', ext_options), @@ -287,10 +286,8 @@ exts_list = [ ('RWekajars', '3.7.11-1', ext_options), ('RWeka', '0.4-23', ext_options), ('slam', '0.1-32', ext_options), - ('spacodiR', '0.13.0115', ext_options), ('tm', '0.6', ext_options), ('TraMineR', '1.8-8', ext_options), - ('untb', '1.7-2', ext_options), ('chemometrics', '1.3.8', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-3', ext_options), @@ -357,11 +354,7 @@ exts_list = [ ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), ('nleqslv', '2.5', ext_options), - ('widgetTools', '1.44.0', bioconductor_options), ('DynDoc', '1.44.0', bioconductor_options), - ('tkWidgets', '1.44.0', bioconductor_options), - ('Mfuzz', '2.26.0', bioconductor_options), - ('maSigPro', '1.38.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '0.7.7', ext_options), -- GitLab From e7a5c6fc2fc877687276fdb337376445403fca4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Feb 2015 19:19:43 +0100 Subject: [PATCH 205/911] remove R pkgs with external deps + any pkgs that depend on them, minor version bump in 2 Bioconductor pkgs --- .../easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 18 ++---------------- .../easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 18 ++---------------- 2 files changed, 4 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index f244aa3da4..a73e438a8c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -220,7 +220,7 @@ exts_list = [ ('Biostrings', '2.34.1', bioconductor_options), ('GenomicRanges', '1.18.4', bioconductor_options), ('Rsamtools', '1.18.2', bioconductor_options), - ('BiocParallel', '1.0.0', bioconductor_options), + ('BiocParallel', '1.0.2', bioconductor_options), ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), @@ -269,7 +269,6 @@ exts_list = [ ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '1.9-8', ext_options), - ('gmp', '0.5-12', ext_options), ('labdsv', '1.6-1', ext_options), ('MatrixModels', '0.3-1.1', ext_options), ('stabs', '0.5-0', ext_options), @@ -278,12 +277,6 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('partitions', '1.9-15', ext_options), - ('rgl', '0.95.1201', ext_options), - ('phangorn', '1.99-11', ext_options), - ('phytools', '0.4-31', ext_options), - ('vegan', '2.2-0', ext_options), - ('picante', '1.6-2', ext_options), ('quantreg', '5.05', ext_options), ('RcppEigen', '0.3.2.3.0', ext_options), ('polspline', '1.1.9', ext_options), @@ -293,10 +286,8 @@ exts_list = [ ('RWekajars', '3.7.11-1', ext_options), ('RWeka', '0.4-23', ext_options), ('slam', '0.1-32', ext_options), - ('spacodiR', '0.13.0115', ext_options), ('tm', '0.6', ext_options), ('TraMineR', '1.8-8', ext_options), - ('untb', '1.7-2', ext_options), ('chemometrics', '1.3.8', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-3', ext_options), @@ -319,7 +310,7 @@ exts_list = [ ('limma', '3.22.4', bioconductor_options), ('RBGL', '1.42.0', bioconductor_options), ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.1', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), ('KEGG.db', '3.0.0', bioconductor_options), ('annaffy', '1.38.0', bioconductor_options), ('gcrma', '2.38.0', bioconductor_options), @@ -363,15 +354,10 @@ exts_list = [ ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), ('nleqslv', '2.5', ext_options), - ('widgetTools', '1.44.0', bioconductor_options), ('DynDoc', '1.44.0', bioconductor_options), - ('tkWidgets', '1.44.0', bioconductor_options), - ('Mfuzz', '2.26.0', bioconductor_options), - ('maSigPro', '1.38.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '0.7.7', ext_options), - ('mixOmics', '5.0-3', ext_options), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), ('openxlsx', '2.2.1', ext_options), diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index f9a3d072b1..99a39db56a 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -220,7 +220,7 @@ exts_list = [ ('Biostrings', '2.34.1', bioconductor_options), ('GenomicRanges', '1.18.4', bioconductor_options), ('Rsamtools', '1.18.2', bioconductor_options), - ('BiocParallel', '1.0.0', bioconductor_options), + ('BiocParallel', '1.0.2', bioconductor_options), ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), @@ -269,7 +269,6 @@ exts_list = [ ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '1.9-8', ext_options), - ('gmp', '0.5-12', ext_options), ('labdsv', '1.6-1', ext_options), ('MatrixModels', '0.3-1.1', ext_options), ('stabs', '0.5-0', ext_options), @@ -278,12 +277,6 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('partitions', '1.9-15', ext_options), - ('rgl', '0.95.1201', ext_options), - ('phangorn', '1.99-11', ext_options), - ('phytools', '0.4-31', ext_options), - ('vegan', '2.2-0', ext_options), - ('picante', '1.6-2', ext_options), ('quantreg', '5.05', ext_options), ('RcppEigen', '0.3.2.3.0', ext_options), ('polspline', '1.1.9', ext_options), @@ -293,10 +286,8 @@ exts_list = [ ('RWekajars', '3.7.11-1', ext_options), ('RWeka', '0.4-23', ext_options), ('slam', '0.1-32', ext_options), - ('spacodiR', '0.13.0115', ext_options), ('tm', '0.6', ext_options), ('TraMineR', '1.8-8', ext_options), - ('untb', '1.7-2', ext_options), ('chemometrics', '1.3.8', ext_options), ('FNN', '1.1', ext_options), ('ipred', '0.9-3', ext_options), @@ -319,7 +310,7 @@ exts_list = [ ('limma', '3.22.4', bioconductor_options), ('RBGL', '1.42.0', bioconductor_options), ('org.Hs.eg.db', '3.0.0', bioconductor_options), - ('AnnotationForge', '1.8.1', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), ('KEGG.db', '3.0.0', bioconductor_options), ('annaffy', '1.38.0', bioconductor_options), ('gcrma', '2.38.0', bioconductor_options), @@ -363,15 +354,10 @@ exts_list = [ ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), ('nleqslv', '2.5', ext_options), - ('widgetTools', '1.44.0', bioconductor_options), ('DynDoc', '1.44.0', bioconductor_options), - ('tkWidgets', '1.44.0', bioconductor_options), - ('Mfuzz', '2.26.0', bioconductor_options), - ('maSigPro', '1.38.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), ('RGCCA', '2.0', ext_options), ('pheatmap', '0.7.7', ext_options), - ('mixOmics', '5.0-3', ext_options), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), ('openxlsx', '2.2.1', ext_options), -- GitLab From e5657e38f95e4db4916e822e6f17d3f99e7e0af0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Feb 2015 20:19:32 +0100 Subject: [PATCH 206/911] fix @boegel's remarks ;-) --- .../easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb | 15 +++++++++++++++ .../easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 3 ++- .../easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 6 +++--- .../f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb | 1 - .../easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 1 - .../easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb | 3 ++- .../easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 7 +++---- 7 files changed, 25 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb new file mode 100644 index 0000000000..5a7003c26f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically +compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical +compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s/'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index e0cb4f9a7d..d7c47ac9d1 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -21,7 +21,6 @@ description = """DNA Sequence Reads Compression is an application designed for c toolchain = {'name': 'dummy', 'version': 'dummy'} -# fi. http://sun.aei.polsl.pl/dsrc/download/2.0rc/dsrc sources = ['%(namelower)s'] source_urls = ['http://sun.aei.polsl.pl/dsrc/download/%(version)s/'] checksums = [('md5', 'bdc40a96e33411cd4cdbe2b58ae285b7')] @@ -31,4 +30,6 @@ sanity_check_paths = { 'dirs': [] } +modextrapaths = {'PATH': ''} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index b750d29bed..9187fc8e42 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -20,12 +20,12 @@ description = """fastqz is a compressor for FASTQ files. FASTQ is the output of toolchain = {'name': 'GCC', 'version': '4.8.2'} toolchainopts = {'opt': True, 'optarch': True} -dependencies = [('ZPAQ', '6.57')] - -# eg. http://mattmahoney.net/dc/fastqz/fastqz15.cpp & http://mattmahoney.net/dc/fastqz/fapack.cpp minver = ''.join(version.split('.')) sources = ['fastqz%s.cpp' % minver, 'fapack.cpp'] source_urls = [homepage] +checksums = ['0a55cd15605ddf32c31dac5af8c0f442', '490efab4389637da5566cf5173b1d274'] + +dependencies = [('ZPAQ', '6.57')] skipsteps = ['source'] diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb index 867cc250e1..522141f705 100644 --- a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -18,7 +18,6 @@ description = """Fqzcomp is a basic fastq compressor, designed primarily for hig toolchain = {'name': 'GCC', 'version': '4.8.2'} -# eg. http://sourceforge.net/projects/fqzcomp/files/fqzcomp-4.6.tar.gz/download sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index 01169de210..4b95315150 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -19,7 +19,6 @@ description = """Quip compresses next-generation sequencing data with extreme pr toolchain = {'name': 'GCC', 'version': '4.8.2'} -# eg. http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz sources = [SOURCELOWER_TAR_GZ] source_urls = [homepage] diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb index 5724bab7ac..c8aea1ea00 100644 --- a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -19,10 +19,11 @@ description = """SCALCE [skeɪlz] is a FASTQ compression tool that uses locally toolchain = {'name': 'GCC', 'version': '4.8.2'} -# eg. http://sourceforge.net/projects/scalce/files/2.7/scalce-v2.7-src.tar.gz/download sources = ['%(namelower)s-v%(version)s-src.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] +dependencies = [('bzip2', '1.0.6')] + preconfigopts = 'cd zlib-1.2.8 &&' buildopts = '-C zlib-1.2.8 && make all' diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index 3ab5b6fbdc..9dabf51cec 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -19,16 +19,15 @@ description = """Quip compresses next-generation sequencing data with extreme pr toolchain = {'name': 'GCC', 'version': '4.8.2'} -# eg. http://mattmahoney.net/dc/zpaq657.zip sources = ['%%(namelower)s%s.zip' % ''.join(version.split('.'))] source_urls = ['http://mattmahoney.net/dc/'] -buildopts = ' && pod2man zpaq.pod > zpaq.1' +buildopts = " && pod2man zpaq.pod > zpaq.1" -files_to_copy = [(["zpaq"], 'bin'), (["zpaq.1"], 'share/man'), (["libzpaq.h", "libzpaq.cpp"], 'include')] +files_to_copy = [(['zpaq'], 'bin'), (['zpaq.1'], 'share/man'), (['libzpaq.h', 'libzpaq.cpp'], 'include')] sanity_check_paths = { - 'files': ["bin/zpaq", "share/man/zpaq.1"], + 'files': ['bin/zpaq', 'share/man/zpaq.1', 'include/libzpaq.h', 'include/libzpqq.cpp'], 'dirs': [] } -- GitLab From 156b7ae1b6b73692b2744c576c2453104c015801 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 6 Feb 2015 07:42:11 +0100 Subject: [PATCH 207/911] fix dates in headers to 2015 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb | 2 +- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index d7c47ac9d1..76c48d1e81 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 9187fc8e42..60a43d46c6 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ diff --git a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb index 522141f705..0f7a6c3ea5 100644 --- a/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fqzcomp/fqzcomp-4.6-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ diff --git a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb index 4b95315150..1cda3a4011 100644 --- a/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/q/Quip/Quip-1.1.8-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ diff --git a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb index c8aea1ea00..f442020c76 100644 --- a/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/s/SCALCE/SCALCE-2.7-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index 9dabf51cec..bee205b447 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2014 NTUA +# Copyright:: Copyright 2012-2015 NTUA # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ -- GitLab From 8c51f6bae5f9716151218889efbb178087507f70 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 6 Feb 2015 07:44:48 +0100 Subject: [PATCH 208/911] oops, fix description for ZPAQ Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb index bee205b447..5421483f0b 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb @@ -13,9 +13,8 @@ name = 'ZPAQ' version = '6.57' homepage = 'http://mattmahoney.net/dc/zpaq.html' -description = """Quip compresses next-generation sequencing data with extreme prejudice. - It supports input and output in the FASTQ and SAM/BAM formats, - compressing large datasets to as little as 15% of their original size.""" +description = """zpaq is a free and open source (GPL v3) incremental, + journaling command-line archiver for Windows, Linux and Mac OS/X""" toolchain = {'name': 'GCC', 'version': '4.8.2'} -- GitLab From f5627c4cb1e283e0c0c34648043df9a560e0cffc Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 6 Feb 2015 07:58:02 +0100 Subject: [PATCH 209/911] bump to ZPAQ/7.00 Signed-off-by: Fotis Georgatos --- .../z/ZPAQ/{ZPAQ-6.57-GCC-4.8.2.eb => ZPAQ-7.00-GCC-4.8.2.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/z/ZPAQ/{ZPAQ-6.57-GCC-4.8.2.eb => ZPAQ-7.00-GCC-4.8.2.eb} (98%) diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb similarity index 98% rename from easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb rename to easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb index 5421483f0b..d3edfe36d4 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-6.57-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb @@ -10,7 +10,7 @@ easyblock = 'MakeCp' name = 'ZPAQ' -version = '6.57' +version = '7.00' homepage = 'http://mattmahoney.net/dc/zpaq.html' description = """zpaq is a free and open source (GPL v3) incremental, -- GitLab From 94a14df36419076164475dc6e06cb495211c6b68 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 6 Feb 2015 08:05:02 +0100 Subject: [PATCH 210/911] bump to ZPAQ/7.00, really, also deps Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 60a43d46c6..50633eb598 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -25,7 +25,7 @@ sources = ['fastqz%s.cpp' % minver, 'fapack.cpp'] source_urls = [homepage] checksums = ['0a55cd15605ddf32c31dac5af8c0f442', '490efab4389637da5566cf5173b1d274'] -dependencies = [('ZPAQ', '6.57')] +dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] -- GitLab From 02468aaca87a1e9c21ac414e0d73b57ac45e0220 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 6 Feb 2015 08:09:06 +0100 Subject: [PATCH 211/911] ZPAQ/7.00 and commit the sanity test bugfix Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb index d3edfe36d4..1950d4e58e 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb @@ -26,7 +26,7 @@ buildopts = " && pod2man zpaq.pod > zpaq.1" files_to_copy = [(['zpaq'], 'bin'), (['zpaq.1'], 'share/man'), (['libzpaq.h', 'libzpaq.cpp'], 'include')] sanity_check_paths = { - 'files': ['bin/zpaq', 'share/man/zpaq.1', 'include/libzpaq.h', 'include/libzpqq.cpp'], + 'files': ['bin/zpaq', 'share/man/zpaq.1', 'include/libzpaq.h', 'include/libzpaq.cpp'], 'dirs': [] } -- GitLab From 8b0b64a9389880fc112d6e3a7e87a1ee3c614920 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Fri, 6 Feb 2015 10:10:00 +0100 Subject: [PATCH 212/911] mpilib, mpiver variables removed --- easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb index 9bc8981a24..b1db91bda9 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.8.3' comp = (compname, compver) -mpilib = 'OpenMPI' -mpiver = '1.6.5' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('OpenMPI', '1.6.5', '', comp), ] moduleclass = 'toolchain' -- GitLab From a596f6d48bb02ba2fb64c0ef95505abbc765c566 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Feb 2015 10:11:19 +0100 Subject: [PATCH 213/911] Added autotools bundle --- .../a/Autotools/Autotools-1.0-GCC.4.9.2.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb new file mode 100644 index 0000000000..2237d09fbc --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'Autotools' +# this version number has no real meaning +version = '1.0' + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [ + ('Autoconf', '2.69'), + ('Automake', '1.15'), + ('libtool', '2.4.2'), +] + +moduleclass = 'devel' -- GitLab From 94b574f278e9a1ce3104459d9076ad5136f1a789 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Feb 2015 10:21:22 +0100 Subject: [PATCH 214/911] Other versioning scheme --- ...-1.0-GCC.4.9.2.eb => Autotools-20150119-GCC.4.9.2.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/a/Autotools/{Autotools-1.0-GCC.4.9.2.eb => Autotools-20150119-GCC.4.9.2.eb} (61%) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC.4.9.2.eb similarity index 61% rename from easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb rename to easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC.4.9.2.eb index 2237d09fbc..067ccdbe63 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-1.0-GCC.4.9.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC.4.9.2.eb @@ -1,8 +1,7 @@ easyblock = 'Bundle' name = 'Autotools' -# this version number has no real meaning -version = '1.0' +version = '20150119' # date of the most recent change homepage = 'http://autotools.io' description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" @@ -10,9 +9,9 @@ description = """This bundle collect the standard GNU build tools: Autoconf, Aut toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [ - ('Autoconf', '2.69'), - ('Automake', '1.15'), - ('libtool', '2.4.2'), + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.5'), # 20150119 ] moduleclass = 'devel' -- GitLab From 4d6148914080f740794bb064e79ccbb1a135a4b6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Feb 2015 10:21:53 +0100 Subject: [PATCH 215/911] New version of libtool --- .../l/libtool/libtool-2.4.5-GCC-4.9.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb new file mode 100644 index 0000000000..01b30a3758 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.5' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' -- GitLab From 311c2dc6936b292e1e4f6a80eed0c5b8f64c8c47 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Fri, 6 Feb 2015 10:39:35 +0100 Subject: [PATCH 216/911] zlib preconfigopts removed --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb index 82920e5897..2c0a2d22d0 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-gompi-1.5.16.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From ed1266e7cc935596ec360dbb25cc22d13bc77190 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Fri, 6 Feb 2015 11:24:18 +0100 Subject: [PATCH 217/911] -bare suffix for Python package --- ...n-2.7.9-gompi-1.5.16.eb => Python-2.7.9-gompi-1.5.16-bare.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/p/Python/{Python-2.7.9-gompi-1.5.16.eb => Python-2.7.9-gompi-1.5.16-bare.eb} (96%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb similarity index 96% rename from easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb rename to easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 4bcf8efac0..583d5df7db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -1,5 +1,6 @@ name = 'Python' version = '2.7.9' +versionsuffix = '-bare' homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." -- GitLab From 0b0a5f0ab03f98dda4f8df26497e120da39fa2af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Feb 2015 22:47:55 +0100 Subject: [PATCH 218/911] add Perl as build dep for ZPAQ --- .../p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb | 17 +++++++++++++++++ .../easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb | 10 +++++++++- 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb new file mode 100644 index 0000000000..df13383ba5 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.20.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb index 1950d4e58e..5325d19c74 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb @@ -21,9 +21,17 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = ['%%(namelower)s%s.zip' % ''.join(version.split('.'))] source_urls = ['http://mattmahoney.net/dc/'] +builddependencies = [ + ('Perl', '5.20.1'), # required for pod2man +] + buildopts = " && pod2man zpaq.pod > zpaq.1" -files_to_copy = [(['zpaq'], 'bin'), (['zpaq.1'], 'share/man'), (['libzpaq.h', 'libzpaq.cpp'], 'include')] +files_to_copy = [ + (['zpaq'], 'bin'), + (['zpaq.1'], 'share/man'), + (['libzpaq.h', 'libzpaq.cpp'], 'include'), +] sanity_check_paths = { 'files': ['bin/zpaq', 'share/man/zpaq.1', 'include/libzpaq.h', 'include/libzpaq.cpp'], -- GitLab From 9ea1a7dedcdd0d2313fc7b50c5e61755605159cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Feb 2015 22:53:06 +0100 Subject: [PATCH 219/911] add easyconfig for bundle of extra R extensions (PoC) --- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb new file mode 100644 index 0000000000..e71e3abf1d --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'R-extra' +rver = '3.1.2' +version = '%s-1.0.0' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('GMP', '6.0.0a'), # for gmp +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('gmp', '0.5-12', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' -- GitLab From 5715d08b9de87430863146c910dd274f4d35adf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Feb 2015 10:05:02 +0100 Subject: [PATCH 220/911] include missing '-bare' versionsuffix for Perl builddep in ZPAQ easyconfig --- easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb index 5325d19c74..6b82f0fc24 100644 --- a/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/z/ZPAQ/ZPAQ-7.00-GCC-4.8.2.eb @@ -22,7 +22,7 @@ sources = ['%%(namelower)s%s.zip' % ''.join(version.split('.'))] source_urls = ['http://mattmahoney.net/dc/'] builddependencies = [ - ('Perl', '5.20.1'), # required for pod2man + ('Perl', '5.20.1', '-bare'), # required for pod2man ] buildopts = " && pod2man zpaq.pod > zpaq.1" -- GitLab From 246386041f3e89739e1782e60bdde94c1d5f0f7a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Feb 2015 11:59:19 +0100 Subject: [PATCH 221/911] Renamed to correct filename --- ...ools-20150119-GCC.4.9.2.eb => Autotools-20150119-GCC-4.9.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/Autotools/{Autotools-20150119-GCC.4.9.2.eb => Autotools-20150119-GCC-4.9.2.eb} (100%) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC.4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC.4.9.2.eb rename to easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb -- GitLab From 3d47126bab32a946dd92356b00e0a0824024e492 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Feb 2015 12:01:20 +0100 Subject: [PATCH 222/911] Add dependency for M4 to libtool --- easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb index 01b30a3758..a0c6a258a8 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.9.2.eb @@ -12,4 +12,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +dependencies = [('M4', '1.4.17')] + moduleclass = 'lib' -- GitLab From d0f788fd1617744ca9bd7d3cee8fd6bf5553799e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Feb 2015 12:06:17 +0100 Subject: [PATCH 223/911] include extra Python packages for Python 2.7.9 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 8ca80a6e43..ddcd75ee83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -91,6 +91,12 @@ exts_list = [ ('pyparsing', '2.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 2bf2418080..295a215baa 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -91,6 +91,12 @@ exts_list = [ ('pyparsing', '2.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 632c8fb490..f686a45b8c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -94,6 +94,12 @@ exts_list = [ ('pyparsing', '2.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), ] moduleclass = 'lang' -- GitLab From 3683989d5d5c85caaca522027d2ce4406abdabf5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Feb 2015 14:23:22 +0100 Subject: [PATCH 224/911] Added ISL-0.14 --- .../easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb new file mode 100644 index 0000000000..7b675a2960 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.14' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints. """ + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['isl-0.14.tar.bz2'] +source_urls = ['http://isl.gforge.inria.fr/'] + +dependencies = [('GMP', '6.0.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.so', 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'compiler' -- GitLab From 8b2c21a3ed6921833897e3d8b777e08d5b18f1b7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Feb 2015 14:24:26 +0100 Subject: [PATCH 225/911] GMP-6.0.0a for GCC 4.9.2 --- .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb new file mode 100644 index 0000000000..08df157950 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ["%(namelower)s-%(version)sa.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From c2c6c8457fef0862eb3f9ade69a4217bc127834c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Feb 2015 14:25:19 +0100 Subject: [PATCH 226/911] WIP for Clang 3.6 --- .../c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb new file mode 100644 index 0000000000..815d5b9a57 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb @@ -0,0 +1,71 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.0" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.2'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +#source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["http://llvm.org/pre-releases/3.6.0/rc2/"] +sources = [ +# "llvm-%(version)src2.src.tar.xz", + "llvm-3.6.0.tar", + "cfe-%(version)src2.src.tar.xz", + "compiler-rt-%(version)src2.src.tar.xz", +# "polly-%(version)src2.src.tar.xz", + "polly-3.6.0.tar", +] + +patches = [ + # Remove some tests that fail because of -DGCC_INSTALL_PREFIX. The issue is + # that hardcoded GCC_INSTALL_PREFIX overrides -sysroot. This probably breaks + # cross-compilation. + # http://lists.cs.uiuc.edu/pipermail/cfe-commits/Week-of-Mon-20130401/077539.html +# 'Clang-%(version)s-failing-tests-due-to-gcc-installation-prefix.patch', +# 'Clang-%(version)s-failing-sanitizer-tests.patch', +# 'Clang-%(version)s-llvm-ar-uid.patch', +# 'lit.patch', +# ('poll-isl.patch', 'tools/polly/'), +] + +builddependencies = [('CMake', '3.1.0')] + +dependencies = [ + ('GMP', '6.0.0'), + ('ISL', '0.14') +] + +sanity_check_paths = { + 'files': ['bin/clang', 'bin/clang++', 'lib/libclang.so', 'lib/clang/%(version)s/include/stddef.h'], + 'dirs': [], +} + +moduleclass = 'compiler' + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +runtest = False + +parallel = 1 + +bootstrap = False -- GitLab From b8af9c7794837e10a66030e674d3c6b907bcc279 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 8 Feb 2015 12:05:01 +0100 Subject: [PATCH 227/911] convert HPCBIOS toolchains to bundles Signed-off-by: Fotis Georgatos --- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index 1919d75c76..f816c5478e 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Bioinfo' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index 07974e95af..928208b06e 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Bioinfo' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 5e0919b8d2..0b0682b5cc 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-05.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Debuggers' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index 105b0630d6..5dc321bbb5 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_LifeSciences' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index 20fb4bbb29..469d57c8d9 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_LifeSciences' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb index 56ceb7f56d..f4b107240d 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-01.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Math' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb index ca6cb154bb..5a7e87852a 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-01.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Math' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb index c4fa0cbf6c..9eead1e8ea 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-01.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Math' version = '20130829' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index 8febd4d488..ae3956c8ea 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html ## -easyblock = "Toolchain" +easyblock = "Bundle" name = 'HPCBIOS_Profilers' version = '20130829' -- GitLab From 2564eacdc7611747fe767c27b9de41c0a3e11484 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 9 Feb 2015 09:37:37 +0100 Subject: [PATCH 228/911] Updated Clang 3.6 ec --- .../c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb | 28 +++---------------- 1 file changed, 4 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb index 815d5b9a57..c46973a974 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb @@ -21,27 +21,12 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -#source_urls = ["http://llvm.org/releases/%(version)s"] -source_urls = ["http://llvm.org/pre-releases/3.6.0/rc2/"] +source_urls = ["http://llvm.org/releases/%(version)s"] sources = [ -# "llvm-%(version)src2.src.tar.xz", - "llvm-3.6.0.tar", + "llvm-%(version)src2.src.tar.xz", "cfe-%(version)src2.src.tar.xz", "compiler-rt-%(version)src2.src.tar.xz", -# "polly-%(version)src2.src.tar.xz", - "polly-3.6.0.tar", -] - -patches = [ - # Remove some tests that fail because of -DGCC_INSTALL_PREFIX. The issue is - # that hardcoded GCC_INSTALL_PREFIX overrides -sysroot. This probably breaks - # cross-compilation. - # http://lists.cs.uiuc.edu/pipermail/cfe-commits/Week-of-Mon-20130401/077539.html -# 'Clang-%(version)s-failing-tests-due-to-gcc-installation-prefix.patch', -# 'Clang-%(version)s-failing-sanitizer-tests.patch', -# 'Clang-%(version)s-llvm-ar-uid.patch', -# 'lit.patch', -# ('poll-isl.patch', 'tools/polly/'), + "polly-%(version)src2.src.tar.xz", ] builddependencies = [('CMake', '3.1.0')] @@ -56,16 +41,11 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'compiler' - assertions = True usepolly = True build_targets = ['X86'] -runtest = False - -parallel = 1 +moduleclass = 'compiler' -bootstrap = False -- GitLab From a728c395f6fce48e0b18c899aaa61397224627de Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 9 Feb 2015 09:37:54 +0100 Subject: [PATCH 229/911] Renamed the Clang easyconfig --- .../{Clang-3.6.0rc2-GCC-4.9.2.eb => Clang-3.6.0-GCC-4.9.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Clang/{Clang-3.6.0rc2-GCC-4.9.2.eb => Clang-3.6.0-GCC-4.9.2.eb} (100%) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/c/Clang/Clang-3.6.0rc2-GCC-4.9.2.eb rename to easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb -- GitLab From 955879553ec246fd909f27e639bc2debca6c911c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 9 Feb 2015 09:40:10 +0100 Subject: [PATCH 230/911] Missed newline --- easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index c46973a974..c22450fce4 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -48,4 +48,3 @@ usepolly = True build_targets = ['X86'] moduleclass = 'compiler' - -- GitLab From 64c97a0a4b3e7f506489953f1972a4cbf28f3a0f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 9 Feb 2015 14:09:00 +0100 Subject: [PATCH 231/911] Added checksums Minor tweaks for consistency --- easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb | 4 ++++ easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb | 4 ++++ easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb | 4 ++++ easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb | 4 ++++ .../easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb | 10 +++++++++- easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb | 7 +++++++ .../easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb | 9 +++++++++ easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb | 7 +++++++ easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb | 12 +++++++++-- .../easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb | 10 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb | 20 +++++++++++++------ .../easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb | 10 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb | 8 ++++++++ easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb | 16 +++++++++++---- .../easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb | 11 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb | 8 ++++++++ .../easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb | 11 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb | 8 ++++++++ .../easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb | 9 +++++++++ easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb | 7 +++++++ .../g/GCC/GCC-4.8.2-CLooG-multilib.eb | 9 +++++++++ .../easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 9 +++++++++ .../easyconfigs/g/GCC/GCC-4.8.2-multilib.eb | 7 +++++++ easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb | 7 +++++++ .../g/GCC/GCC-4.8.3-CLooG-multilib.eb | 9 +++++++++ easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb | 7 +++++++ .../g/GCC/GCC-4.8.4-CLooG-multilib.eb | 9 +++++++++ .../easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb | 9 +++++++++ easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb | 7 +++++++ .../g/GCC/GCC-4.9.0-CLooG-multilib.eb | 15 +++++++++++--- .../easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb | 15 +++++++++++--- easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb | 13 +++++++++--- .../g/GCC/GCC-4.9.1-CLooG-multilib.eb | 15 +++++++++++--- .../easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb | 15 +++++++++++--- easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb | 13 +++++++++--- .../g/GCC/GCC-4.9.2-CLooG-multilib.eb | 15 +++++++++++--- .../easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb | 15 +++++++++++--- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 13 +++++++++--- 38 files changed, 341 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb index 42a1d25324..15db97e462 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dep source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = [ + 'a4a3eb15c96030906d8494959eeda23c', # gcc-4.1.2.tar.bz2 +] + dependencies = [ ('GMP', '4.3.2'), ('MPFR', '2.4.2'), diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb index 3ccecb918f..690c94392b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dep source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = [ + 'd79f553e7916ea21c556329eacfeaa16', # gcc-4.2.4.tar.bz2 +] + dependencies = [ ('GMP', '4.3.2'), ('MPFR', '2.4.2'), diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb index b182cdcc48..d2df4b4c42 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dep source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = [ + '55ddf934bc9f8d1eaff7a77e7d598a85', # gcc-4.3.6.tar.bz2 +] + dependencies = [ ('GMP', '4.3.2'), ('MPFR', '2.4.2'), diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb index dd92bece57..584afb9b7c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dep source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = [ + '295709feb4441b04e87dea3f1bab4281', # gcc-4.4.7.tar.bz2 +] + dependencies = [ ('GMP', '4.3.2'), ('MPFR', '2.4.2'), diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb index 910274c9af..bcb7fd7639 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb @@ -20,7 +20,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies, for PPL and CLooG-PPL 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - sources = [ SOURCELOWER_TAR_GZ, 'gmp-5.0.2.tar.gz', @@ -30,6 +29,15 @@ sources = [ 'ppl-%s.tar.gz' % pplver, ] +checksums = [ + 'bf100d5b3b88f7938752e43c90e48f48', # gcc-4.5.3.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz + '060ae4df6fb8176e021b4d033a6c0b9e', # cloog-ppl-0.15.11.tar.gz + 'ba527ec0ffc830ce16fad8a4195a337e', # ppl-0.11.tar.gz +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb index 625423d639..9a31d20e93 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-0.8.2.tar.gz', ] +checksums = [ + 'bf100d5b3b88f7938752e43c90e48f48', # gcc-4.5.3.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb index 212d837eb2..3a9114bc86 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb @@ -29,6 +29,15 @@ sources = [ 'ppl-%s.tar.gz' % pplver, ] +checksums = [ + 'c51e55130ab9ca3e5f34014cac15dd39', # gcc-4.6.3.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz + '060ae4df6fb8176e021b4d033a6c0b9e', # cloog-ppl-0.15.11.tar.gz + '47a5548d4e3d98cf6b97e4fd3e5db513', # ppl-0.12.tar.gz +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb index 97b63a7dfa..884bd3660e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-0.9.tar.gz', ] +checksums = [ + 'c51e55130ab9ca3e5f34014cac15dd39', # gcc-4.6.3.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb index 612489b92c..6d06e3dc27 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb @@ -20,10 +20,18 @@ sources = [ 'mpc-1.0.1.tar.gz', ] -languages = ['c', 'c++', 'fortran'] - patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + 'a8f15fc233589924ccd8cc8140b0ca3c', # gcc-4.6.4.tar.gz + '2fa018a7cd193c78494525f236d02dd6', # gmp-5.1.1.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + +languages = ['c', 'c++', 'fortran'] + # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb index 30d7d0fa79..b46830b3c9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb @@ -31,6 +31,16 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + 'ef5117788e27ffef05f8b8adf46f91d8', # gcc-4.7.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + '10968131acc26d79311ac4f8982ff078', # mpfr-3.1.0.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz + '947123350d1ff6dcb4b0774947ac015a', # cloog-0.16.1.tar.gz + '47a5548d4e3d98cf6b97e4fd3e5db513', # ppl-0.12.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb index 1782b94bb7..25a490f355 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb @@ -7,21 +7,29 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = [ - SOURCELOWER_TAR_GZ, - 'gmp-5.0.4.tar.bz2', - 'mpfr-3.1.0.tar.gz', - 'mpc-0.9.tar.gz', -] source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.1.0.tar.gz', + 'mpc-0.9.tar.gz', +] patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + 'ef5117788e27ffef05f8b8adf46f91d8', # gcc-4.7.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + '10968131acc26d79311ac4f8982ff078', # mpfr-3.1.0.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb index 4b5d149d00..6c58ae7bc6 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb @@ -31,6 +31,16 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + '3d06e24570635c91eed6b114687513a6', # gcc-4.7.1.tar.gz + '041487d25e9c230b0c42b106361055fe', # gmp-5.0.5.tar.bz2 + '769411e241a3f063ae1319eb5fac2462', # mpfr-3.1.1.tar.gz + '13370ceb2e266c5eeb2f7e78c24b7858', # mpc-1.0.tar.gz + 'a0f8a241cd1c4f103f8d2c91642b3498', # cloog-0.16.3.tar.gz + '47a5548d4e3d98cf6b97e4fd3e5db513', # ppl-0.12.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb index ca98da2565..b3ad3f8087 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb @@ -22,6 +22,14 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + '3d06e24570635c91eed6b114687513a6', # gcc-4.7.1.tar.gz + '041487d25e9c230b0c42b106361055fe', # gmp-5.0.5.tar.bz2 + '769411e241a3f063ae1319eb5fac2462', # mpfr-3.1.1.tar.gz + '13370ceb2e266c5eeb2f7e78c24b7858', # mpc-1.0.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb index 12e831324b..decee62a58 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb @@ -8,10 +8,10 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR - 'http://www.multiprecision.org/mpc/download', # MPC official + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official ] sources = [ SOURCELOWER_TAR_GZ, @@ -22,6 +22,14 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + '5199d34506d4fa6528778ddba362d3f4', # gcc-4.7.2.tar.gz + '041487d25e9c230b0c42b106361055fe', # gmp-5.0.5.tar.bz2 + '769411e241a3f063ae1319eb5fac2462', # mpfr-3.1.1.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb index b9d63d8009..8f5cae195c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb @@ -34,6 +34,17 @@ patches = [ 'mpfr-3.1.0-changes_fix.patch', ] +checksums = [ + 'd518eace24a53aef59c2c69498ea4989', # gcc-4.7.3.tar.gz + '7e3516128487956cd825fef01aafe4bc', # gmp-5.1.2.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'a0f8a241cd1c4f103f8d2c91642b3498', # cloog-0.16.3.tar.gz + 'cec8144f2072ac45a850214cca97d075', # ppl-0.12.1.tar.gz + 'b6153bac75ee9e2a78e08ee97bf045f2', # ppl-0.12.1-mpfr.patch + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb index 09e9dae03b..03f65ea5f0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb @@ -22,6 +22,14 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + 'd518eace24a53aef59c2c69498ea4989', # gcc-4.7.3.tar.gz + '2fa018a7cd193c78494525f236d02dd6', # gmp-5.1.1.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb index e5ae9ca655..da943f7026 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb @@ -34,6 +34,17 @@ patches = [ 'mpfr-3.1.0-changes_fix.patch', ] +checksums = [ + 'f07a9c4078dbccdcc18bc840ab5e0fe9', # gcc-4.7.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'a0f8a241cd1c4f103f8d2c91642b3498', # cloog-0.16.3.tar.gz + 'cec8144f2072ac45a850214cca97d075', # ppl-0.12.1.tar.gz + 'b6153bac75ee9e2a78e08ee97bf045f2', # ppl-0.12.1-mpfr.patch + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb index 986014a36d..5d688569b0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb @@ -22,6 +22,14 @@ sources = [ patches = ['mpfr-3.1.0-changes_fix.patch'] +checksums = [ + 'f07a9c4078dbccdcc18bc840ab5e0fe9', # gcc-4.7.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'fa4095252d843d465ac9aa5e2d760dd8', # mpfr-3.1.0-changes_fix.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 5ccb3091a1..97ecab725e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + '74cc12b7afe051ab7d0e00269e49fc9b', # gcc-4.8.1.tar.gz + '7e3516128487956cd825fef01aafe4bc', # gmp-5.1.2.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb index d59607eece..18a5c26a04 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-1.0.1.tar.gz', ] +checksums = [ + '74cc12b7afe051ab7d0e00269e49fc9b', # gcc-4.8.1.tar.gz + '7e3516128487956cd825fef01aafe4bc', # gmp-5.1.2.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 64fb3ab48a..0cc4d2d8be 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + 'deca88241c1135e2ff9fa5486ab5957b', # gcc-4.8.2.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index 64e4242a83..76ee08688e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + 'deca88241c1135e2ff9fa5486ab5957b', # gcc-4.8.2.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb index 1e4a0b8b5b..45168e2586 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -21,6 +21,13 @@ sources = [ 'mpc-1.0.1.tar.gz', ] +checksums = [ + 'deca88241c1135e2ff9fa5486ab5957b', # gcc-4.8.2.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + languages = ['c', 'c++', 'fortran'] multilib = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb index dcddef3500..4f8e1b941b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-1.0.1.tar.gz', ] +checksums = [ + 'deca88241c1135e2ff9fa5486ab5957b', # gcc-4.8.2.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index 35b2688a1c..cdf28092c4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + 'e2c60f5ef918be2db08df96c7d97d0c4', # gcc-4.8.3.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb index b72eb0f106..10a1ebfca0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-1.0.1.tar.gz', ] +checksums = [ + 'e2c60f5ef918be2db08df96c7d97d0c4', # gcc-4.8.3.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index ed620cefc6..621a6661ef 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index f700348861..7dd0f5df24 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -26,6 +26,15 @@ sources = [ 'isl-0.11.1.tar.bz2', ] +checksums = [ + '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz + 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb index fa49500c29..5ac47478fb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb @@ -20,6 +20,13 @@ sources = [ 'mpc-1.0.1.tar.gz', ] +checksums = [ + '0c92ac45af5b280e301ca56b40fdaea2', # gcc-4.8.4.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index 965fc73198..f77a70efc3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '9709b49ae0e904cbb0a6a1b62853b556', # gcc-4.9.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 9a94681363..9974833bba 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '9709b49ae0e904cbb0a6a1b62853b556', # gcc-4.9.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb index 3f14a7a026..cd09534c39 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb @@ -7,15 +7,14 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -25,6 +24,14 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '9709b49ae0e904cbb0a6a1b62853b556', # gcc-4.9.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index 77bc3a952c..a3c67d644e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + 'fddf71348546af523353bd43d34919c1', # gcc-4.9.1.tar.gz + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index c6f4f49acc..b78ac53014 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + 'fddf71348546af523353bd43d34919c1', # gcc-4.9.1.tar.gz + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb index c888d0b270..21e41342d3 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb @@ -7,15 +7,14 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -25,6 +24,14 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + 'fddf71348546af523353bd43d34919c1', # gcc-4.9.1.tar.gz + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index 338efeb6d4..0906283ab2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index 82dd583d70..1af6bd9c36 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -8,6 +8,8 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP @@ -17,9 +19,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -31,6 +30,16 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'e039bfcfb6c2ab039b8ee69bf883e824', # isl-0.12.2.tar.bz2 + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] withcloog = True diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index f1c7b80023..cb9f3aa4f2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -7,15 +7,14 @@ description = """The GNU Compiler Collection includes front ends for C, C++, Obj toolchain = {'name': 'dummy', 'version': 'dummy'} +mpfr_version = '3.1.2' + source_urls = [ 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror 'http://ftpmirror.gnu.org/gmp', # idem for GMP 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR 'http://www.multiprecision.org/mpc/download', # MPC official ] - -mpfr_version = '3.1.2' - sources = [ SOURCELOWER_TAR_BZ2, 'gmp-6.0.0a.tar.bz2', @@ -25,6 +24,14 @@ sources = [ patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + languages = ['c', 'c++', 'fortran'] # building GCC sometimes fails if make parallelism is too high, so let's limit it -- GitLab From 46359e89b96e87545ae741210900feef997932b7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 10:24:59 +0100 Subject: [PATCH 232/911] bump to hwloc/1.10.1-GCC-4.8.4 Signed-off-by: Fotis Georgatos --- ...GCC-4.8.4.eb => hwloc-1.10.1-GCC-4.8.4.eb} | 2 +- .../n/numactl/numactl-2.0.9-GCC-4.8.4.eb | 24 ------------------- .../o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 2 +- 3 files changed, 2 insertions(+), 26 deletions(-) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.10.0-GCC-4.8.4.eb => hwloc-1.10.1-GCC-4.8.4.eb} (98%) delete mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb similarity index 98% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb index 48456705b1..117203c855 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' -version = "1.10.0" +version = "1.10.1" homepage = 'http://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb deleted file mode 100644 index 631c25771b..0000000000 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.9-GCC-4.8.4.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'numactl' -version = '2.0.9' - -homepage = 'http://oss.sgi.com/projects/libnuma/' -description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. -It does this by supplying a NUMA memory policy to the operating system before running your program. -The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" - -sources = [SOURCE_TAR_GZ] -source_urls = ["ftp://oss.sgi.com/www/projects/libnuma/download/"] - -toolchain = {'name': 'GCC', 'version': '4.8.4'} - -skipsteps = ['configure'] -installopts = "PREFIX=%(installdir)s libdir='${prefix}/lib'" - -sanity_check_paths = { - 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], - 'dirs': ['share/man', 'include'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index bf74f56b70..31dfab1648 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -dependencies = [('hwloc', '1.10.0')] +dependencies = [('hwloc', '1.10.1')] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -- GitLab From d81646903c3f36ceb4b8a760bf39d4b92f12ac48 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 10:34:25 +0100 Subject: [PATCH 233/911] bump to libtool/2.4.5 Signed-off-by: Fotis Georgatos --- .../{libtool-2.4.2-GCC-4.8.4.eb => libtool-2.4.5-GCC-4.8.4.eb} | 2 +- easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libtool/{libtool-2.4.2-GCC-4.8.4.eb => libtool-2.4.5-GCC-4.8.4.eb} (95%) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb similarity index 95% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb rename to easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb index 82d1212976..f9f513b45f 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libtool' -version = '2.4.2' +version = '2.4.5' homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb index 4e761b0ac5..6e81e95581 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_GZ] builddependencies = [ ('Automake', '1.15'), - ('libtool', '2.4.2'), + ('libtool', '2.4.5'), ] preconfigopts = './autogen.sh && ' -- GitLab From 3e2c4d52bbc8424e5ae27fe1c8ca4ce374d1e85e Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 10:55:24 +0100 Subject: [PATCH 234/911] update #1294 as per comments in PR Signed-off-by: Fotis Georgatos --- ...TW-3.3.4-gompi-1.6.20.eb => FFTW-3.3.4-gompi-1.7.20.eb} | 2 +- .../g/gompi/{gompi-1.6.20.eb => gompi-1.7.20.eb} | 7 ++----- .../g/goolf/{goolf-1.6.20.eb => goolf-1.7.20.eb} | 2 +- .../{HPL-2.1-goolf-1.6.20.eb => HPL-2.1-goolf-1.7.20.eb} | 2 +- easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb | 6 +++--- .../easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb | 5 ++--- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 6 +----- ...ACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb} | 2 +- 8 files changed, 12 insertions(+), 20 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-gompi-1.6.20.eb => FFTW-3.3.4-gompi-1.7.20.eb} (96%) rename easybuild/easyconfigs/g/gompi/{gompi-1.6.20.eb => gompi-1.7.20.eb} (81%) rename easybuild/easyconfigs/g/goolf/{goolf-1.6.20.eb => goolf-1.7.20.eb} (98%) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-goolf-1.6.20.eb => HPL-2.1-goolf-1.7.20.eb} (92%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb => ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb} (92%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.7.20.eb similarity index 96% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.7.20.eb index 002bd8dda5..716715a07e 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.20.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.7.20.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '1.6.20'} +toolchain = {'name': 'gompi', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb b/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb similarity index 81% rename from easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb rename to easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb index a2dd8f90be..62fc761f97 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.6.20.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'gompi' -version = '1.6.20' +version = '1.7.20' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, @@ -13,13 +13,10 @@ compname = 'GCC' compver = '4.8.4' comp = (compname, compver) -mpilib = 'OpenMPI' -mpiver = '1.8.4' - # compiler toolchain dependencies dependencies = [ comp, - (mpilib, mpiver, '', comp), + ('OpenMPI', '1.8.4', '', comp), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb b/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb similarity index 98% rename from easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb rename to easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb index 635ab13824..63245fe52b 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.20.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'goolf' -version = '1.6.20' +version = '1.7.20' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb similarity index 92% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb index c245a1d304..fd109a8fed 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.6.20.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.7.20.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'goolf', 'version': '1.6.20'} +toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb index 117203c855..6adedf3a5d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb @@ -13,11 +13,11 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.4'} +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb index 6e81e95581..e56d4ba751 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GCC-4.8.4.eb @@ -3,8 +3,6 @@ easyblock = 'ConfigureMake' name = 'numactl' version = '2.0.10' -checksums = ['682c38305b2596967881f3d77bc3fc9c'] - homepage = 'http://oss.sgi.com/projects/libnuma/' description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. @@ -15,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + builddependencies = [ ('Automake', '1.15'), ('libtool', '2.4.5'), @@ -22,7 +22,6 @@ builddependencies = [ preconfigopts = './autogen.sh && ' - sanity_check_paths = { 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], 'dirs': ['share/man', 'include'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 31dfab1648..4450b68758 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -19,11 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb similarity index 92% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 7c911189b3..94cfcc38e5 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -5,7 +5,7 @@ homepage = 'http://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '1.6.20'} +toolchain = {'name': 'gompi', 'version': '1.7.20'} toolchainopts = {'pic': True} source_urls = [homepage] -- GitLab From 201e790ba97e5034af0637f9a06219e85175842b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 10 Feb 2015 12:11:12 +0100 Subject: [PATCH 235/911] Consistently use CLooG 0.18.0 for GCC 4.8 series --- easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb | 4 ++-- easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index cdf28092c4..8f71a86f5f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -22,7 +22,7 @@ sources = [ 'gmp-5.1.3.tar.bz2', 'mpfr-3.1.2.tar.gz', 'mpc-1.0.1.tar.gz', - 'cloog-0.18.1.tar.gz', + 'cloog-0.18.0.tar.gz', 'isl-0.11.1.tar.bz2', ] @@ -31,7 +31,7 @@ checksums = [ 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz - 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 ] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index 621a6661ef..a553c070ef 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -22,7 +22,7 @@ sources = [ 'gmp-5.1.3.tar.bz2', 'mpfr-3.1.2.tar.gz', 'mpc-1.0.1.tar.gz', - 'cloog-0.18.1.tar.gz', + 'cloog-0.18.0.tar.gz', 'isl-0.11.1.tar.bz2', ] @@ -31,7 +31,7 @@ checksums = [ 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz - 'e34fca0540d840e5d0f6427e98c92252', # cloog-0.18.1.tar.gz + 'be78a47bd82523250eb3e91646db5b3d', # cloog-0.18.0.tar.gz 'bce1586384d8635a76d2f017fb067cd2', # isl-0.11.1.tar.bz2 ] -- GitLab From 9b3aaff010f87324ca2cc854fb58d7677dc16263 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 16:32:01 +0100 Subject: [PATCH 236/911] add M4 as builddep Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb index f9f513b45f..f1e3238f19 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-GCC-4.8.4.eb @@ -9,6 +9,8 @@ description = """GNU libtool is a generic library support script. Libtool hides toolchain = {'name': 'GCC', 'version': '4.8.4'} +builddependencies = [('M4', '1.4.17')] + sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -- GitLab From 0b384057c93037c57d80dd61726501efb5bece5a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 10 Feb 2015 17:11:51 +0100 Subject: [PATCH 237/911] added toolchain intel-2015.02.eb --- .../i/icc/icc-2015.2.164-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../iccifort/iccifort-2015.2.164-GCC-4.9.2.eb | 17 +++++++++++++ .../i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 24 ++++++++++++++++++ .../i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb | 21 ++++++++++++++++ .../imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb | 22 ++++++++++++++++ ...5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb | 20 +++++++++++++++ .../easyconfigs/i/intel/intel-2015.02.eb | 21 ++++++++++++++++ 7 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2015.02.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..64131e9b0c --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +name = 'icc' +version = '2015.2.164' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +gcc = 'GCC' +gccver = '4.9.2' +versionsuffix = '-%s-%s' % (gcc, gccver) + +dependencies = [(gcc, gccver)] + +dontcreateinstalldir = 'True' + +# license file +#import os +#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = '/import/bc2/soft/source/i/icc/COM_L__CPP_RSCN-FRFDSRTL.lic' + +moduleclass = 'compiler' + diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..26bfe2f84a --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,17 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.2.164' +versionsuffix = '-GCC-4.9.2' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C, C++ and Fortran compilers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..3c57e6d8fe --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,24 @@ +name = 'ifort' +version = '2015.2.164' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +gcc = 'GCC' +gccver = '4.9.2' +versionsuffix = '-%s-%s' % (gcc, gccver) + +dependencies = [(gcc, gccver)] + +dontcreateinstalldir = 'True' + +# license file +#import os +#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = '/import/bc2/soft/source/i/ifort/COM_L__FOR_RRB4-H33RVJNV.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb new file mode 100644 index 0000000000..62c0e1ff30 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.2.5' +versionsuffix = '-GCC-4.9.2' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '2.164' +compver = '2015.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.0.2.044', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb new file mode 100644 index 0000000000..aadf66c552 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iimpi-7.2.5-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.2.164' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.2.5-GCC-4.9.2'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..a71dcd21b3 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,20 @@ +name = 'impi' +version = '5.0.2.044' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = '/import/bc2/soft/source/i/impi/COM_L___LL96-5ZMJC2LJ.lic' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb new file mode 100644 index 0000000000..dc1797ac5a --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2015.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.2.164' +gccsuff = '-GCC-4.9.2' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.0.2.044', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.2.2.164', '', ('iimpi', '7.2.5%s' % gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From e583665ad10131df3c7543bbffaa9108913edc22 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 17:52:07 +0100 Subject: [PATCH 238/911] add Lmod/5.9 for GCC/4.8.[2,4] Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.2.eb | 27 +++++++++++++++++++ .../easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.4.eb | 27 +++++++++++++++++++ .../l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb | 24 +++++++++++++++++ .../n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 15 +++++++++++ 4 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.2.eb new file mode 100644 index 0000000000..e86305d642 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "5.9" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +sources = [SOURCE_TAR_BZ2] +source_urls = [ + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.4.eb new file mode 100644 index 0000000000..e44bacb20b --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.9-GCC-4.8.4.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "5.9" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCE_TAR_BZ2] +source_urls = [ + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb new file mode 100644 index 0000000000..a407b62d7d --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb @@ -0,0 +1,24 @@ +name = "Lua" +version = "5.1.4-8" + +homepage = "http://www.lua.org/" +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb new file mode 100644 index 0000000000..6031386c0f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' -- GitLab From cf6d219ae347d47ab39f99d230de9ba153347fdf Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 20:54:17 +0100 Subject: [PATCH 239/911] oh yes, add easyblock = 'ConfigureMake' for everybody Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb | 2 ++ easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb index a407b62d7d..a84e128f02 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = "Lua" version = "5.1.4-8" diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 6031386c0f..946a1c5338 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' -- GitLab From c200b00a7a58a72ab8ce922fb518efa8600a20f9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Feb 2015 21:25:35 +0100 Subject: [PATCH 240/911] also edit text files in favor of Lmod/5.9.5-GCC-4.8.4 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/README.rst | 10 +++++----- easybuild/easyconfigs/l/Lmod/sourceme | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/README.rst b/easybuild/easyconfigs/l/Lmod/README.rst index d3231b25ad..3c0886718f 100644 --- a/easybuild/easyconfigs/l/Lmod/README.rst +++ b/easybuild/easyconfigs/l/Lmod/README.rst @@ -10,14 +10,14 @@ Howto Assuming you have successfully used the bootstrap procedure of EasyBuild, you should be able to initiate a recursive build of the following bits:: - EASYBUILD_OPTARCH= time eb Lmod-5.8.5-GCC-4.8.2.eb -r + EASYBUILD_OPTARCH= time eb Lmod-5.9-GCC-4.8.4.eb -r which is going to build the following modules/easyconfigs:: - g/GCC/GCC-4.8.2.eb ## if this breaks use: --try-amend=parallel=1 - n/ncurses/ncurses-5.9-GCC-4.8.2.eb ## On MacOSX, this should pick a special patch - l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb ## Lmod is written in Lua, which needs ncurses - l/Lmod/Lmod-5.8.5-GCC-4.8.2.eb ## Lmod should be built with -r, to build the above + g/GCC/GCC-4.8.4.eb ## if this breaks use: --try-amend=parallel=1 + n/ncurses/ncurses-5.9-GCC-4.8.4.eb ## On MacOSX, this should pick a special patch + l/Lua/Lua-5.1.4-8-GCC-4.8.4.eb ## Lmod is written in Lua, which needs ncurses + l/Lmod/Lmod-5.9-GCC-4.8.4.eb ## Lmod should be built with -r, to build the above This operation is expected to be the needed substrate to launch you towards Lmod; Lmod facility gets activated with the `sourceme` script available next to this file:: diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index cf5748704a..804f0ede35 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -2,17 +2,17 @@ # # This script helps to implement policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html # -# prereq: Lmod/5.8.5-GCC-4.8.2 -# prereq: Lua/5.1.4-8-GCC-4.8.2 +# prereq: Lmod/5.9.5-GCC-4.8.4 +# prereq: Lua/5.1.4-8-GCC-4.8.4 # -# build prereqs, take a note: GCC/4.8.2 & ncurses/5.9 +# build prereqs, take a note: GCC/4.8.4 & ncurses/5.9 ## Remember to change the following, as per individual case EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} -TOOLCHAIN="GCC-4.8.2" +TOOLCHAIN="GCC-4.8.4" VERSIONLUA="5.1.4-8" -VERSIONLMOD="5.8.5" +VERSIONLMOD="5.9" PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD -- GitLab From 979a532426bc3b0cad5842e66ce1a2ef09929a32 Mon Sep 17 00:00:00 2001 From: Bart Verleye Date: Wed, 11 Feb 2015 10:27:33 +1300 Subject: [PATCH 241/911] updating python file --- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 113 ++++-------------- 1 file changed, 24 insertions(+), 89 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 33fd2ef2d0..df184b1c3e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -3,107 +3,56 @@ version = '2.7.8' homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.8.2' +numpyversion = '1.8.1' scipyversion = '0.14.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package dependencies = [ - ('bzip2', '1.0.6'), # for bz2 package -# ('zlib', '1.2.8'), # use version selected by libxslt below - ('libreadline', '6.2'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), ('ncurses', '5.9'), - ('LLVM', '3.2'), # for Numba - ('SQLite', '3.8.4.3'), # for IPython and general use - ('libxslt', '1.1.28'), # for lxml. brings in libxml2 and zlib dependencies. - ('CUDA', '6.0.37','', True), # for pycuda, duh. -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons - - ('libjpeg-turbo','1.3.0'), # For matplotlib and Pillow - ('libpng','1.6.10'), # For matplotlib and Pillow - ('freetype', '2.5.3'), # For matplotlib and Pillow - +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] +osdependencies = [('openssl-devel', 'libssl-dev')] + # order is important! +# Version updated 08/JULY/2014 exts_list = [ - ('setuptools', '5.7', { + ('setuptools', '5.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('ipython', '2.2.0', { - 'modulename': 'IPython', - 'source_urls': ['http://pypi.python.org/packages/source/i/ipython/'], - }), ('pip', '1.5.6', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('virtualenv', '1.11.6', { - 'source_urls': ['http://pypi.python.org/packages/source/v/virtualenv/'], - }), ('nose', '1.3.3', { 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), - ('line_profiler', '1.0b3', { - 'source_urls': ['http://pypi.python.org/packages/source/l/line_profiler/'], - }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % ('1.8.1' if numpyversion.startswith('1.8') else numpyversion), + 'numpy-%s-mkl.patch' % numpyversion, ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), - ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - - - ('networkx', '1.9', { - 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], - 'modulename': 'Bio', - }), - ('biopython', '1.64', { - 'source_urls': ['https://pypi.python.org/packages/source/b/biopython/'], - 'modulename': 'Bio', - }), - - ('Pillow', '2.5.3', { - 'source_tmpl': SOURCE_ZIP, #'%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/P/Pillow/'], - 'modulename': 'PIL', - }), - ('matplotlib', '1.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), - ('skimage', '0.10.1', { - 'source_tmpl': 'scikit-image-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/s/scikit-image/'], - }), - - ('lxml', '3.3.5', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], - }), - ('pycuda', '2014.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycuda/'], - }), - #('pyopencl', '2014.1', { - # 'source_urls': ['https://pypi.python.org/packages/source/p/puopencl/'], - #}), - ('pysam', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pysam/'], - }), - ('pytz', '2014.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['https://mpi4py.googlecode.com/files/'], + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], @@ -114,12 +63,15 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { - 'source_urls': ['http://pypi.python.org/packages/source/d/deap/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], @@ -135,26 +87,9 @@ exts_list = [ ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), - ('llvmpy', '0.12.7', { -# 'source_urls': ['https://pypi.python.org/packages/source/l/llvmpy/'], - 'source_urls': ['https://github.com/llvmpy/llvmpy/archive/'], # since pypi tarball is incomplete - 'source_tmpl': '%(version)s.zip', - }), - ('numba', '0.13.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - }), - ('numexpr', '2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr/'], - }), - ('Bottleneck', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/B/Bottleneck/'], + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), - ('pandas', '0.14.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], - }), - ] -osdependencies = [('openssl-devel', 'libssl-dev')] - moduleclass = 'lang' -- GitLab From 822c5ff12504e3177e9aa8706e42eb8c38f2a9ac Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 11 Feb 2015 02:20:03 +0100 Subject: [PATCH 242/911] add comment for source as requested Signed-off-by: Fotis Georgatos --- .../easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb index 1c4c98b0f0..ab71f3a9fb 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb @@ -21,6 +21,7 @@ description = """The rCUDA Framework enables the concurrent usage of CUDA-compat toolchain = {'version': 'dummy', 'name': 'dummy'} +# Obtain source via http://www.rcuda.net/index.php/software-request-form.html sources = ['rCUDA_%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { -- GitLab From 32d6b80d049418487f1f5fa325f80c746f2f0ed7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Feb 2015 09:31:12 +0100 Subject: [PATCH 243/911] add easyconfig for JUBE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb new file mode 100644 index 0000000000..0044a1ec87 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -0,0 +1,22 @@ +easyblock = "VersionIndependentPythonPackage" + +name = "JUBE" +version = "2.0.3" + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +sources = [SOURCELOWER_TAR_GZ] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From e839997611c0d2e83efe55ce1c6f077b6acc66d1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 11 Feb 2015 14:27:48 +0100 Subject: [PATCH 244/911] add rCUDA_5.0_linux_64_scientificLinux6.eb Signed-off-by: Fotis Georgatos --- .../rCUDA_5.0_linux_64_scientificLinux6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb new file mode 100644 index 0000000000..5169448939 --- /dev/null +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html +## + +easyblock = "Tarball" + +name = "rCUDA" +version = "5.0" +versionsuffix = "_linux_64_scientificLinux6" + +homepage = 'http://www.rcuda.net/' +description = """The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['rCUDA_%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ["framework/common/rCUDAcommIB.so", "framework/common/rCUDAcommTCP.so", + "framework/rCUDAl/libcudart.so", "framework/rCUDAd/getGPUNo"], + 'dirs': [] +} + +moduleclass = 'system' -- GitLab From 5eaf52feaa38920470b26a5fd10cc83855c67038 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 11 Feb 2015 14:28:54 +0100 Subject: [PATCH 245/911] header fix for rCUDA/4.0.1 Signed-off-by: Fotis Georgatos --- .../easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb index 1c4c98b0f0..0bf2a17ba2 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb @@ -1,8 +1,8 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB -# Authors:: Fotis Georgatos , +# Copyright:: Copyright 2012-2014 NTUA +# Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ # -- GitLab From 4397a59636475ae58f72738fa6b89f214ae97cbe Mon Sep 17 00:00:00 2001 From: Danilo Guerrera Date: Wed, 11 Feb 2015 14:32:36 +0100 Subject: [PATCH 246/911] support for MVAPICH2 vs 2.0.1 and a toolchain with GCC 4.8.4 --- .../b/Bison/Bison-2.7-GCC-4.8.4.eb | 22 +++++++++++++++++++ .../g/gmvapich2/gmvapich2-1.7.20.eb | 22 +++++++++++++++++++ .../m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb | 17 ++++++++++++++ 3 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.4.eb create mode 100644 easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb create mode 100644 easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.4.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.4.eb new file mode 100644 index 0000000000..308a68920e --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.4.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb new file mode 100644 index 0000000000..22b6c5bfc3 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = "Toolchain" + +name = 'gmvapich2' +version = '1.7.20' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including MVAPICH2 for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.4' +comp = (compname, compver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('MVAPICH2', '2.0.1', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb new file mode 100644 index 0000000000..bf2762a1a1 --- /dev/null +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-2.0.1-GCC-4.8.4.eb @@ -0,0 +1,17 @@ +name = 'MVAPICH2' +version = '2.0.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/overview/mvapich2/' +description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH." + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/'] +sources = [SOURCELOWER_TAR_GZ] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['77bba29442f81e196155e87869cdceda'] + +builddependencies = [('Bison', '2.7')] + +moduleclass = 'mpi' -- GitLab From 2143edd9f67667536dd6c3ad4ebfd9255dad3761 Mon Sep 17 00:00:00 2001 From: Danilo Guerrera Date: Wed, 11 Feb 2015 14:38:24 +0100 Subject: [PATCH 247/911] new GMVOLF toolchain, based on GCC 4.8.4, MVAPICH2 v2.0.1 --- .../f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb | 34 +++++++++++++++++ .../easyconfigs/g/gmvolf/gmvolf-1.7.20.eb | 37 +++++++++++++++++++ ...ch2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb create mode 100644 easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb new file mode 100644 index 0000000000..c0222caee5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gmvapich2-1.7.20.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gmvapich2', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb new file mode 100644 index 0000000000..5c496f8a67 --- /dev/null +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'gmvolf' +version = '1.7.20' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.8.4' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build gmvolf dependencies +comp_mpi_tc_name = 'gmvapich2' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and MVAPICH2 as explicit dependencies instead of gmvapivh2 toolchain +# because of toolchain preperation functions +dependencies = [ + ('GCC', '4.8.4'), + ('MVAPICH2', '2.0.1', '', comp), + (blaslib, blasver, blassuff, comp), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..4792a692ea --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gmvapich2', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.8.4'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 89a6a9367194fa2224250b503114a0caa657d573 Mon Sep 17 00:00:00 2001 From: Danilo Guerrera Date: Wed, 11 Feb 2015 14:40:01 +0100 Subject: [PATCH 248/911] HPL v2.1 built on top of GMVOLF 1.7.20 toolchain --- .../easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb new file mode 100644 index 0000000000..dda08f35b9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-gmvolf-1.7.20.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gmvolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 69ccaa4cdd228049b2dc9d6080f382fac864d9c5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 12 Feb 2015 09:52:05 +0100 Subject: [PATCH 249/911] removed site specific license path --- easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb | 5 ++--- easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 64131e9b0c..edbddbc36d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -17,9 +17,8 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -#import os -#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -license_file = '/import/bc2/soft/source/i/icc/COM_L__CPP_RSCN-FRFDSRTL.lic' +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 3c57e6d8fe..4f376249d8 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -17,8 +17,7 @@ dependencies = [(gcc, gccver)] dontcreateinstalldir = 'True' # license file -#import os -#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -license_file = '/import/bc2/soft/source/i/ifort/COM_L__FOR_RRB4-H33RVJNV.lic' +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'compiler' -- GitLab From 75703b90c024a99bab19e620630ef64119196a99 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 12 Feb 2015 09:53:46 +0100 Subject: [PATCH 250/911] added HPL easyconfig for intel-2015.02 toolchain --- .../easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb new file mode 100644 index 0000000000..7597cf43f8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2015.02'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From e9db7b144c938f08209941e414319263be21f872 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 12 Feb 2015 10:08:27 +0100 Subject: [PATCH 251/911] added java 1.7.0_75 --- easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb new file mode 100644 index 0000000000..72fde0f6bc --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_75' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From ad1597209504a1856f3df960c425537dd415bb7d Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 12 Feb 2015 10:19:45 +0100 Subject: [PATCH 252/911] updated picard to latest java --- easybuild/easyconfigs/p/picard/picard-1.119.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/picard/picard-1.119.eb b/easybuild/easyconfigs/p/picard/picard-1.119.eb index cb362554cd..b6b8db08ef 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119.eb @@ -9,6 +9,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] -dependencies = [('Java', '1.7.0_10')] +dependencies = [('Java', '1.7.0_75')] moduleclass = 'bio' -- GitLab From 949caa1d64850968fbb4ec9f450f382bd7df0a6b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 12 Feb 2015 10:35:44 +0100 Subject: [PATCH 253/911] updated to latest intel-mpi --- easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb | 2 +- ....2.eb => impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb} | 5 ++--- easybuild/easyconfigs/i/intel/intel-2015.02.eb | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/i/impi/{impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb => impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb} (74%) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb index 62c0e1ff30..2c890a5549 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb @@ -15,7 +15,7 @@ compver = '2015.%s' % suff dependencies = [ ('icc', compver, versionsuffix), ('ifort', compver, versionsuffix), - ('impi', '5.0.2.044', '', ('iccifort', '%s%s' % (compver, versionsuffix))), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, versionsuffix))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb similarity index 74% rename from easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb rename to easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index a71dcd21b3..d23a27639e 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -1,5 +1,5 @@ name = 'impi' -version = '5.0.2.044' +version = '5.0.3.048' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message @@ -14,7 +14,6 @@ dontcreateinstalldir = 'True' # license file import os -#license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -license_file = '/import/bc2/soft/source/i/impi/COM_L___LL96-5ZMJC2LJ.lic' +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb index dc1797ac5a..ab8507944b 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -14,7 +14,7 @@ gccsuff = '-GCC-4.9.2' dependencies = [ ('icc', compver, gccsuff), ('ifort', compver, gccsuff), - ('impi', '5.0.2.044', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, gccsuff))), ('imkl', '11.2.2.164', '', ('iimpi', '7.2.5%s' % gccsuff)), ] -- GitLab From 0f558843477fc0bea296063453ab266cf65e11c2 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 12 Feb 2015 11:22:32 +0100 Subject: [PATCH 254/911] style fixes --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 53d9ac4058..84a819596b 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java','1.7.0_75', '', True), + ('Java', '1.7.0_75', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb index 76687da80e..a00dce23ff 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java','1.7.0_75', '', True), + ('Java', '1.7.0_75', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index f15ea8b602..15878afe16 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java','1.7.0_75', '', True), + ('Java', '1.7.0_75', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " -- GitLab From 22a27248154007a4f6d1bbad4f2a16dc442ca4c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Feb 2015 11:49:59 +0100 Subject: [PATCH 255/911] rename GenomeAnalysisTk easyconfigs to GATK --- .../GenomeAnalysisTK-1.0.5083.eb => GATK/GATK-1.0.5083.eb} | 0 .../GATK-2.7-4.eb}/GenomeAnalysisTK-2.7-4.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/{GenomeAnalysisTK/GenomeAnalysisTK-1.0.5083.eb => GATK/GATK-1.0.5083.eb} (100%) rename easybuild/easyconfigs/g/{GenomeAnalysisTK => GATK/GATK-2.7-4.eb}/GenomeAnalysisTK-2.7-4.eb (100%) diff --git a/easybuild/easyconfigs/g/GenomeAnalysisTK/GenomeAnalysisTK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb similarity index 100% rename from easybuild/easyconfigs/g/GenomeAnalysisTK/GenomeAnalysisTK-1.0.5083.eb rename to easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb diff --git a/easybuild/easyconfigs/g/GenomeAnalysisTK/GenomeAnalysisTK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb similarity index 100% rename from easybuild/easyconfigs/g/GenomeAnalysisTK/GenomeAnalysisTK-2.7-4.eb rename to easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb -- GitLab From bec2794c6b7c4252ed00c270435e3b7a57eb0454 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Feb 2015 11:59:00 +0100 Subject: [PATCH 256/911] fix rename screwup --- .../{GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb => GATK-2.7-4.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GATK/{GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb => GATK-2.7-4.eb} (100%) diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb similarity index 100% rename from easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb/GenomeAnalysisTK-2.7-4.eb rename to easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb -- GitLab From 332179371685a2dd1babbbc91f6e39d83e349e4e Mon Sep 17 00:00:00 2001 From: Adam Mazur Date: Thu, 12 Feb 2015 12:03:46 +0100 Subject: [PATCH 257/911] easyconfig for Coot --- easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb | 27 ++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb b/easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb new file mode 100644 index 0000000000..54e36207e0 --- /dev/null +++ b/easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Mazur +# Research IT +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'Coot' +version = '0.8.1' +versionsuffix = '-binary-Linux-x86_64-rhel-6-python-gtk2' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot' +description = """Coot is for macromolecular model building, model completion +and validation, particularly suitable for protein modelling using X-ray data.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/coot" ], + 'dirs': ["bin"] +} + +moduleclass = 'bio' + -- GitLab From a002266ec091a8c286958521cf465ac1406280f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Feb 2015 12:09:50 +0100 Subject: [PATCH 258/911] revert back to v1.7.0_10 for compatibility with HPCBIOS easyconfigs --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 84a819596b..ae4e3793e6 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_75', '', True), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb index a00dce23ff..f3660e8c90 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-4.1.13.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_75', '', True), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index 15878afe16..f34568c037 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -22,7 +22,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_75', '', True), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " -- GitLab From a25e81ed2166db04b225cd934dff9b9e39e3762e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Feb 2015 12:20:35 +0100 Subject: [PATCH 259/911] fix name/sources in renamed GATK easyconfigs --- easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb | 6 +++--- easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index b0b8f69c3e..bf84cfb541 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -1,4 +1,4 @@ -name = 'GenomeAnalysisTK' +name = 'GATK' version = '1.0.5083' homepage = 'http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit' @@ -9,8 +9,8 @@ description = """The GATK is a structured software library that makes writing ef toolchain = {'name': 'dummy', 'version': 'dummy'} -# download via http://www.broadinstitute.org/gatk/download (requires registration) -sources = [SOURCE_TAR_BZ2] +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 6f476f6eff..8d820b457c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -1,4 +1,4 @@ -name = 'GenomeAnalysisTK' +name = 'GATK' version = '2.7-4' homepage = 'http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit' @@ -9,8 +9,8 @@ description = """The GATK is a structured software library that makes writing ef toolchain = {'name': 'dummy', 'version': 'dummy'} -# download via http://www.broadinstitute.org/gatk/download (requires registration) -sources = [SOURCE_TAR_BZ2] +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] -- GitLab From 37e080af91f24a43f3c5b46983bab8162a69a027 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 12 Feb 2015 12:21:02 +0100 Subject: [PATCH 260/911] bugfix filename of MAFFT for ictce/5.3.0 Signed-off-by: Fotis Georgatos --- ...MAFFT-7.130-ictce-5.3.0-with-extensions.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb new file mode 100644 index 0000000000..6bf747d607 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-ictce-5.3.0-with-extensions.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.130' +versionsuffix = '-with-extensions' + +homepage = 'http://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 16e6b57e586555ca09b09a548343957365bb4534 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 12 Feb 2015 12:35:04 +0100 Subject: [PATCH 261/911] really bugfix this MAFFT Signed-off-by: Fotis Georgatos --- ...MAFFT-7.130-with-extensions-ictce-5.3.0.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb deleted file mode 100644 index 6bf747d607..0000000000 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-ictce-5.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel - -easyblock = 'ConfigureMake' - -name = 'MAFFT' -version = '7.130' -versionsuffix = '-with-extensions' - -homepage = 'http://mafft.cbrc.jp/alignment/software/' -description = """MAFFT is a multiple sequence alignment program - for unix-like operating systems. It offers a range of multiple - alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), - FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = [homepage] -sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] - -skipsteps = ['configure'] -start_dir = 'core' -installopts = 'PREFIX=%(installdir)s' - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -sanity_check_paths = { - 'files': ['bin/mafft'], - 'dirs': [], -} - -moduleclass = 'bio' -- GitLab From ff0235fb00d9a2c7c4f86964feb66c9aec996658 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Feb 2015 12:41:53 +0100 Subject: [PATCH 262/911] use Tarball easyblock for renamed GATK easyconfigs --- easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb | 9 +++++++++ easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index bf84cfb541..ddd5712d6f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -1,3 +1,5 @@ +easyblock = 'Tarball' + name = 'GATK' version = '1.0.5083' @@ -14,4 +16,11 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 8d820b457c..98e7df7db8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -1,3 +1,5 @@ +easyblock = 'Tarball' + name = 'GATK' version = '2.7-4' @@ -14,4 +16,11 @@ sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] dependencies = [('Java', '1.7.0_10')] +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + moduleclass = 'bio' -- GitLab From 9eaecd9c12622df49a0a556df6994f87eb7d221b Mon Sep 17 00:00:00 2001 From: Adam Mazur Date: Thu, 12 Feb 2015 12:42:08 +0100 Subject: [PATCH 263/911] renamed the easyconfig file name --- ....1.eb => Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Coot/{Coot-0.8.1.eb => Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb} (100%) diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb similarity index 100% rename from easybuild/easyconfigs/c/Coot/Coot-0.8.1.eb rename to easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb -- GitLab From 792312016a7f7dece347a37e7add6cf00f133443 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 12 Feb 2015 13:05:42 +0100 Subject: [PATCH 264/911] iomkl-2015.02 --- ...oc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb | 20 +++++++++++ .../i/imkl/imkl-11.2.2.164-iompi-2015.02.eb | 21 +++++++++++ .../easyconfigs/i/iomkl/iomkl-2015.02.eb | 20 +++++++++++ .../easyconfigs/i/iompi/iompi-2015.02.eb | 20 +++++++++++ ...MPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 36 +++++++++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2015.02.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..6a875c1d32 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.0' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' + diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb new file mode 100644 index 0000000000..82eec3eecb --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.2.164-iompi-2015.02.eb @@ -0,0 +1,21 @@ +name = 'imkl' +version = '11.2.2.164' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines +for science, engineering, and financial applications that require maximum performance. Core math functions include +BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iompi', 'version': '2015.02'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +interfaces = True + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb new file mode 100644 index 0000000000..544ad6da2e --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2015.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.2.164-GCC-4.9.2' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.8.4', '', ('iccifort', compver)), + ('imkl', '11.2.2.164', '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb new file mode 100644 index 0000000000..698ba1f804 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2015.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.2.164-GCC-4.9.2' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.8.4', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb new file mode 100644 index 0000000000..23433689d8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += ' CC=icc FC=ifort CXX=icpc ' +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +dependencies = [('hwloc', '1.10.0')] + +# needed for --with-openib +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 89ee72e0a470a568a889c5524ce78f3648eda4ac Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 12 Feb 2015 13:10:01 +0100 Subject: [PATCH 265/911] added HPL-2.1-iomkl-2015.02.eb --- .../easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb new file mode 100644 index 0000000000..28511646d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2015.02.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2015.02'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 96060d2f318003c44b3b7cb3e05cde290367a490 Mon Sep 17 00:00:00 2001 From: Adam Mazur Date: Thu, 12 Feb 2015 17:11:59 +0100 Subject: [PATCH 266/911] pmw python library --- .../Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..e2f286887c --- /dev/null +++ b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Mazur +# Research IT +# Biozentrum, University of Basel + +easyblock = "PythonPackage" + +name = 'Pmw' +version = '1.3.3' + +homepage = 'http://pmw.sourceforge.net' +description = """Pmw is a toolkit for building high-level compound widgets in Python + using the Tkinter module. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/%(namelower)s/files/%(name)s/%(name)s.%(version)s/', '/download'] +sources = ['%(name)s.%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +options = {'modulename': 'Pmw'} + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%s-%s-py%s.egg-info' % (pyshortver, name, version, pyshortver)], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From b6a9297bc3958fbb331324c778005fe4c88b3498 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 12 Feb 2015 20:53:15 +0100 Subject: [PATCH 267/911] rename rCUDA_5.0_linux_64_scientificLinux6.eb as rCUDA-5.0* Signed-off-by: Fotis Georgatos --- ...scientificLinux6.eb => rCUDA-5.0_linux_64_scientificLinux6.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/r/rCUDA/{rCUDA_5.0_linux_64_scientificLinux6.eb => rCUDA-5.0_linux_64_scientificLinux6.eb} (100%) diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb similarity index 100% rename from easybuild/easyconfigs/r/rCUDA/rCUDA_5.0_linux_64_scientificLinux6.eb rename to easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb -- GitLab From 96eadea73ee77fb689b185578200ef7417ebb0a5 Mon Sep 17 00:00:00 2001 From: Adam Mazur Date: Fri, 13 Feb 2015 16:57:21 +0100 Subject: [PATCH 268/911] removed the 'download/' string from the source_urls list --- .../easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb index e2f286887c..c8749eca4a 100644 --- a/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/Pmw/Pmw-1.3.3-goolf-1.4.10-Python-2.7.5.eb @@ -14,7 +14,7 @@ description = """Pmw is a toolkit for building high-level compound widgets in Py toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://sourceforge.net/projects/%(namelower)s/files/%(name)s/%(name)s.%(version)s/', '/download'] +source_urls = ['http://sourceforge.net/projects/%(namelower)s/files/%(name)s/%(name)s.%(version)s/'] sources = ['%(name)s.%(version)s.tar.gz'] python = 'Python' -- GitLab From c8d8b591b6e516e5318e471b9097bae7b201af06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Feb 2015 10:53:03 +0100 Subject: [PATCH 269/911] add easyconfig file for GAMESS-US 2014.12.05-R1, including patch to make rungms work with SLURM --- .../GAMESS-US-2014.12.05-R1-intel-2015a.eb | 21 ++++++ .../g/GAMESS-US/GAMESS-US_rungms-slurm.patch | 67 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb new file mode 100644 index 0000000000..88ffa942b9 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'GAMESS-US' +version = '20141205-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +sources = ['gamess-%(version)s.tar.gz'] + +patches = ['GAMESS-US_rungms-slurm.patch'] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch new file mode 100644 index 0000000000..93831aab9e --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch @@ -0,0 +1,67 @@ +This patch adds support for the SLURM scheduler (without removing support for +the PBS or SGE schedulers). + +Written by Benjamin Roberts, New Zealand eScience Infrastructure +University of Auckland, Auckland, New Zealand +--- gamess.orig/rungms 2013-05-18 04:15:11.000000000 +1200 ++++ gamess/rungms 2015-01-29 17:39:53.359679532 +1300 +@@ -86,6 +92,7 @@ + set SCHED=none + if ($?PBS_O_LOGNAME) set SCHED=PBS + if ($?SGE_O_LOGNAME) set SCHED=SGE ++if ($?SLURM_JOB_ID) set SCHED=SLURM + if ($SCHED == SGE) then + set SCR=$TMPDIR + echo "SGE has assigned the following compute nodes to this run:" +@@ -96,6 +103,13 @@ + echo "PBS has assigned the following compute nodes to this run:" + uniq $PBS_NODEFILE + endif ++if ($SCHED == SLURM) then ++ # SCR is for large binary temporary files. Accordingly, it should only be ++ # set to a network file system if the connection to that file system is fast. ++ set SCR=$SCRATCH_DIR ++ echo "SLURM has assigned the following compute nodes to this run:" ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq ++endif + # + echo "Available scratch disk space (Kbyte units) at beginning of the job is" + df -k $SCR +@@ -594,6 +608,11 @@ + set NNODES=`wc -l $HOSTFILE` + set NNODES=$NNODES[1] + endif ++ if ($SCHED == SLURM) then ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq > $HOSTFILE ++ set NNODES=`wc -l $HOSTFILE` ++ set NNODES=$NNODES[1] ++ endif + endif + # uncomment next lines if you need to debug host configuration. + #--echo '-----debug----' +@@ -825,8 +844,12 @@ + unset echo + endif + set echo +- mpiexec.hydra -f $PROCFILE -n $NPROCS \ ++ if ($SCHED == SLURM) then ++ srun $GMSPATH/gamess.$VERNO.x < /dev/null ++ else ++ mpiexec.hydra -f $PROCFILE -n $NPROCS \ + $GMSPATH/gamess.$VERNO.x < /dev/null ++ endif + unset echo + breaksw + # +@@ -906,6 +929,11 @@ + set NNODES=`wc -l $HOSTFILE` + set NNODES=$NNODES[1] + endif ++ if ($SCHED == SLURM) then ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq > $HOSTFILE ++ set NNODES=`wc -l $HOSTFILE` ++ set NNODES=$NNODES[1] ++ endif + endif + # uncomment next lines if you need to debug host configuration. + #--echo '-----debug----' -- GitLab From bcf9de7c70b68a488d1b867ed25e4d8a451fac5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Feb 2015 13:45:42 +0100 Subject: [PATCH 270/911] fix easyconfig file name for GAMESS-US --- ....05-R1-intel-2015a.eb => GAMESS-US-20141205-R1-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GAMESS-US/{GAMESS-US-2014.12.05-R1-intel-2015a.eb => GAMESS-US-20141205-R1-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-2014.12.05-R1-intel-2015a.eb rename to easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb -- GitLab From 3209efcbfe2dc20fe572c16a43281e655628ab8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Feb 2015 20:37:45 +0100 Subject: [PATCH 271/911] include checksum for GAMESS-US source tarball, add easyconfig for GAMESS-US v20130501-R1 with ictce/6.2.5 (thanks @pescobar) --- .../GAMESS-US-20130501-R1-ictce-6.1.5.eb | 23 +++++++++++++++++++ .../GAMESS-US-20141205-R1-intel-2015a.eb | 2 ++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb new file mode 100644 index 0000000000..da31b958ee --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb @@ -0,0 +1,23 @@ +name = 'GAMESS-US' +version = '20130501-R1' + +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} +toolchainopts = {'usempi': True} + +# manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version +sources = ['gamess-%(version)s.tar.gz'] +checksums = ['977a01a8958238c67b707f125999fcec'] + +patches = ['GAMESS-US_rungms-slurm.patch'] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb index 88ffa942b9..00832c574c 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20141205-R1-intel-2015a.eb @@ -9,7 +9,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': True} # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version sources = ['gamess-%(version)s.tar.gz'] +checksums = ['6403592eaa885cb3691505964d684516'] patches = ['GAMESS-US_rungms-slurm.patch'] -- GitLab From 75f3623885563aaf55607d513af710329482b71e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Feb 2015 20:44:01 +0100 Subject: [PATCH 272/911] sync GAMESS-US easyconfig for goolf/1.5.14-no-OFED with #1406 --- ...ESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 19 ++++++---- .../easyconfigs/g/GAMESS-US/gamess_TMP.patch | 36 ------------------- 2 files changed, 12 insertions(+), 43 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb index c2b22536d1..fdb027a1ed 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb @@ -1,18 +1,23 @@ name = 'GAMESS-US' version = '20130501-R1' -homepage = 'http://www.msg.ameslab.gov/gamess/' -description = """The General Atomic and Molecular Electronic Structure System (GAMESS) - is a general ab initio quantum chemistry package.""" +homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' +description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) + is a general ab initio quantum chemistry package. """ toolchain = {'name': 'goolf', 'version': '1.5.14-no-OFED'} -toolchainopts = {'usempi': True, 'optarch': False} +toolchainopts = {'usempi': True} # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) +# rename gamess-current.tar.gz by changing 'current' to the proper version sources = ['gamess-%(version)s.tar.gz'] -patches = ['gamess_TMP.patch'] +checksums = ['977a01a8958238c67b707f125999fcec'] -maxcpus = 4 -maxnodes = 1 +patches = ['GAMESS-US_rungms-slurm.patch'] + +# increase these numbers if your system is bigger in terms of cores-per-node or number of nodes +# it's OK if these values are larger than what your system provides +maxcpus = '1000' +maxnodes = '100000' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch b/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch deleted file mode 100644 index 795144d2dc..0000000000 --- a/easybuild/easyconfigs/g/GAMESS-US/gamess_TMP.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- gamess/compall.orig 2014-06-11 18:37:54.000000000 +0200 -+++ gamess/compall 2014-06-11 18:40:44.000000000 +0200 -@@ -97,7 +97,7 @@ - # Debian uses the -m flag, since its -p replies "unknown" - # Gentoo uses the -m flag, since its -p gives an unusable multiword reply - if ($TARGET == linux64) then -- set chip=(`uname -p`) -+ set chip=(`uname -m`) - if (${#chip} > 1) set chip=unknown - if ($chip == unknown) set chip=`uname -m` - if ($chip == x86_64) set extraflags='-DLINUX64 -m64' ---- gamess/comp.orig 2014-06-11 21:26:28.000000000 +0200 -+++ gamess/comp 2014-06-11 21:26:03.000000000 +0200 -@@ -1806,6 +1804,8 @@ - breaksw - case 4.6: - case 4.7: -+ case 4.8: -+ case 4.9: - set EXTRAOPT="$EXTRAOPT -fno-whole-file" - breaksw - default: ---- gamess/source/zunix.c.orig 2014-06-12 08:52:56.000000000 +0200 -+++ gamess/source/zunix.c 2014-06-12 08:53:05.000000000 +0200 -@@ -443,7 +443,7 @@ - #ifdef LINUX64 - - #include --#include -+#include - - #define FORTINT long - -[?25l[?12l[?25h[?1049h[?1h=[?12;25h[?12l[?25h[?25l"diff" [New File]~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ [?12l[?25h[?25lType :quit to exit Vim[?12l[?25h[?1l>[?1049lVim: Error reading input, exiting... -Vim: Finished. -2 files to edit -- GitLab From 113777fd072dd181b3ea9aee0e611bbd10ed94a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Feb 2015 20:46:07 +0100 Subject: [PATCH 273/911] include patch file for GAMESS-uS rungms script --- .../g/GAMESS-US/GAMESS-US_rungms-slurm.patch | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch new file mode 100644 index 0000000000..93831aab9e --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US_rungms-slurm.patch @@ -0,0 +1,67 @@ +This patch adds support for the SLURM scheduler (without removing support for +the PBS or SGE schedulers). + +Written by Benjamin Roberts, New Zealand eScience Infrastructure +University of Auckland, Auckland, New Zealand +--- gamess.orig/rungms 2013-05-18 04:15:11.000000000 +1200 ++++ gamess/rungms 2015-01-29 17:39:53.359679532 +1300 +@@ -86,6 +92,7 @@ + set SCHED=none + if ($?PBS_O_LOGNAME) set SCHED=PBS + if ($?SGE_O_LOGNAME) set SCHED=SGE ++if ($?SLURM_JOB_ID) set SCHED=SLURM + if ($SCHED == SGE) then + set SCR=$TMPDIR + echo "SGE has assigned the following compute nodes to this run:" +@@ -96,6 +103,13 @@ + echo "PBS has assigned the following compute nodes to this run:" + uniq $PBS_NODEFILE + endif ++if ($SCHED == SLURM) then ++ # SCR is for large binary temporary files. Accordingly, it should only be ++ # set to a network file system if the connection to that file system is fast. ++ set SCR=$SCRATCH_DIR ++ echo "SLURM has assigned the following compute nodes to this run:" ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq ++endif + # + echo "Available scratch disk space (Kbyte units) at beginning of the job is" + df -k $SCR +@@ -594,6 +608,11 @@ + set NNODES=`wc -l $HOSTFILE` + set NNODES=$NNODES[1] + endif ++ if ($SCHED == SLURM) then ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq > $HOSTFILE ++ set NNODES=`wc -l $HOSTFILE` ++ set NNODES=$NNODES[1] ++ endif + endif + # uncomment next lines if you need to debug host configuration. + #--echo '-----debug----' +@@ -825,8 +844,12 @@ + unset echo + endif + set echo +- mpiexec.hydra -f $PROCFILE -n $NPROCS \ ++ if ($SCHED == SLURM) then ++ srun $GMSPATH/gamess.$VERNO.x < /dev/null ++ else ++ mpiexec.hydra -f $PROCFILE -n $NPROCS \ + $GMSPATH/gamess.$VERNO.x < /dev/null ++ endif + unset echo + breaksw + # +@@ -906,6 +929,11 @@ + set NNODES=`wc -l $HOSTFILE` + set NNODES=$NNODES[1] + endif ++ if ($SCHED == SLURM) then ++ scontrol show hostnames $SLURM_JOB_NODELIST | sort | uniq > $HOSTFILE ++ set NNODES=`wc -l $HOSTFILE` ++ set NNODES=$NNODES[1] ++ endif + endif + # uncomment next lines if you need to debug host configuration. + #--echo '-----debug----' -- GitLab From 3ea75c4d5fff471c1e6624eea2afc6fdcb5f09f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Feb 2015 15:41:53 +0100 Subject: [PATCH 274/911] replace GAMESS-US 20130501-R1 easyconfig using ictce/6.2.5 with one using intel/2015a --- ...1-R1-ictce-6.1.5.eb => GAMESS-US-20130501-R1-intel-2015a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/GAMESS-US/{GAMESS-US-20130501-R1-ictce-6.1.5.eb => GAMESS-US-20130501-R1-intel-2015a.eb} (94%) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-intel-2015a.eb similarity index 94% rename from easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb rename to easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-intel-2015a.eb index da31b958ee..9ef05a983e 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-intel-2015a.eb @@ -5,7 +5,7 @@ homepage = 'http://www.msg.chem.iastate.edu/gamess/index.html' description = """ The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. """ -toolchain = {'name': 'ictce', 'version': '6.2.5'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': True} # manually download via http://www.msg.chem.iastate.edu/gamess/download.html (requires registration) -- GitLab From 71b420fcdb733a4cc3c96bd5ba41b5d7cfad3f5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Feb 2015 09:04:18 +0100 Subject: [PATCH 275/911] add easyconfig for worker framework --- .../w/worker/worker-1.5.1-intel-2015a.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb new file mode 100644 index 0000000000..ca46ed7819 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.5.1' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.20.1', '-bare') +] + +moduleclass = 'tools' -- GitLab From 2b41f30c4f0a3b02ea48f0dea2be70372367c013 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Feb 2015 09:18:16 +0100 Subject: [PATCH 276/911] enable 'usempi' in worker easyconfig --- easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index ca46ed7819..600c35a7cd 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -9,6 +9,7 @@ description = """The Worker framework has been developed to help deal with param see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] -- GitLab From 86ecd3e263325dd2260060451c52a697a2586597 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 16 Feb 2015 10:50:40 +0100 Subject: [PATCH 277/911] Small fix in ISL easyconfig --- easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 7b675a2960..3ba25676db 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -4,12 +4,12 @@ name = 'ISL' version = '0.14' homepage = 'http://isl.gforge.inria.fr/' -description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints. """ +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = ['isl-0.14.tar.bz2'] source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] dependencies = [('GMP', '6.0.0')] @@ -18,4 +18,4 @@ sanity_check_paths = { 'dirs': ['include/isl'] } -moduleclass = 'compiler' +moduleclass = 'math' -- GitLab From e802ef4de074572663983ea57f2eed1dca73fa35 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 16 Feb 2015 10:52:56 +0100 Subject: [PATCH 278/911] Added newer CMake version --- .../c/CMake/CMake-3.1.3-GCC-4.9.2.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb new file mode 100644 index 0000000000..674ad2c737 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c25baf6baf94eeb0bbb20bee69bc8bd1512a9e16 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 16 Feb 2015 10:53:14 +0100 Subject: [PATCH 279/911] Use newer CMake --- easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index c22450fce4..1fa4fc4b47 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -29,7 +29,7 @@ sources = [ "polly-%(version)src2.src.tar.xz", ] -builddependencies = [('CMake', '3.1.0')] +builddependencies = [('CMake', '3.1.3')] dependencies = [ ('GMP', '6.0.0'), -- GitLab From 54ac2b4927e8db845f48b726090f0453da36b14f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Feb 2015 12:28:11 +0100 Subject: [PATCH 280/911] add postinstallcmds in worker easyconfig file --- .../easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb index 600c35a7cd..e3023d8f2c 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.5.1-intel-2015a.eb @@ -18,4 +18,14 @@ dependencies = [ ('Perl', '5.20.1', '-bare') ] +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', # tweak this + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', # tweak this (maybe) + 'sed -i "s@ mpi_module = .*@ mpi_module = intel/2015a@g" %(installdir)s/conf/worker.conf', # tweak this (maybe) +] + moduleclass = 'tools' -- GitLab From f1f1bef8d7a3db8bdd0b5340fdfc35c937d25a1c Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 17 Feb 2015 15:55:07 +0100 Subject: [PATCH 281/911] Fixed style issue --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index e311f5fe2d..131eedc724 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'Octave' version = '3.8.2' -- GitLab From 662aa111a1977f3f57405f8b1e4be10669bc37c0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 18 Feb 2015 13:23:59 +0100 Subject: [PATCH 282/911] Dummy --- .../easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f747925bf5 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb @@ -0,0 +1 @@ +DUMMY -- GitLab From 662d8eeba0f855a57297b0d89baec39216897bf9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 18 Feb 2015 13:32:06 +0100 Subject: [PATCH 283/911] Revert "Autoconf dep removed" This reverts commit 7bcb5ac31cf03ffd1559e4f91a163ec59e7c0109. Get lost in time and space --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index ae2c3c32ff..e3c5f86d83 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -24,6 +24,7 @@ sources = ['ocaml-%(version)s.tar.gz'] sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] +builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " -- GitLab From 0e65ccdc46d930869e2971b9704aff735b485a09 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 18 Feb 2015 13:33:06 +0100 Subject: [PATCH 284/911] Revert "Autoconf dep removed" This reverts commit 7bcb5ac31cf03ffd1559e4f91a163ec59e7c0109. Get Lost In Time And Space --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb index ae2c3c32ff..e3c5f86d83 100644 --- a/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -24,6 +24,7 @@ sources = ['ocaml-%(version)s.tar.gz'] sourcedir = name.lower() + '-' + '.'.join(version.split('.')[0:-1]) source_urls = ['http://caml.inria.fr/pub/distrib/%s' % sourcedir] +builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " -- GitLab From 9d3a7ca103b2e49be9a784e9b794f7445aecf819 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 18 Feb 2015 15:29:49 +0100 Subject: [PATCH 285/911] Real --- .../BLAST-2.2.30-intel-2015a-Python-2.7.9.eb | 44 +++++ .../BLAST-2.2.30-intel2015a-Python-2.7.9.eb | 1 - .../b/BLAST/BLAST-2.2.30_basename-fixes.patch | 173 ++++++++++++++++++ .../b/BLAST/BLAST-2.2.30_ictce-fixes.patch | 12 ++ 4 files changed, 229 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..66879c0ee8 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST' +version = '2.2.30' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-%(version)s_ictce-fixes.patch', + '%(name)s-%(version)s_basename-fixes.patch' +] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb deleted file mode 100644 index f747925bf5..0000000000 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel2015a-Python-2.7.9.eb +++ /dev/null @@ -1 +0,0 @@ -DUMMY diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch new file mode 100644 index 0000000000..25b21c2317 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch @@ -0,0 +1,173 @@ +#Let configure(.ac) determine the absolute path to basename, rather +#than having Makefile.in.top hardcode /usr/bin/basename, which fails on +#at least stock CentOS 6 (which supplies only /bin/basename). +#http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 +#B. Hajgato 02/18/2015 +--- trunk/c++/src/build-system/Makefile.in.top 2014/11/12 15:16:56 65203 ++++ trunk/c++/src/build-system/Makefile.in.top 2014/11/12 16:41:55 65204 +@@ -11,6 +11,7 @@ + libdir = @libdir@ + includedir = @includedir@ + pincludedir = $(includedir)/$(PACKAGE_NAME) ++BASENAME = @BASENAME@ + INSTALL = @INSTALL@ + LN_S = @LN_S@ + +@@ -46,7 +47,7 @@ + -rm -f $(libdir)/lib*-static.a + cd $(libdir) && \ + for x in *.a; do \ +- $(LN_S) "$$x" "`/usr/bin/basename \"$$x\" .a`-static.a"; \ ++ $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \ + done + cd $(includedir0) && find * -name CVS -prune -o -print |\ + cpio -pd $(pincludedir) +--- trunk/c++/src/build-system/configure 2014/11/12 15:16:56 65203 ++++ trunk/c++/src/build-system/configure 2014/11/12 16:41:55 65204 +@@ -682,6 +682,7 @@ + DISTCC + CCACHE + TAIL ++BASENAME + SED + TOUCH + GREP +@@ -8413,6 +8414,46 @@ + echo "${ECHO_T}no" >&6; } + fi + ++# Extract the first word of "basename", so it can be a program name with args. ++set dummy basename; ac_word=$2 ++{ echo "$as_me:$LINENO: checking for $ac_word" >&5 ++echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6; } ++if test "${ac_cv_path_BASENAME+set}" = set; then ++ echo $ECHO_N "(cached) $ECHO_C" >&6 ++else ++ case $BASENAME in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_BASENAME="$BASENAME" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++for as_dir in $PATH ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_BASENAME="$as_dir/$ac_word$ac_exec_ext" ++ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++BASENAME=$ac_cv_path_BASENAME ++if test -n "$BASENAME"; then ++ { echo "$as_me:$LINENO: result: $BASENAME" >&5 ++echo "${ECHO_T}$BASENAME" >&6; } ++else ++ { echo "$as_me:$LINENO: result: no" >&5 ++echo "${ECHO_T}no" >&6; } ++fi ++ ++ + # Extract the first word of "sed", so it can be a program name with args. + set dummy sed; ac_word=$2 + { echo "$as_me:$LINENO: checking for $ac_word" >&5 +@@ -41750,6 +41791,7 @@ + DISTCC!$DISTCC$ac_delim + CCACHE!$CCACHE$ac_delim + TAIL!$TAIL$ac_delim ++BASENAME!$BASENAME$ac_delim + SED!$SED$ac_delim + TOUCH!$TOUCH$ac_delim + GREP!$GREP$ac_delim +@@ -41772,7 +41814,6 @@ + GCRYPT_INCLUDE!$GCRYPT_INCLUDE$ac_delim + GCRYPT_LIBS!$GCRYPT_LIBS$ac_delim + LIBGNUTLS_CONFIG!$LIBGNUTLS_CONFIG$ac_delim +-GNUTLS_INCLUDE!$GNUTLS_INCLUDE$ac_delim + _ACEOF + + if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then +@@ -41814,6 +41855,7 @@ + ac_delim='%!_!# ' + for ac_last_try in false false false false false :; do + cat >conf$$subs.sed <<_ACEOF ++GNUTLS_INCLUDE!$GNUTLS_INCLUDE$ac_delim + GNUTLS_LIBS!$GNUTLS_LIBS$ac_delim + OPENSSL_INCLUDE!$OPENSSL_INCLUDE$ac_delim + OPENSSL_LIBS!$OPENSSL_LIBS$ac_delim +@@ -41910,7 +41952,6 @@ + status_dir!$status_dir$ac_delim + builddir!$builddir$ac_delim + runpath!$runpath$ac_delim +-ncbi_runpath!$ncbi_runpath$ac_delim + _ACEOF + + if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then +@@ -41952,6 +41993,7 @@ + ac_delim='%!_!# ' + for ac_last_try in false false false false false :; do + cat >conf$$subs.sed <<_ACEOF ++ncbi_runpath!$ncbi_runpath$ac_delim + c_ncbi_runpath!$c_ncbi_runpath$ac_delim + LINK!$LINK$ac_delim + C_LINK!$C_LINK$ac_delim +@@ -42048,7 +42090,6 @@ + BZ2_LIB!$BZ2_LIB$ac_delim + PCREPOSIX_LIBS!$PCREPOSIX_LIBS$ac_delim + PCRE_LIB!$PCRE_LIB$ac_delim +-OPENSSL_STATIC_LIBS!$OPENSSL_STATIC_LIBS$ac_delim + _ACEOF + + if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then +@@ -42090,6 +42131,7 @@ + ac_delim='%!_!# ' + for ac_last_try in false false false false false :; do + cat >conf$$subs.sed <<_ACEOF ++OPENSSL_STATIC_LIBS!$OPENSSL_STATIC_LIBS$ac_delim + TLS_INCLUDE!$TLS_INCLUDE$ac_delim + TLS_LIBS!$TLS_LIBS$ac_delim + SYBASE_PATH!$SYBASE_PATH$ac_delim +@@ -42186,7 +42228,6 @@ + AVRO_STATIC_LIBS!$AVRO_STATIC_LIBS$ac_delim + MONGODB_STATIC_LIBS!$MONGODB_STATIC_LIBS$ac_delim + ncbi_xreader_pubseqos!$ncbi_xreader_pubseqos$ac_delim +-ncbi_xreader_pubseqos2!$ncbi_xreader_pubseqos2$ac_delim + _ACEOF + + if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 97; then +@@ -42228,6 +42269,7 @@ + ac_delim='%!_!# ' + for ac_last_try in false false false false false :; do + cat >conf$$subs.sed <<_ACEOF ++ncbi_xreader_pubseqos2!$ncbi_xreader_pubseqos2$ac_delim + UNLESS_PUBSEQOS!$UNLESS_PUBSEQOS$ac_delim + PERL_INCLUDE!$PERL_INCLUDE$ac_delim + PERL_LIBS!$PERL_LIBS$ac_delim +@@ -42266,7 +42308,7 @@ + LTLIBOBJS!$LTLIBOBJS$ac_delim + _ACEOF + +- if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 36; then ++ if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 37; then + break + elif $ac_last_try; then + { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +--- trunk/c++/src/build-system/configure.ac 2014/11/12 15:16:56 65203 ++++ trunk/c++/src/build-system/configure.ac 2014/11/12 16:41:55 65204 +@@ -2255,6 +2255,7 @@ + AC_MSG_RESULT(no) + fi + ++AC_PATH_PROG(BASENAME, basename) + AC_PATH_PROG(SED, sed) + AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) + dnl AC_PATH_PROG(GREP, grep) + diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch new file mode 100644 index 0000000000..c43727c4bb --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch @@ -0,0 +1,12 @@ +diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/configure ncbi-blast-2.2.30+-src/c++/src/build-system/configure +--- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/configure 2014-08-08 17:36:55.000000000 +0200 ++++ ncbi-blast-2.2.30+-src/c++/src/build-system/configure 2015-01-18 13:53:21.006190873 +0100 +@@ -6537,6 +6537,8 @@ + mips-sgi-irix*:KCC ) + ARCH_CFLAGS="-64" + ;; ++ *:ICC ) ++ ;; + * ) + { { echo "$as_me:$LINENO: error: Do not know how to compile 64-bit with compiler $CXX $compiler_ver $host:$compiler" >&5 + echo "$as_me: error: Do not know how to compile 64-bit with compiler $CXX $compiler_ver $host:$compiler" >&2;} -- GitLab From 6c237bc9e30c49543f36abc8e845f8cf56757d6d Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 20 Feb 2015 11:05:36 -0500 Subject: [PATCH 286/911] bump in version --- .../s/SAMtools/SAMtools-1.2-foss-2015a.eb | 33 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb new file mode 100644 index 0000000000..227c52d47d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..15cb82566e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] + +parallel = 1 + +moduleclass = 'bio' -- GitLab From 5aed0f0efe6b1386ba4a4c0d9b5ef47e5e5c963c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 11:04:57 +0100 Subject: [PATCH 287/911] add easyconfig + patch for Hoard --- .../h/Hoard/Hoard-3.10-intel-2015a.eb | 26 ++++++++++++++ .../easyconfigs/h/Hoard/Hoard-3.x_CXX.patch | 34 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/Hoard/Hoard-3.x_CXX.patch diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb new file mode 100644 index 0000000000..c1298de331 --- /dev/null +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Hoard' +version = '3.10' + +homepage = 'http://www.hoard.org/' +description = """Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/emeryberger/Hoard/releases/download/%(version)s'] +sources = ['Hoard-%(version)s-source.tar.gz'] +patches = ['Hoard-%(version_major)s.x_CXX.patch'] + +start_dir = 'src' + +buildopts = 'linux-gcc-x86-64' + +files_to_copy = [(['libhoard.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libhoard.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.x_CXX.patch b/easybuild/easyconfigs/h/Hoard/Hoard-3.x_CXX.patch new file mode 100644 index 0000000000..0b3f914c43 --- /dev/null +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.x_CXX.patch @@ -0,0 +1,34 @@ +--- Hoard/src/Makefile.orig 2015-02-23 10:46:55.000000000 +0100 ++++ Hoard/src/Makefile 2015-02-23 10:51:28.000000000 +0100 +@@ -1,6 +1,7 @@ + # Commands to compile Hoard for various targets. + # Run make (with no arguments) to see the complete target list. + ++CXX ?= g++ + CPPFLAGS = -O3 + + all: +@@ -53,17 +54,17 @@ + + MACOS_COMPILE_DEBUG = clang++ -ftemplate-depth=1024 -arch i386 -arch x86_64 -pipe -g -O0 -Wall $(INCLUDES) -D_REENTRANT=1 -compatibility_version 1 -current_version 1 -dynamiclib $(MACOS_SRC) -o libhoard.dylib -ldl -lpthread + +-LINUX_GCC_x86_COMPILE = g++ $(CPPFLAGS) -I/usr/include/nptl -ffast-math -g -malign-double -pipe -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread ++LINUX_GCC_x86_COMPILE = $(CXX) $(CPPFLAGS) -I/usr/include/nptl -ffast-math -g -malign-double -pipe -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread + +-LINUX_GCC_x86_64_COMPILE = g++ $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -pipe -fPIC -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread ++LINUX_GCC_x86_64_COMPILE = $(CXX) $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -pipe -fPIC -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread + +-LINUX_GCC_x86_64_COMPILE_DEBUG = g++ $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -pipe -fPIC $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread ++LINUX_GCC_x86_64_COMPILE_DEBUG = $(CXX) $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -pipe -fPIC $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread + +-LINUX_GCC_x86_COMPILE_STATIC = g++ $(CPPFLAGS) -g -I/usr/include/nptl -static -pipe -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -c $(GNU_SRC) ; ar cr libhoard.a libhoard.o ++LINUX_GCC_x86_COMPILE_STATIC = $(CXX) $(CPPFLAGS) -g -I/usr/include/nptl -static -pipe -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -c $(GNU_SRC) ; ar cr libhoard.a libhoard.o + +-LINUX_GCC_x86_64_COMPILE_STATIC = g++ $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -static -pipe -fPIC -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared -c $(GNU_SRC) -Bsymbolic ; ar cr libhoard.a libhoard.o ++LINUX_GCC_x86_64_COMPILE_STATIC $(CXX) $(CPPFLAGS) -g -W -Wconversion -Wall -I/usr/include/nptl -static -pipe -fPIC -finline-limit=20000 -finline-functions -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -shared -c $(GNU_SRC) -Bsymbolic ; ar cr libhoard.a libhoard.o + +-LINUX_GCC_x86_COMPILE_DEBUG = g++ $(CPPFLAGS) -fPIC -fno-inline -I/usr/include/nptl -g -pipe $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread ++LINUX_GCC_x86_COMPILE_DEBUG $(CXX) $(CPPFLAGS) -fPIC -fno-inline -I/usr/include/nptl -g -pipe $(INCLUDES) -D_REENTRANT=1 -shared $(GNU_SRC) -Bsymbolic -o libhoard.so -ldl -lpthread + + SOLARIS_SUNW_SPARC_COMPILE_32_DEBUG = CC -dalign -xbuiltin=%all -fast -mt -g -xildoff -xthreadvar=dynamic -L/usr/lib/lwp -R/usr/lib/lwp -DNDEBUG $(INCLUDES) -D_REENTRANT=1 -G -PIC $(SUNW_SRC) Heap-Layers/wrappers/arch-specific/sparc-interchange.il -o libhoard_32.so -lthread -ldl -lCrun + -- GitLab From 3674daac256d9fc96b88bdb4117dfdabf63fa416 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 11:40:56 +0100 Subject: [PATCH 288/911] add easyconfig for jemalloc --- .../j/jemalloc/jemalloc-3.6.0-intel-2015a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb new file mode 100644 index 0000000000..6777300bd6 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '3.6.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.canonware.com/download/jemalloc/'] +sources = [SOURCE_TAR_BZ2] + +moduleclass = 'lib' -- GitLab From 4f39459cade9f2c1db2dc4835d407290c69fbffe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 11:42:29 +0100 Subject: [PATCH 289/911] fix remark --- easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb index c1298de331..38e2d6db59 100644 --- a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://github.com/emeryberger/Hoard/releases/download/%(version)s'] sources = ['Hoard-%(version)s-source.tar.gz'] + patches = ['Hoard-%(version_major)s.x_CXX.patch'] start_dir = 'src' -- GitLab From f6d1a8065cf1fe47cf01d3e828e67a3595835171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 12:16:14 +0100 Subject: [PATCH 290/911] add custom sanity check in jemalloc easyconfig --- .../easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb index 6777300bd6..ac8c2523c3 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb @@ -12,4 +12,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://www.canonware.com/download/jemalloc/'] sources = [SOURCE_TAR_BZ2] +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.so', + 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + moduleclass = 'lib' -- GitLab From d9efa0a8d531052268ee41d1ffbae92ef92ccdf5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 13:25:17 +0100 Subject: [PATCH 291/911] arpack-ng for intel/2015a --- .../arpack-ng-3.2.0-intel-2015a-mt.eb | 23 +++++++++++++++++++ .../arpack-ng/arpack-ng-3.2.0-intel-2015a.eb | 22 ++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb new file mode 100644 index 0000000000..995ad2d16f --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.2.0' +versionsuffix = '-mt' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb new file mode 100644 index 0000000000..a7d64515a1 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.2.0' + +homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' + +sanity_check_paths = { + 'files': ["lib/libarpack.a", "lib/libarpack.so"], + 'dirs': [] +} + +moduleclass = 'numlib' -- GitLab From dd87620ede22d5237e69fc92d4a85c4bf6c9ec9b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 13:28:04 +0100 Subject: [PATCH 292/911] arpack: fix mpi version --- .../easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb index a7d64515a1..3493bc2699 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb @@ -12,7 +12,7 @@ toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] sources = ['%(version)s.tar.gz'] -configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"' +configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { 'files': ["lib/libarpack.a", "lib/libarpack.so"], -- GitLab From 21a8398c3d4529586635dea30b18feee28ee90d0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 23 Feb 2015 14:21:51 +0100 Subject: [PATCH 293/911] Copy&Paste is a bitch --- .../easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb index 995ad2d16f..5f89014f6e 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a-mt.eb @@ -7,7 +7,7 @@ versionsuffix = '-mt' homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" -toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb index 3493bc2699..9f6edb0eef 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.2.0-intel-2015a.eb @@ -6,7 +6,7 @@ version = '3.2.0' homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/' description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" -toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True} source_urls = ['https://github.com/opencollab/arpack-ng/archive/'] -- GitLab From 2a5491524d51e383b83240bb5e535ac4ffa9588f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 16:16:23 +0100 Subject: [PATCH 294/911] add easyconfig for Hadoop seagate variants with native libs --- easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb | 22 ++++++++++++++++ .../Hadoop-2.4.0-seagate-722af1-native.eb | 26 +++++++++++++++++++ .../easyconfigs/p/protobuf/protobuf-2.5.0.eb | 19 ++++++++++++++ 3 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb new file mode 100644 index 0000000000..d2b515088f --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb new file mode 100644 index 0000000000..814e2f970f --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -0,0 +1,26 @@ +name = 'Hadoop' +version = '2.4.0' +commit = '722af1' +versionsuffix = '-seagate-%s-native' % commit + +homepage = 'https://github.com/Seagate/hadoop-on-lustre2' +description = """Hadoop MapReduce for Parallel File Systems as provided by Seagate""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%s.tar.gz' % commit] +source_urls = ['https://github.com/Seagate/hadoop-on-lustre2/archive'] + +java = 'Java' +javaver = '1.7.0_40' + +builddependencies = [ + ('Maven', '3.2.3'), + ('protobuf', '2.5.0'), + ('CMake', '3.1.3'), +] +dependencies = [(java, javaver)] + +build_native_libs = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb new file mode 100644 index 0000000000..7a7091bb5e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://code.google.com/p/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GOOGLECODE_SOURCE] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 126cda77d3f0e951935669b128d35807ac1c39b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 16:27:06 +0100 Subject: [PATCH 295/911] update to latest Java dep in Hadoop easyconfig --- .../Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb | 2 +- easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb | 15 +++++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 814e2f970f..3066cf90e5 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -12,7 +12,7 @@ sources = ['%s.tar.gz' % commit] source_urls = ['https://github.com/Seagate/hadoop-on-lustre2/archive'] java = 'Java' -javaver = '1.7.0_40' +javaver = '1.7.0_76' builddependencies = [ ('Maven', '3.2.3'), diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb new file mode 100644 index 0000000000..7e3b9df3d0 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_76' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 5efce5c1211a076d7188410b590d0fa701ea8fcf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 16:39:07 +0100 Subject: [PATCH 296/911] add missing easyconfig for ncurses 5.9 with dummy toolchain --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb new file mode 100644 index 0000000000..6ab79de61f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' -- GitLab From 352e5db28d1ca8ad0527b63fb55c3e5bbfe5020c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Feb 2015 16:52:29 +0100 Subject: [PATCH 297/911] change moduleclass for Hadoop to 'tools' --- .../easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 3066cf90e5..1a2bc6a274 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -23,4 +23,4 @@ dependencies = [(java, javaver)] build_native_libs = True -moduleclass = 'devel' +moduleclass = 'tools' -- GitLab From 521153144fe0ae6326d76eae9a4ea808b33d1be2 Mon Sep 17 00:00:00 2001 From: "Dominik L. Borkowski" Date: Mon, 23 Feb 2015 21:39:52 -0500 Subject: [PATCH 298/911] add SLES11 package to openssl devel os dependency A lot of existing easyconfigs used 'openssl-devel' and 'libssl-dev' under osdependencies to indicate the need to have development files for openssl. SLES 11 uses 'libopenssl-devel', so we add that as a third option. --- easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.40.0-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.40.0-intel-2015a.eb | 2 +- .../easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb | 2 +- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 2 +- .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 2 +- 56 files changed, 56 insertions(+), 56 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb index 3b257ff22b..90466f7075 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2014b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] #dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb index 044a3da83e..82fe8da72a 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-intel-2015a.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] #dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-GCC-4.9.2.eb index 7009ac53e5..c62cc48307 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-GCC-4.9.2.eb @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] # dependencies = [('OpenSSL', '1.0.1k')] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # configopts = "--with-ssl=$EBROOTOPENSSL" diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb index a8c7d1b972..f28780066a 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-foss-2015a.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] sanity_check_paths = { 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-intel-2015a.eb index 7a5f70d693..c9c8c7db48 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.40.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.40.0-intel-2015a.eb @@ -18,7 +18,7 @@ source_urls = ['http://curl.haxx.se/download/'] # dependencies = [('OpenSSL', '1.0.1k')] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # configopts = "--with-ssl=$EBROOTOPENSSL" diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb index 39773d3294..b14d94df84 100644 --- a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.20-intel-2014b-clientonly.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] dependencies = [ ('libevent', '2.0.21'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index 279bdd8c99..a0f450f70f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index f9f346f7bc..53b6064132 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index 66cb466a25..ed1944c3f2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index 781b45ed3f..d9118da106 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index c8bc196270..da9bd1c2a4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -21,6 +21,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index 79512f826c..ae0e9d0e08 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index f949db90c2..6d976f526f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 09f3055b4f..1634c92386 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 42193d47f3..9da359d558 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index 1afb913fc7..1f7939f4ae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index e06519fa69..ad3be578b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index d2a397a75d..87842fb428 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 911d601c84..2831a2cc23 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index fc55e54136..b776fb0b02 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index ddb8cca034..78603dc07b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index 30918d38a9..ed4e0133ca 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 4134226fe7..05b7c9748b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 3674e8503a..aa705e3789 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index c79f20595e..5ff8d51fe5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 35b2b5b200..b5fe2d5275 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 7aebaedcf4..811713df94 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 664ee1f1a8..130b9064da 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index bc49ef2fca..3b99a9a692 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 0c368fb252..b1cf4f2c33 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index 9bb670b9f9..61bbf93bff 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 50f7775759..4702e95c66 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 2ddde79dbd..6b7e21c3ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index f1a9ed5672..50bb8eaa10 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 1fba318bda..d5bc39c85f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -26,7 +26,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index f9fa5f9c80..ab16192e19 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index d5ea67a210..8450ef1ade 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index ad9bec4d24..84e3eb01be 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 727caedb4d..8fc41a9000 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 7c555315ab..e1f4863c86 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -28,7 +28,7 @@ dependencies = [ # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # Version updated 08/JULY/2014 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 606015815c..37561dbbd7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # Version updated 08/JULY/2014 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 8f5509ad1f..ad901ece9f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -97,6 +97,6 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 3ee92cdc84..0c37e9ea68 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -21,7 +21,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # bare installation: no extensions included exts_list = [] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index ddcd75ee83..ee34812203 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Jan 19th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 583d5df7db..2d2b758eb9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -19,6 +19,6 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 295a215baa..51b20dc349 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Jan 19th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2a6be35eb..b906a68722 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -21,7 +21,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # bare installation: no extensions included exts_list = [] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index f686a45b8c..9107501405 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # package versions updated Jan 19th 2015 diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 5908968a8a..ff366c2d52 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index f3672941f6..1a46862919 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index 46621b251d..bfaa166f08 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 202bdb8ade..92a41bf7e7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index ccb66beda5..c462546fe3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -22,7 +22,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index b8c6c3ff36..51dd82cdf9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index 9f533cb4ea..f1f4f3af6b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index aa223ede51..648a65cc92 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -25,7 +25,7 @@ dependencies = [ # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! # Version updated 08/JULY/2014 -- GitLab From 16827a044da6d84ab2e2e5ba550b52a52a9b2573 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 24 Feb 2015 14:10:37 +0100 Subject: [PATCH 299/911] added perl as a build dependency for parallel --- .../p/Parallel/Parallel-20141122-GCC-4.9.2.eb | 4 ++++ .../parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb | 10 +++++++--- .../p/parallel/parallel-20130122-goolf-1.4.10.eb | 10 +++++++--- .../p/parallel/parallel-20130122-ictce-4.0.6.eb | 10 +++++++--- .../p/parallel/parallel-20130122-ictce-5.3.0.eb | 11 +++++++---- 5 files changed, 32 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb index 370f2c2b26..d9ace2eab9 100644 --- a/easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb @@ -11,6 +11,10 @@ source_urls = ['http://ftp.gnu.org/gnu/parallel'] toolchain = {'name': 'GCC', 'version': '4.9.2'} +builddependencies = [ + ('Perl', '5.20.1', '-bare'), # required for pod2man +] + sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb index cfd2944d18..775324e831 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb @@ -23,9 +23,13 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +builddependencies = [ + ('Perl', '5.20.1', '-bare'), # required for pod2man +] + sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] - } + 'files': ['bin/parallel'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb index dc28a0e211..2fbe84589d 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb @@ -21,11 +21,15 @@ description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] +builddependencies = [ + ('Perl', '5.20.1', '-bare'), # required for pod2man +] + toolchain = {'name': 'goolf', 'version': '1.4.10'} sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] - } + 'files': ['bin/parallel'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb index 355352cf8e..14b3713165 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -23,9 +23,13 @@ source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} +builddependencies = [ + ('Perl', '5.20.1', '-bare'), # required for pod2man +] + sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] - } + 'files': ['bin/parallel'], + 'dirs': [] +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb index a00d8552bf..a8c81fe5d4 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb @@ -21,12 +21,15 @@ description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] - toolchain = {'name': 'ictce', 'version': '5.3.0'} +builddependencies = [ + ('Perl', '5.20.1', '-bare'), # required for pod2man +] + sanity_check_paths = { - 'files': ['bin/parallel'], - 'dirs': [] - } + 'files': ['bin/parallel'], + 'dirs': [] +} moduleclass = 'tools' -- GitLab From 4b09258328a23b65c862e24965a962a1cba811aa Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 24 Feb 2015 14:31:37 +0100 Subject: [PATCH 300/911] moved Parallel to parallel --- .../parallel-20141122-GCC-4.9.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/{Parallel/Parallel-20141122-GCC-4.9.2.eb => parallel/parallel-20141122-GCC-4.9.2.eb} (100%) diff --git a/easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb similarity index 100% rename from easybuild/easyconfigs/p/Parallel/Parallel-20141122-GCC-4.9.2.eb rename to easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb -- GitLab From 16f4d473216c701109a9e07b43c5f68dae048961 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 24 Feb 2015 15:20:36 +0100 Subject: [PATCH 301/911] actually, parallel is a perl script, so it's more then a build dependency --- .../p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb | 4 ++-- .../easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb index 775324e831..07a89393a8 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb @@ -23,7 +23,7 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -builddependencies = [ +dependencies = [ ('Perl', '5.20.1', '-bare'), # required for pod2man ] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb index 2fbe84589d..978e1f0baf 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb @@ -21,8 +21,8 @@ description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] -builddependencies = [ - ('Perl', '5.20.1', '-bare'), # required for pod2man +dependencies = [ + ('Perl', '5.20.1', '-bare'), ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb index 14b3713165..73c8501eb4 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -23,8 +23,8 @@ source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} -builddependencies = [ - ('Perl', '5.20.1', '-bare'), # required for pod2man +dependencies = [ + ('Perl', '5.20.1', '-bare'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb index a8c81fe5d4..1e2ee3feeb 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb @@ -23,8 +23,8 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} -builddependencies = [ - ('Perl', '5.20.1', '-bare'), # required for pod2man +dependencies = [ + ('Perl', '5.20.1', '-bare'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb index d9ace2eab9..58e05fec2b 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb @@ -11,8 +11,8 @@ source_urls = ['http://ftp.gnu.org/gnu/parallel'] toolchain = {'name': 'GCC', 'version': '4.9.2'} -builddependencies = [ - ('Perl', '5.20.1', '-bare'), # required for pod2man +dependencies = [ + ('Perl', '5.20.1', '-bare'), ] sanity_check_paths = { -- GitLab From d4ad7234491642639a8f41259dcaf0f5a9d2ae58 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 25 Feb 2015 11:54:22 +0100 Subject: [PATCH 302/911] changed perl version to older perl where you had one, left older (broken?) easyconfigs where we have no perl for the toolchain the way there were --- .../p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb | 4 ---- .../p/parallel/parallel-20130122-goolf-1.4.10.eb | 2 +- .../p/parallel/parallel-20130122-ictce-4.0.6.eb | 4 ---- .../p/parallel/parallel-20130122-ictce-5.3.0.eb | 2 +- .../easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb | 7 ++++--- 5 files changed, 6 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb index 07a89393a8..ff68a75587 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb @@ -23,10 +23,6 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -dependencies = [ - ('Perl', '5.20.1', '-bare'), # required for pod2man -] - sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb index 978e1f0baf..59543e9cd3 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb @@ -22,7 +22,7 @@ sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] dependencies = [ - ('Perl', '5.20.1', '-bare'), + ('Perl', '5.16.3', '-bare'), ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb index 73c8501eb4..6286cb7ed1 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -23,10 +23,6 @@ source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} -dependencies = [ - ('Perl', '5.20.1', '-bare'), -] - sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb index 1e2ee3feeb..268bcb3414 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb @@ -24,7 +24,7 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ - ('Perl', '5.20.1', '-bare'), + ('Perl', '5.16.3', '-bare'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb index 58e05fec2b..65d2e1f27b 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb @@ -11,9 +11,10 @@ source_urls = ['http://ftp.gnu.org/gnu/parallel'] toolchain = {'name': 'GCC', 'version': '4.9.2'} -dependencies = [ - ('Perl', '5.20.1', '-bare'), -] +# warning, parallel is a perl script and should depend on perl +# dependencies = [ +# ('Perl', '5.20.1', '-bare'), +#] sanity_check_paths = { 'files': ['bin/parallel'], -- GitLab From 8b28742fa7d4d577b9bdbdeb4527b37f9c1b7549 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 25 Feb 2015 12:14:20 +0100 Subject: [PATCH 303/911] parallel has lowercase p --- easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb index 65d2e1f27b..e9be3039e9 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'Parallel' +name = 'parallel' version = '20141122' homepage = 'http://savannah.gnu.org/projects/parallel/' -- GitLab From 5d81fce68288b804bb5c576e1ea8d8c3ff13dcf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Feb 2015 17:08:04 +0100 Subject: [PATCH 304/911] add missing Perl deps for parallel easyconfigs --- .../Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb | 16 ++++++++++++++++ .../p/Perl/Perl-5.16.3-goolf-1.4.10-bare.eb | 4 ++-- .../p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb | 18 ++++++++++++++++++ .../p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb | 6 ++++-- .../p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb | 2 ++ .../p/Perl/Perl-5.20.1-GCC-4.9.2-bare.eb | 19 +++++++++++++++++++ .../parallel-20130122-goalf-1.1.0-no-OFED.eb | 6 +++++- .../parallel-20130122-goolf-1.4.10.eb | 4 ++-- .../parallel/parallel-20130122-ictce-4.0.6.eb | 6 +++++- .../parallel/parallel-20130122-ictce-5.3.0.eb | 4 ++-- .../p/parallel/parallel-20141122-GCC-4.9.2.eb | 11 +++++------ 11 files changed, 80 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.9.2-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb new file mode 100644 index 0000000000..c5a2760a68 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goalf-1.1.0-no-OFED-bare.eb @@ -0,0 +1,16 @@ +name = 'Perl' +version = '5.16.3' +versionsuffix = "-bare" + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goolf-1.4.10-bare.eb index af7ea2a52c..b0a376e62e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goolf-1.4.10-bare.eb @@ -1,5 +1,6 @@ name = 'Perl' version = '5.16.3' +versionsuffix = "-bare" homepage = 'http://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language""" @@ -9,8 +10,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] -runtest = 'test' -versionsuffix = "-bare" +runtest = 'test' moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb new file mode 100644 index 0000000000..9e108b5b00 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb @@ -0,0 +1,18 @@ +name = 'Perl' +version = '5.16.3' +versionsuffix = "-bare" + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['exitcode_error.patch'] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb index 0c3f3f991c..63c4aa7e73 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.1.13-bare.eb @@ -1,16 +1,18 @@ name = 'Perl' version = '5.16.3' +versionsuffix = "-bare" homepage = 'http://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language""" + toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.cpan.org/src/5.0'] sources = [SOURCELOWER_TAR_GZ] + patches = ['exitcode_error.patch'] -runtest = 'test' -versionsuffix = "-bare" +runtest = 'test' moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb index df13383ba5..5d0f51129b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.8.2-bare.eb @@ -14,4 +14,6 @@ sources = [SOURCELOWER_TAR_GZ] # bare, no extensions exts_list = [] +runtest = 'test' + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000..331ab4d45f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.1-GCC-4.9.2-bare.eb @@ -0,0 +1,19 @@ +name = 'Perl' +version = '5.20.1' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb index ff68a75587..3804c6ccaa 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb @@ -18,10 +18,14 @@ version = '20130122' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +dependencies = [ + ('Perl', '5.16.3', '-bare'), +] sanity_check_paths = { 'files': ['bin/parallel'], diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb index 59543e9cd3..3810b2de94 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb @@ -18,6 +18,8 @@ version = '20130122' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] @@ -25,8 +27,6 @@ dependencies = [ ('Perl', '5.16.3', '-bare'), ] -toolchain = {'name': 'goolf', 'version': '1.4.10'} - sanity_check_paths = { 'files': ['bin/parallel'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb index 6286cb7ed1..df8ba6abaf 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -18,10 +18,14 @@ version = '20130122' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" +toolchain = {'version': '4.0.6', 'name': 'ictce'} + sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] -toolchain = {'version': '4.0.6', 'name': 'ictce'} +dependencies = [ + ('Perl', '5.16.3', '-bare'), +] sanity_check_paths = { 'files': ['bin/parallel'], diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb index 268bcb3414..fc4fbe41bc 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb @@ -18,11 +18,11 @@ version = '20130122' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] -toolchain = {'name': 'ictce', 'version': '5.3.0'} - dependencies = [ ('Perl', '5.16.3', '-bare'), ] diff --git a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb index e9be3039e9..87af6fceee 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20141122-GCC-4.9.2.eb @@ -6,15 +6,14 @@ version = '20141122' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/parallel'] -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -# warning, parallel is a perl script and should depend on perl -# dependencies = [ -# ('Perl', '5.20.1', '-bare'), -#] +dependencies = [ + ('Perl', '5.20.1', '-bare'), +] sanity_check_paths = { 'files': ['bin/parallel'], -- GitLab From 4c9dff5e212778d7e2482e7b09edb044c6c8f6f4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 20:46:53 +0100 Subject: [PATCH 305/911] Added PSI4 git rev 3815c4672b2 --- .../PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch | 115 ++++++++++++++++++ .../PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb | 29 +++++ 2 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch new file mode 100644 index 0000000000..c756debf48 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch @@ -0,0 +1,115 @@ +# fixes the order in which libs get linked in the final executable +# if the order is wrong, you will get linking errors +diff -ur psi4public-3815c4672b20557818d653694ff2cb5c78819708.org/src/lib/libPsiUtil/CMakeLists.txt psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/lib/libPsiUtil/CMakeLists.txt +--- psi4public-3815c4672b20557818d653694ff2cb5c78819708.org/src/lib/libPsiUtil/CMakeLists.txt 2015-02-18 19:36:31.000000000 +0100 ++++ psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/lib/libPsiUtil/CMakeLists.txt 2015-02-26 10:36:56.000000000 +0100 +@@ -1,21 +1,41 @@ +-set(SRC ProgressBar.h +- PsiMap.h +- PsiRdmNumGen.h +- PythonFxn.h +- Timer.h +- Units.h +- AtomicData.h +- Implementations/UnitsGuts.hh +- Implementations/PrefixConverter.cc +- Implementations/Timer.cc +- Implementations/BaseUnitConverter.cc +- Implementations/PythonFxnGuts.cc +- Implementations/AtomicData.cc +- Implementations/ProgressBar.cc +-) +-add_library(PsiUtil ${SRC}) ++set(headers_list "") ++# List of headers ++list(APPEND ProgressBar.h PsiMap.h PsiRdmNumGen.h PythonFxn.h Timer.h Units.h AtomicData.h Implementations/UnitsGuts.hh ) ++ ++# If you want to remove some headers specify them explictly here ++if(DEVELOPMENT_CODE) ++ list(REMOVE_ITEM headers_list "") ++else() ++ list(REMOVE_ITEM headers_list "") ++endif() ++# Sort alphabetically ++list(SORT headers_list) ++ ++set(sources_list "") ++# List of sources ++list(APPEND sources_list Implementations/PrefixConverter.cc Implementations/Timer.cc Implementations/BaseUnitConverter.cc Implementations/PythonFxnGuts.cc Implementations/AtomicData.cc Implementations/ProgressBar.cc ) ++ ++# If you want to remove some sources specify them explictly here ++if(DEVELOPMENT_CODE) ++ list(REMOVE_ITEM sources_list "") ++else() ++ list(REMOVE_ITEM sources_list "") ++endif() ++ ++# Write list of files to be passed to cloc for counting lines of code. ++# Only files that are actually compiled are counted. ++set(to_count "${sources_list}" "${headers_list}") ++write_to_cloc_list("${to_count}") ++ ++# Build static library ++add_library(PsiUtil STATIC ${sources_list}) ++# Specify dependencies for the library (if any) + add_dependencies(PsiUtil parallel2) +-include_directories(libparallel2) ++set(libs_to_merge PsiUtil ${libs_to_merge} PARENT_SCOPE) + if(BUILD_CUSTOM_BOOST) + add_dependencies(PsiUtil custom_boost) + endif() ++install(TARGETS PsiUtil ARCHIVE DESTINATION lib) ++ ++# Sets install directory for all the headers in the list ++install_list_FILES("${headers_list}" include/libPsiUtil) +diff --git a/CMakeLists.txt b/CMakeLists.txt +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -203,8 +203,12 @@ if(NOT LIBINT_OPT_AM) + set(LIBINT_OPT_AM 5) + endif() + ++get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) ++set(include_dir_externals ${dirs}) ++ + # Psi4-specific includes and libraries + set(CMAKE_INCLUDE_CURRENT_DIR ON) ++ + include_directories( + ${PROJECT_BINARY_DIR}/include + ${PROJECT_SOURCE_DIR}/include +@@ -225,7 +229,8 @@ set(PSILIB mints_wrapper dfmp2 dfocc scf ccenergy ccsort psimrcc transqt2 + cchbar cclambda ccdensity transqt ccresponse detci occ mrcc fnocc + cceom adc thermo functional disp thce 3index deriv_wrapper optking + findif mints trans dpd chkpt iwl psio qt ciomr options moinfo psi4util +- stable deriv scfgrad int diis plugin parallel parallel2 babel frag efp_solver efp) ++ stable deriv scfgrad int diis plugin parallel parallel2 babel frag efp_solver efp ++ parallel parallel2 PsiUtil) + + # PCMSolver + if(ENABLE_PCMSOLVER) +@@ -303,9 +308,11 @@ add_subdirectory(lib) + # Handle creation of Makefile for plugins + get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) + get_property(defs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY COMPILE_DEFINITIONS) +-foreach(dir ${dirs}) ++foreach(dir ${include_dir_externals}) + set(PLUGIN_INCLUDE_DIRECTORIES "-I${dir} ${PLUGIN_INCLUDE_DIRECTORIES}") + endforeach() ++set(PLUGIN_INCLUDE_DIRECTORIES "-I$ENV{PSI_SRC_INSTALL_DIR}/include -I$ENV{PSI_SRC_INSTALL_DIR}/src/lib/ -I$ENV{PSI_OBJ_INSTALL_DIR}/include -I$ENV{PSI_OBJ_INSTALL_DIR}/src/lib/ ${PLUGIN_INCLUDE_DIRECTORIES}") ++ + foreach(def ${defs}) + set(PLUGIN_DEFINES "-D${def} ${PLUGIN_DEFINES}") + endforeach() +diff --git a/include/psiconfig.h.cmake.in b/include/psiconfig.h.cmake.in +--- a/include/psiconfig.h.cmake.in ++++ b/include/psiconfig.h.cmake.in +@@ -20,7 +20,7 @@ + #define PLUGIN_DEFINES "@PLUGIN_DEFINES@" + #define PLUGIN_FLAGS "@CXX_FLAGS_PLUGIN@" + #define PLUGIN_INCLUDES "@PLUGIN_INCLUDE_DIRECTORIES@" +-#define PLUGIN_OBJDIR "@PROJECT_BINARY_DIR@" ++#define PLUGIN_OBJDIR "@CMAKE_INSTALL_PREFIX@/obj" + + /* The PSI4 Datadir */ + #define INSTALLEDPSIDATADIR "@CMAKE_INSTALL_PREFIX@/share/psi" diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb new file mode 100644 index 0000000000..3cdeb9cb5e --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb @@ -0,0 +1,29 @@ +name = 'PSI' +commit = '3815c4672b2' +version = '4.0b6-%s' % commit +versionsuffix = '-mt' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/psi4/psi4public/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['PSI-%(version)s-fix-cmake.patch'] + +python = 'Python' +pyver = '2.7.9' + +dependencies = [ + (python, pyver), + ('Boost', '1.57.0', '-%s-%s' % (python, pyver)), +] + +builddependencies = [('CMake', '3.1.3', '', ('GCC', '4.9.2'))] + +moduleclass = 'chem' -- GitLab From 958518448e8bccfaea7f72630a19e96106a4da50 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:01:47 +0100 Subject: [PATCH 306/911] CMake 3.1.3 --- .../c/CMake/CMake-3.1.3-GCC-4.9.2.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb new file mode 100644 index 0000000000..674ad2c737 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From c1454f5a5400940e40bd0a5bd9235b84ca8c2236 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:36:06 +0100 Subject: [PATCH 307/911] Added patch for zlib to detect icc --- .../easyconfigs/z/zlib/zlib-detected-icc.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch diff --git a/easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch b/easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch new file mode 100644 index 0000000000..7fc52f886b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch @@ -0,0 +1,13 @@ +# the configure script doesn't know that icc is equivalent +# with gcc +--- configure.orig 2015-02-26 21:32:25.239440052 +0100 ++++ configure 2015-02-26 21:31:53.238819720 +0100 +@@ -100,7 +100,7 @@ + cflags=${CFLAGS-"-O3"} + # to force the asm version use: CFLAGS="-O3 -DASMV" ./configure + case "$cc" in +- *gcc*) gcc=1 ;; ++ *gcc* | *icc* ) gcc=1 ;; + esac + + if test "$gcc" -eq 1 && ($cc -c $cflags $test.c) 2>/dev/null; then -- GitLab From f7b8d576a70e0c5da1379141326d00b272e70d70 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:38:44 +0100 Subject: [PATCH 308/911] Add icc patch to selected zlib versions --- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb | 2 ++ easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb | 2 ++ easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb | 2 ++ easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb | 3 ++- easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb | 2 ++ easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb | 2 ++ easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb | 2 ++ 7 files changed, 14 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb index 8eedf49cf6..d733aaf922 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb index 1bcd57dece..03bd01986c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb index 4a778d2bba..b90ca21c08 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb index 46d721cc9d..e6c3a85399 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb @@ -8,13 +8,14 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb index 2135132db6..ba51d59fe5 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb index 719603c67b..57c8954b85 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb index 8f93afc07c..e130029888 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 475aa59e21dfc8abafe06a9ccf2a043a1f207d76 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:47:17 +0100 Subject: [PATCH 309/911] Added and moved patch for zlib --- ...etected-icc.patch => zlib-1.2.5-detected-icc.patch} | 0 .../easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch | 10 ++++++++++ 2 files changed, 10 insertions(+) rename easybuild/easyconfigs/z/zlib/{zlib-detected-icc.patch => zlib-1.2.5-detected-icc.patch} (100%) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch diff --git a/easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-detected-icc.patch similarity index 100% rename from easybuild/easyconfigs/z/zlib/zlib-detected-icc.patch rename to easybuild/easyconfigs/z/zlib/zlib-1.2.5-detected-icc.patch diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch new file mode 100644 index 0000000000..6c1524262e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch @@ -0,0 +1,10 @@ +--- configure.orig 2012-05-02 06:17:08.000000000 +0200 ++++ configure 2015-02-26 21:46:25.275559445 +0100 +@@ -174,6 +174,7 @@ + case "$cc" in + *gcc*) gcc=1 ;; + *clang*) gcc=1 ;; ++ *icc*) gcc=1 ;; + esac + case `$cc -v 2>&1` in + *gcc*) gcc=1 ;; -- GitLab From 87ebe23a6b945bb68dd8a0bb8314bc21c6193d7c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:49:24 +0100 Subject: [PATCH 310/911] Use correct version of patch in zlib --- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb index d733aaf922..d01a7f9d72 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-3.2.2.u3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb index 03bd01986c..69d5b76957 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.0.6.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb index b90ca21c08..47b80f9b8b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-4.1.13.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb index e6c3a85399..a0237792fe 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb index ba51d59fe5..b0a946a39d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-3.2.2.u3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb index 57c8954b85..34070b60f4 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-iqacml-3.7.3.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], -- GitLab From e0084f1ea380b0ea297c313966a9cc266cfd3f7d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 21:51:57 +0100 Subject: [PATCH 311/911] Added comment in patch --- easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch index 6c1524262e..f94b26caee 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-detected-icc.patch @@ -1,3 +1,5 @@ +# the configure script doesn't know that icc is equivalent +# with gcc --- configure.orig 2012-05-02 06:17:08.000000000 +0200 +++ configure 2015-02-26 21:46:25.275559445 +0100 @@ -174,6 +174,7 @@ -- GitLab From 8839e9944a1ff4a92dfc980a06b6c8769237c2df Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 22:28:45 +0100 Subject: [PATCH 312/911] Add git version to exec --- .../p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch index c756debf48..ab31858bd0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch @@ -113,3 +113,13 @@ diff --git a/include/psiconfig.h.cmake.in b/include/psiconfig.h.cmake.in /* The PSI4 Datadir */ #define INSTALLEDPSIDATADIR "@CMAKE_INSTALL_PREFIX@/share/psi" +diff -ur psi4public-3815c4672b20557818d653694ff2cb5c78819708.orig/src/bin/psi4/gitversion.py.in psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/bin/psi4/gitversion.py.in +--- psi4public-3815c4672b20557818d653694ff2cb5c78819708.orig/src/bin/psi4/gitversion.py.in 2015-02-18 19:36:31.000000000 +0100 ++++ psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/bin/psi4/gitversion.py.in 2015-02-26 22:27:18.000000000 +0100 +@@ -47,4 +47,6 @@ + except: + branch = "detached?" + ++version = "3815c4672b2055" ++branch = "master" + write_version(version, branch) -- GitLab From 45ffb7a9ef1c6bb6b91a6b7d34d54848a27bfa55 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 26 Feb 2015 22:30:53 +0100 Subject: [PATCH 313/911] Fix error in zlib-1.2.8-iqacml-3.7.3 Doesn't need the patch, I hope? --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb index e130029888..8f93afc07c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -patches = ['zlib-detected-icc.patch'] - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From f9afb3717bb357c63e6d7d8690c62e515962213f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Feb 2015 10:22:11 +0100 Subject: [PATCH 314/911] speed up unit tests by switching to fetch_parameters_from_easyconfig --- test/easyconfigs/easyconfigs.py | 12 ++++-------- test/easyconfigs/suite.py | 3 +++ 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0dac782165..20c3cab4f7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -43,8 +43,9 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig, fetch_parameter_from_easyconfig_file +from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig from easybuild.framework.easyconfig.easyconfig import get_easyblock_class +from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config from easybuild.tools.module_naming_scheme import GENERAL_CLASS @@ -60,9 +61,6 @@ single_tests_ok = True class EasyConfigTest(TestCase): """Baseclass for easyconfig testcases.""" - if LooseVersion(sys.version) >= LooseVersion('2.6'): - os.environ['EASYBUILD_DEPRECATED'] = '2.0' - # initialize configuration (required for e.g. default modules_tool setting) eb_go = eboptions.parse_options() config.init(eb_go.options, eb_go.get_options_by_section('config')) @@ -221,13 +219,11 @@ def template_easyconfig_test(self, spec): msg = "Filename '%s' of parsed easconfig matches expected filename '%s'" % (spec, expected_fn) self.assertEqual(os.path.basename(spec), expected_fn, msg) + name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) + # sanity check for software name - name = fetch_parameter_from_easyconfig_file(spec, 'name') self.assertTrue(ec['name'], name) - # try and fetch easyblock spec from easyconfig - easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock') - # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index f936405be6..65497da038 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -45,6 +45,9 @@ import test.easyconfigs.easyconfigs as e fancylogger.disableDefaultHandlers() fancylogger.setLogLevelError() +# make sure no deprecated behaviour is triggered +os.environ['EASYBUILD_DEPRECATED'] = '10000' + os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') # call suite() for each module and then run them all -- GitLab From 46bd43ccbc4bd149c53f370fdc369973a68f1c56 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 11:47:01 +0100 Subject: [PATCH 315/911] Added icc patch to iqacml build of zlib --- easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb index 8f93afc07c..c0491f7dc7 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-iqacml-3.7.3.eb @@ -14,6 +14,8 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +patches = ['zlib-1.2.7-detected-icc.patch'] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 9813262abbe04ded936b30c01875db935336489a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 15:22:09 +0100 Subject: [PATCH 316/911] GDB 7.9 for GCC/4.9.2 --- .../easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb new file mode 100644 index 0000000000..a1ba41f0f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.9' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [('ncurses', '5.9')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' -- GitLab From e9c91700a6e47f9416d59665658ebf2914104a49 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 17:22:02 +0100 Subject: [PATCH 317/911] Renamed PSI easyconfig from git commit to date --- ...c4672b2-fix-cmake.patch => PSI-4.0b6-20150218-fix-cmake.patch} | 0 ...2b2-intel-2015a-mt.eb => PSI-4.0b6-20150218-intel-2015a-mt.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b6-3815c4672b2-fix-cmake.patch => PSI-4.0b6-20150218-fix-cmake.patch} (100%) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb => PSI-4.0b6-20150218-intel-2015a-mt.eb} (100%) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-fix-cmake.patch rename to easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-fix-cmake.patch diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb similarity index 100% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b6-3815c4672b2-intel-2015a-mt.eb rename to easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb -- GitLab From a31b8b26bdf5c018ffbf963261b0fae8d674c8ec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 17:23:18 +0100 Subject: [PATCH 318/911] And now with the actual file included --- .../easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb index 3cdeb9cb5e..6cb0e25154 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb @@ -1,6 +1,6 @@ name = 'PSI' -commit = '3815c4672b2' -version = '4.0b6-%s' % commit +commit = '' +version = '4.0b6-20150218' versionsuffix = '-mt' homepage = 'http://www.psicode.org/' @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': False} source_urls = ['https://github.com/psi4/psi4public/archive/'] -sources = ['%s.tar.gz' % commit] +sources = ['3815c4672b2.tar.gz'] patches = ['PSI-%(version)s-fix-cmake.patch'] -- GitLab From 6a7248d574621f340e592cae0b8b2bdd1927e2aa Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 17:23:52 +0100 Subject: [PATCH 319/911] Delete unneeded line --- easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb index 6cb0e25154..2aefad5fbc 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb @@ -1,5 +1,4 @@ name = 'PSI' -commit = '' version = '4.0b6-20150218' versionsuffix = '-mt' -- GitLab From c8c9ffbde0b7fbca00828f79e9b3be395636e1a0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 21:47:23 +0100 Subject: [PATCH 320/911] Fix files for Clang 3.6 --- easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 1fa4fc4b47..138e25fb82 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -23,10 +23,10 @@ toolchainopts = {'optarch': False} source_urls = ["http://llvm.org/releases/%(version)s"] sources = [ - "llvm-%(version)src2.src.tar.xz", - "cfe-%(version)src2.src.tar.xz", - "compiler-rt-%(version)src2.src.tar.xz", - "polly-%(version)src2.src.tar.xz", + "llvm-%(version).src.tar.xz", + "cfe-%(version).src.tar.xz", + "compiler-rt-%(version).src.tar.xz", + "polly-%(version).src.tar.xz", ] builddependencies = [('CMake', '3.1.3')] -- GitLab From ebb344e4118c23574f1c01d4cfe539b8a27341ba Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 27 Feb 2015 22:08:09 +0100 Subject: [PATCH 321/911] Fix typo --- easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 138e25fb82..5be4ff6781 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -23,10 +23,10 @@ toolchainopts = {'optarch': False} source_urls = ["http://llvm.org/releases/%(version)s"] sources = [ - "llvm-%(version).src.tar.xz", - "cfe-%(version).src.tar.xz", - "compiler-rt-%(version).src.tar.xz", - "polly-%(version).src.tar.xz", + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", ] builddependencies = [('CMake', '3.1.3')] -- GitLab From 09f072b119b1d56782a54001a013969c66d2aa58 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 28 Feb 2015 14:05:31 +0100 Subject: [PATCH 322/911] Changed CMake from GCC to intel toolchain --- .../c/CMake/CMake-3.1.3-intel-2015a.eb | 22 +++++++++++++++++++ .../PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2015a.eb new file mode 100644 index 0000000000..be08430cf4 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb index 2aefad5fbc..b55af44caa 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb @@ -23,6 +23,6 @@ dependencies = [ ('Boost', '1.57.0', '-%s-%s' % (python, pyver)), ] -builddependencies = [('CMake', '3.1.3', '', ('GCC', '4.9.2'))] +builddependencies = [('CMake', '3.1.3')] moduleclass = 'chem' -- GitLab From 0e7a24598d5702b26107aa33ebad03dd409aa3e5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 1 Mar 2015 18:52:22 +0100 Subject: [PATCH 323/911] Newer git version of PSI4 Fixes serveral issues --- ...tch => PSI-4.0b6-20150228-fix-cmake.patch} | 65 +++++++++++++++---- ...b => PSI-4.0b6-20150228-intel-2015a-mt.eb} | 4 +- 2 files changed, 56 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b6-20150218-fix-cmake.patch => PSI-4.0b6-20150228-fix-cmake.patch} (68%) rename easybuild/easyconfigs/p/PSI/{PSI-4.0b6-20150218-intel-2015a-mt.eb => PSI-4.0b6-20150228-intel-2015a-mt.eb} (89%) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch similarity index 68% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-fix-cmake.patch rename to easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch index ab31858bd0..9035ed8df9 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-fix-cmake.patch +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch @@ -78,16 +78,6 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt include_directories( ${PROJECT_BINARY_DIR}/include ${PROJECT_SOURCE_DIR}/include -@@ -225,7 +229,8 @@ set(PSILIB mints_wrapper dfmp2 dfocc scf ccenergy ccsort psimrcc transqt2 - cchbar cclambda ccdensity transqt ccresponse detci occ mrcc fnocc - cceom adc thermo functional disp thce 3index deriv_wrapper optking - findif mints trans dpd chkpt iwl psio qt ciomr options moinfo psi4util -- stable deriv scfgrad int diis plugin parallel parallel2 babel frag efp_solver efp) -+ stable deriv scfgrad int diis plugin parallel parallel2 babel frag efp_solver efp -+ parallel parallel2 PsiUtil) - - # PCMSolver - if(ENABLE_PCMSOLVER) @@ -303,9 +308,11 @@ add_subdirectory(lib) # Handle creation of Makefile for plugins get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) @@ -120,6 +110,59 @@ diff -ur psi4public-3815c4672b20557818d653694ff2cb5c78819708.orig/src/bin/psi4/g except: branch = "detached?" -+version = "3815c4672b2055" ++version = "14c78eabdca86f8e094576890518d93d300d2500" +branch = "master" write_version(version, branch) +diff --git a/doc/sphinxman/CMakeLists.txt b/doc/sphinxman/CMakeLists.txt +--- a/doc/sphinxman/CMakeLists.txt ++++ b/doc/sphinxman/CMakeLists.txt +@@ -256,6 +256,24 @@ if(PERL_FOUND AND SPHINX_FOUND) + add_custom_target(sphinxpdf + DEPENDS sphinxman + COMMENT "Preparing Sphinx HTML and PDF documentation build") ++ ++ # * full, proper build with latex builder ++ add_custom_command( ++ TARGET sphinxpdf POST_BUILD ++ COMMAND ${SPHINX_EXECUTABLE} ++ -b latex # builder ++ -d ${CCBD}/_doctrees # cache w/ pickled reST ++ -c ${CCBD}/source # whereabouts of conf.py ++ ${CCBD}/source # build from ++ ${CCBD}/latex # build to ++ COMMENT "Building latex documentation ...") ++ add_custom_command( ++ TARGET sphinxpdf POST_BUILD ++ COMMAND ${PDFLATEX_COMPILER} ++ -interaction=nonstopmode ++ "Psi4.tex" > /dev/null 2>&1 ++ WORKING_DIRECTORY ${CCBD}/latex ++ COMMENT "Building remarkably ugly PDF documentation from LaTeX ... (ignore the make exit error)") + endif() + + +@@ -295,24 +313,5 @@ if(PERL_FOUND AND SPHINX_FOUND) + ${CCBD}/html + COMMENT "Building abridged html documentation ...") + +- # * full, proper build with latex builder +- add_custom_command( +- TARGET sphinxpdf POST_BUILD +- COMMAND ${SPHINX_EXECUTABLE} +- -b latex # builder +- -d ${CCBD}/_doctrees # cache w/ pickled reST +- -c ${CCBD}/source # whereabouts of conf.py +- ${CCBD}/source # build from +- ${CCBD}/latex # build to +- COMMENT "Building latex documentation ...") +- add_custom_command( +- TARGET sphinxpdf POST_BUILD +- COMMAND ${PDFLATEX_COMPILER} +- -interaction=nonstopmode +- "Psi4.tex" > /dev/null 2>&1 +- WORKING_DIRECTORY ${CCBD}/latex +- COMMENT "Building remarkably ugly PDF documentation from LaTeX ... (ignore the make exit error)") +- +- + endif(PERL_FOUND AND SPHINX_FOUND) + diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb similarity index 89% rename from easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb rename to easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index b55af44caa..160241465f 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150218-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -1,5 +1,5 @@ name = 'PSI' -version = '4.0b6-20150218' +version = '4.0b6-20150228' versionsuffix = '-mt' homepage = 'http://www.psicode.org/' @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'usempi': False} source_urls = ['https://github.com/psi4/psi4public/archive/'] -sources = ['3815c4672b2.tar.gz'] +sources = ['14c78eabdca86f8e094576890518d93d300d2500.tar.gz'] patches = ['PSI-%(version)s-fix-cmake.patch'] -- GitLab From 3be6fddaa8019b702a79710b70e392f754ba223c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 2 Mar 2015 09:58:19 +0100 Subject: [PATCH 324/911] PSI: run tests --- .../easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index 160241465f..c585277151 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -25,4 +25,6 @@ dependencies = [ builddependencies = [('CMake', '3.1.3')] +runtest = 'all test' + moduleclass = 'chem' -- GitLab From 9e897b722cf997d27b60f46fb7023e9551aa29f2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 2 Mar 2015 10:20:58 +0100 Subject: [PATCH 325/911] Updated comments in PSI patch --- .../easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch index 9035ed8df9..9f4ec23cf2 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch @@ -1,5 +1,10 @@ -# fixes the order in which libs get linked in the final executable -# if the order is wrong, you will get linking errors +# This fixes several issues with the CMake build system: +# - Sync the CMakeLists for libPsiUtil with the other libs +# - Let the plugin makefile system work with our install system: patch the +# directory path to correspond with our install directory +# - Add the git revision in the version (as we download a git snapshot for the moment) +# - Fix a bug in the CMakeLists of the documentation (target didn't exists) +# 02/03/2015 - wpoely86@gmail.com diff -ur psi4public-3815c4672b20557818d653694ff2cb5c78819708.org/src/lib/libPsiUtil/CMakeLists.txt psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/lib/libPsiUtil/CMakeLists.txt --- psi4public-3815c4672b20557818d653694ff2cb5c78819708.org/src/lib/libPsiUtil/CMakeLists.txt 2015-02-18 19:36:31.000000000 +0100 +++ psi4public-3815c4672b20557818d653694ff2cb5c78819708/src/lib/libPsiUtil/CMakeLists.txt 2015-02-26 10:36:56.000000000 +0100 -- GitLab From ef84018eb5c86e0a5a1c4a12e35f1ecff28d5f59 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 2 Mar 2015 12:46:19 +0100 Subject: [PATCH 326/911] Disable some tests in PSI4 --- ...SI-4.0b6-20150228-disable-some-tests.patch | 64 +++++++++++++++++++ .../PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb | 5 +- 2 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-disable-some-tests.patch diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-disable-some-tests.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-disable-some-tests.patch new file mode 100644 index 0000000000..f324b80712 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-disable-some-tests.patch @@ -0,0 +1,64 @@ +# Disable some tests of which we know that they will fail... +diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt +index df55cd6..ccd85ab 100644 +--- a/tests/CMakeLists.txt ++++ b/tests/CMakeLists.txt +@@ -154,18 +154,18 @@ add_subdirectory(fci-h2o-fzcv) + add_subdirectory(fci-tdm) + add_subdirectory(fci-tdm-2) + add_subdirectory(fd-freq-energy) +-add_subdirectory(fd-freq-energy-large) ++#add_subdirectory(fd-freq-energy-large) + add_subdirectory(fd-freq-gradient) + add_subdirectory(fd-freq-gradient-large) + add_subdirectory(fd-gradient) + add_subdirectory(fnocc1) +-add_subdirectory(fnocc2) ++#add_subdirectory(fnocc2) + add_subdirectory(fnocc3) + add_subdirectory(fnocc4) +-add_subdirectory(frac) ++#add_subdirectory(frac) + add_subdirectory(ghosts) + add_subdirectory(gibbs) +-add_subdirectory(large_atoms) ++#add_subdirectory(large_atoms) + add_subdirectory(matrix1) + add_subdirectory(mcscf1) + add_subdirectory(mcscf2) +@@ -213,12 +213,12 @@ add_subdirectory(omp3-4) + add_subdirectory(omp3-5) + add_subdirectory(omp3-grad1) + add_subdirectory(omp3-grad2) +-add_subdirectory(opt-lindep-change) ++#add_subdirectory(opt-lindep-change) + add_subdirectory(opt1) + add_subdirectory(opt1-fd) + add_subdirectory(opt2) + add_subdirectory(opt2-fd) +-add_subdirectory(opt3) ++#add_subdirectory(opt3) + add_subdirectory(opt4) + add_subdirectory(opt5) + add_subdirectory(opt6) +@@ -235,7 +235,7 @@ add_subdirectory(psimrcc-fd-freq2) + add_subdirectory(psimrcc-pt2) + add_subdirectory(psimrcc-sp1) + add_subdirectory(psithon1) +-add_subdirectory(psithon2) ++#add_subdirectory(psithon2) + add_subdirectory(pubchem1) + add_subdirectory(pywrap-alias) + add_subdirectory(pywrap-all) +@@ -259,9 +259,9 @@ add_subdirectory(sad1) + add_subdirectory(sapt1) + add_subdirectory(sapt2) + add_subdirectory(sapt3) +-add_subdirectory(sapt4) ++#add_subdirectory(sapt4) + add_subdirectory(sapt5) +-add_subdirectory(scf-bz2) ++#add_subdirectory(scf-bz2) + add_subdirectory(scf-guess-read) + add_subdirectory(scf1) + add_subdirectory(scf11-freq-from-energies) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index c585277151..a0905e7a9d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -13,7 +13,10 @@ toolchainopts = {'usempi': False} source_urls = ['https://github.com/psi4/psi4public/archive/'] sources = ['14c78eabdca86f8e094576890518d93d300d2500.tar.gz'] -patches = ['PSI-%(version)s-fix-cmake.patch'] +patches = [ + 'PSI-%(version)s-fix-cmake.patch', + 'PSI-%(version)s-disable-some-tests.patch', +] python = 'Python' pyver = '2.7.9' -- GitLab From 6fe340122d5a3599ed6032177ae391ac9e8655e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 2 Mar 2015 17:04:43 +0100 Subject: [PATCH 327/911] Limit tests for PSI --- .../easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index a0905e7a9d..3b8a97485f 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -28,6 +28,7 @@ dependencies = [ builddependencies = [('CMake', '3.1.3')] -runtest = 'all test' +# Execute only the 'quick' tests and run 4 in parallel +runtest = 'ARGS="-V -L quicktests -j 4" test' moduleclass = 'chem' -- GitLab From e6bb9ef3d4974ba5a079c6324da7eaea4347b0f1 Mon Sep 17 00:00:00 2001 From: gjbex Date: Tue, 3 Mar 2015 11:07:06 +0100 Subject: [PATCH 328/911] Version of Python easyconfigs that include SQLite as dependency --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 3 +-- .../easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 3 +-- 4 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 3ee92cdc84..b5ab1b4ed0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -17,8 +17,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + ('SQLite', '3.8.8.1'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index ddcd75ee83..052500e6c3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -19,8 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + ('SQLite', '3.8.8.1'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2a6be35eb..42fbb947fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -17,8 +17,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + ('SQLite', '3.8.8.1'), ] osdependencies = [('openssl-devel', 'libssl-dev')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index f686a45b8c..c388acc157 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -19,8 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's -# nice to have an up to date openssl for security reasons + ('SQLite', '3.8.8.1'), ] osdependencies = [('openssl-devel', 'libssl-dev')] -- GitLab From e113a627ea5816c4d96ed4c5c1485d24d50129a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 11:10:09 +0100 Subject: [PATCH 329/911] add required patch files for GAMESS-US goolf easyconfig --- ...ESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 6 +++- ...ESS-US-20130501-R1_config-recent-gcc.patch | 29 +++++++++++++++++ .../GAMESS-US-20130501-R1_openblas.patch | 31 +++++++++++++++++++ 3 files changed, 65 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb index fdb027a1ed..b4cfc07622 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True} sources = ['gamess-%(version)s.tar.gz'] checksums = ['977a01a8958238c67b707f125999fcec'] -patches = ['GAMESS-US_rungms-slurm.patch'] +patches = [ + 'GAMESS-US_rungms-slurm.patch', + 'GAMESS-US-%(version)s_config-recent-gcc.patch', + 'GAMESS-US-%(version)s_openblas.patch', +] # increase these numbers if your system is bigger in terms of cores-per-node or number of nodes # it's OK if these values are larger than what your system provides diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch new file mode 100644 index 0000000000..55700478bc --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch @@ -0,0 +1,29 @@ +--- config.orig 2015-03-03 10:33:00.023695000 +0100 ++++ config 2015-03-03 10:33:37.858993156 +0100 +@@ -452,6 +452,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: +@@ -823,6 +825,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: +@@ -879,6 +883,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch new file mode 100644 index 0000000000..a0cf3ef61c --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch @@ -0,0 +1,31 @@ +--- config.orig 2015-03-03 10:45:24.562802000 +0100 ++++ config 2015-03-03 10:48:31.411157020 +0100 +@@ -569,7 +569,7 @@ + echo "Type 'ls /usr/lib64/atlas' to look for Atlas" + endif + echo " " +-echo -n "Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none': " ++echo -n "Enter your choice of 'mkl' or 'atlas' or 'acml' or 'openblas' or 'none': " + set GMS_MATHLIB=$< + # + switch ($GMS_MATHLIB) +@@ -773,6 +773,19 @@ + endif + breaksw + ++ case openblas: ++ badopenblas: ++ echo -n "Enter full path to OpenBLAS libraries (without 'lib' subdirectory): " ++ set openblaspath=$< ++ if (!(-d $openblaspath)) then ++ echo " " ++ echo "The directory $openblaspath does not exist." ++ echo " " ++ goto badopenblas ++ endif ++ set GMS_MATHLIB_PATH=$openblaspath ++ breaksw ++ + default: + echo "You didn't provide a valid math library name, try again." + echo " " -- GitLab From e1a8b87bd58a1a403ac4bcf5c049cfe81a92ddee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 12:10:00 +0100 Subject: [PATCH 330/911] enhance patches for recent GCC + OpenBLAS --- ...ESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 2 +- ...ESS-US-20130501-R1_config-recent-gcc.patch | 29 -------- .../GAMESS-US-20130501-R1_openblas.patch | 16 ++++- .../GAMESS-US-20130501-R1_recent-gcc.patch | 67 +++++++++++++++++++ 4 files changed, 83 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch create mode 100644 easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb index b4cfc07622..5c7679d343 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb @@ -15,7 +15,7 @@ checksums = ['977a01a8958238c67b707f125999fcec'] patches = [ 'GAMESS-US_rungms-slurm.patch', - 'GAMESS-US-%(version)s_config-recent-gcc.patch', + 'GAMESS-US-%(version)s_recent-gcc.patch', 'GAMESS-US-%(version)s_openblas.patch', ] diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch deleted file mode 100644 index 55700478bc..0000000000 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_config-recent-gcc.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- config.orig 2015-03-03 10:33:00.023695000 +0100 -+++ config 2015-03-03 10:33:37.858993156 +0100 -@@ -452,6 +452,8 @@ - breaksw - case 4.6: - case 4.7: -+ case 4.8: -+ case 4.9: - echo " Good, the newest gfortran can compile REAL*16 data type." - breaksw - default: -@@ -823,6 +825,8 @@ - breaksw - case 4.6: - case 4.7: -+ case 4.8: -+ case 4.9: - echo " Good, the newest gfortran can compile REAL*16 data type." - breaksw - default: -@@ -879,6 +883,8 @@ - breaksw - case 4.6: - case 4.7: -+ case 4.8: -+ case 4.9: - echo " Good, the newest gfortran can compile REAL*16 data type." - breaksw - default: diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch index a0cf3ef61c..3125b9d0be 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch @@ -23,9 +23,23 @@ + echo " " + goto badopenblas + endif -+ set GMS_MATHLIB_PATH=$openblaspath ++ set GMS_MATHLIB_PATH=$openblaspath/lib + breaksw + default: echo "You didn't provide a valid math library name, try again." echo " " +--- lked.orig 2015-03-03 12:03:13.657079000 +0100 ++++ lked 2015-03-03 12:03:58.829061256 +0100 +@@ -473,6 +473,11 @@ + set BLAS=' ' + breaksw + ++ case openblas: ++ set MATHLIBS="$GMS_MATHLIB_PATH/libopenblas.a" ++ set BLAS=' ' ++ breaksw ++ + case none: + default: + echo "Warning. No math library was found, you should install one." diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch new file mode 100644 index 0000000000..e93717f078 --- /dev/null +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch @@ -0,0 +1,67 @@ +--- config.orig 2015-03-03 10:33:00.023695000 +0100 ++++ config 2015-03-03 10:33:37.858993156 +0100 +@@ -452,6 +452,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: +@@ -823,6 +825,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: +@@ -879,6 +883,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + echo " Good, the newest gfortran can compile REAL*16 data type." + breaksw + default: +--- comp.orig 2015-03-03 11:41:57.287089000 +0100 ++++ comp 2015-03-03 11:43:02.574753319 +0100 +@@ -1612,6 +1612,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + set EXTRAOPT="$EXTRAOPT -fno-whole-file" + breaksw + default: +@@ -1804,6 +1806,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + set EXTRAOPT="$EXTRAOPT -fno-whole-file" + breaksw + default: +@@ -2041,6 +2045,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + set EXTRAOPT="$EXTRAOPT -fno-whole-file" + breaksw + default: +@@ -2099,6 +2105,8 @@ + breaksw + case 4.6: + case 4.7: ++ case 4.8: ++ case 4.9: + set EXTRAOPT="$EXTRAOPT -fno-whole-file" + breaksw + default: -- GitLab From 146ed598b4eacfcb081d5a24a3d5893cecb12631 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 12:12:35 +0100 Subject: [PATCH 331/911] add easyconfig with OpenFOAM 2.2.2 + required patches --- .../o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb | 32 +++ .../o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch | 235 ++++++++++++++++++ .../o/OpenFOAM/cleanup-ThirdParty-2.2.2.patch | 18 ++ 3 files changed, 285 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.2.2.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000..13fb5726c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb @@ -0,0 +1,32 @@ +name = 'OpenFOAM' +version = '2.2.2' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.0_esmumps'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch new file mode 100644 index 0000000000..b3cf4117c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch @@ -0,0 +1,235 @@ +diff -ru OpenFOAM-2.2.2.orig/etc/bashrc OpenFOAM-2.2.2/etc/bashrc +--- OpenFOAM-2.2.2.orig/etc/bashrc 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/etc/bashrc 2015-03-03 10:39:07.817538712 +0100 +@@ -63,7 +63,7 @@ + + #- Compiler: + # WM_COMPILER = Gcc | Gcc43 | Gcc44 | Gcc45 | Gcc46 | Clang | Icc (Intel icc) +-export WM_COMPILER=Gcc ++: ${WM_COMPILER:=Gcc}; export WM_COMPILER + unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH + + #- Architecture: +@@ -81,7 +81,7 @@ + #- MPI implementation: + # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI + # | GAMMA | MPI | QSMPI | SGIMPI +-export WM_MPLIB=OPENMPI ++: ${WM_MPLIB:=OPENMPI}; export WM_MPLIB + + #- Operating System: + # WM_OSTYPE = POSIX | ??? +@@ -115,7 +115,7 @@ + + # Location of third-party software + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION ++: ${WM_THIRD_PARTY_DIR:=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION}; export WM_THIRD_PARTY_DIR + + # Location of site-specific templates etc + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +diff -ru OpenFOAM-2.2.2.orig/etc/config/scotch.sh OpenFOAM-2.2.2/etc/config/scotch.sh +--- OpenFOAM-2.2.2.orig/etc/config/scotch.sh 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/etc/config/scotch.sh 2015-03-03 10:39:07.817538712 +0100 +@@ -33,7 +33,11 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.0 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++if [ -n "${SCOTCH_ROOT}" ] ; then ++ export SCOTCH_ARCH_PATH="${SCOTCH_ROOT}" ++else ++ export SCOTCH_VERSION=scotch_6.0.0 ++ export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++fi + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-2.2.2.orig/etc/config/settings.csh OpenFOAM-2.2.2/etc/config/settings.csh +--- OpenFOAM-2.2.2.orig/etc/config/settings.csh 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/etc/config/settings.csh 2015-03-03 10:39:07.817538712 +0100 +@@ -373,7 +373,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + switch ("$WM_MPLIB") + case SYSTEMOPENMPI: +diff -ru OpenFOAM-2.2.2.orig/etc/config/settings.sh OpenFOAM-2.2.2/etc/config/settings.sh +--- OpenFOAM-2.2.2.orig/etc/config/settings.sh 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/etc/config/settings.sh 2015-03-03 10:39:07.817538712 +0100 +@@ -395,7 +395,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + case "$WM_MPLIB" in + SYSTEMOPENMPI) +@@ -563,6 +563,11 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++ ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C +--- OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-03-03 10:39:07.827538901 +0100 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/Make/options 2015-03-03 10:39:07.827538901 +0100 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-03-03 10:39:07.827538901 +0100 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-2.2.2/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-2.2.2.orig/src/parallel/decompose/scotchDecomp/Make/options 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/src/parallel/decompose/scotchDecomp/Make/options 2015-03-03 10:39:07.827538901 +0100 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c 2015-03-03 10:39:07.827538901 +0100 +@@ -2,7 +2,7 @@ + + cWARN = -Wall + +-cc = gcc -m64 ++cc = $(MPICC) + + include $(RULES)/c$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c++ OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c++ +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c++ 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c++ 2015-03-03 10:39:07.827538901 +0100 +@@ -2,7 +2,7 @@ + + c++WARN = -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor + +-CC = g++ -m64 ++CC = $(MPICXX) + + include $(RULES)/c++$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/cOpt OpenFOAM-2.2.2/wmake/rules/linux64Gcc/cOpt +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/cOpt 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Gcc/cOpt 2015-03-03 10:39:07.827538901 +0100 +@@ -1,3 +1,3 @@ + cDBUG = +-cOPT = -O3 ++cOPT = $(CFLAGS) + # -fprefetch-loop-arrays +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c++Opt OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c++Opt +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Gcc/c++Opt 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Gcc/c++Opt 2015-03-03 10:39:07.827538901 +0100 +@@ -1,3 +1,3 @@ + c++DBUG = +-c++OPT = -O3 ++c++OPT = $(CXXFLAGS) + # -fprefetch-loop-arrays +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c OpenFOAM-2.2.2/wmake/rules/linux64Icc/c +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Icc/c 2015-03-03 10:39:07.827538901 +0100 +@@ -2,7 +2,7 @@ + + cWARN = + +-cc = icc ++cc = $(MPICC) + + include $(RULES)/c$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c++ OpenFOAM-2.2.2/wmake/rules/linux64Icc/c++ +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c++ 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Icc/c++ 2015-03-03 10:39:07.827538901 +0100 +@@ -2,7 +2,7 @@ + + c++WARN = -wd327,654,819,1125,1476,1505,1572 + +-CC = icpc -std=c++0x ++CC = $(MPICXX) + + include $(RULES)/c++$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/cOpt OpenFOAM-2.2.2/wmake/rules/linux64Icc/cOpt +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/cOpt 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Icc/cOpt 2015-03-03 10:39:07.827538901 +0100 +@@ -1,2 +1,2 @@ + cDBUG = +-cOPT = -O3 -no-prec-div ++cOPT = $(CFLAGS) +diff -ru OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c++Opt OpenFOAM-2.2.2/wmake/rules/linux64Icc/c++Opt +--- OpenFOAM-2.2.2.orig/wmake/rules/linux64Icc/c++Opt 2013-10-03 12:28:16.000000000 +0200 ++++ OpenFOAM-2.2.2/wmake/rules/linux64Icc/c++Opt 2015-03-03 10:39:45.158231466 +0100 +@@ -1,2 +1,2 @@ + c++DBUG = +-c++OPT = -xHost -O2 -no-prec-div ++c++OPT = $(CXXFLAGS) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.2.2.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.2.2.patch new file mode 100644 index 0000000000..b3bb8665db --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.2.2.patch @@ -0,0 +1,18 @@ +diff -ru ThirdParty-2.2.2.orig/Allwmake ThirdParty-2.2.2/Allwmake +--- ThirdParty-2.2.2.orig/Allwmake 2013-03-05 19:09:55.000000000 +0100 ++++ ThirdParty-2.2.2/Allwmake 2013-05-15 09:06:16.834069000 +0200 +@@ -110,12 +110,12 @@ + ;; + + MPICH) +- if [ -r $MPI_ARCH_PATH/lib/libmpich.so ] ++ if [ -r $MPI_ARCH_PATH/lib64/libmpich.so ] + then + echo " have $WM_MPLIB shared library ($FOAM_MPI)" + echo + echo +- elif [ -r $MPI_ARCH_PATH/lib/libmpich.a ] ++ elif [ -r $MPI_ARCH_PATH/lib64/libmpich.a ] + then + echo " have $WM_MPLIB static library ($FOAM_MPI)" + echo -- GitLab From 6ac577e60b626dc84b488e2b8f2d0638970b3840 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 12:21:36 +0100 Subject: [PATCH 332/911] add SCOTCH easyconfig as dep for OpenFOAM --- .../s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb new file mode 100644 index 0000000000..04430d4385 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.0_esmumps' + +homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From 05c3701209d22bad746769e15263e80bed318028 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 13:35:48 +0100 Subject: [PATCH 333/911] Added perl as build dep to PSI --- .../easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb index 3b8a97485f..2550e2c136 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-intel-2015a-mt.eb @@ -26,7 +26,10 @@ dependencies = [ ('Boost', '1.57.0', '-%s-%s' % (python, pyver)), ] -builddependencies = [('CMake', '3.1.3')] +builddependencies = [ + ('CMake', '3.1.3'), + ('Perl', '5.20.1', '-bare'), # for the test suite +] # Execute only the 'quick' tests and run 4 in parallel runtest = 'ARGS="-V -L quicktests -j 4" test' -- GitLab From b21a84291e892d684aff6f6310bb7ae18d223780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 14:08:05 +0100 Subject: [PATCH 334/911] fix remark, bump SCOTCH version to 6.0.3 --- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.0.1.patch | 2 ++ easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.1.1.patch | 2 ++ easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.0.patch | 2 ++ easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch | 2 ++ easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.0.patch | 2 ++ ...0.0_esmumps-intel-2015a.eb => SCOTCH-6.0.3-intel-2015a.eb} | 4 ++-- 7 files changed, 13 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/s/SCOTCH/{SCOTCH-6.0.0_esmumps-intel-2015a.eb => SCOTCH-6.0.3-intel-2015a.eb} (82%) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb index 13fb5726c9..fa74bb2b42 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2015a.eb @@ -23,7 +23,7 @@ patches = [ dependencies = [ ('libreadline', '6.3'), - ('SCOTCH', '6.0.0_esmumps'), + ('SCOTCH', '6.0.3'), ('ncurses', '5.9'), ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.0.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.0.1.patch index 22a30fd75b..a3c524a23b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.0.1.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.0.1.patch @@ -1,3 +1,5 @@ +patch to avoid hardcoding of settings, so defaults can be set on the outside by defining environment variables +author: Kenneth Hoste (Ghent University) diff -ru OpenFOAM-2.0.1.ORIG/etc/bashrc OpenFOAM-2.0.1/etc/bashrc --- OpenFOAM-2.0.1.ORIG/etc/bashrc 2011-08-03 11:42:18.000000000 +0200 +++ OpenFOAM-2.0.1/etc/bashrc 2014-07-01 10:58:53.980635981 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.1.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.1.1.patch index c497399edc..6abdad8e03 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.1.1.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.1.1.patch @@ -1,3 +1,5 @@ +patch to avoid hardcoding of settings, so defaults can be set on the outside by defining environment variables +author: kenneth hoste (ghent university) diff -ru OpenFOAM-2.1.1.ORIG/etc/bashrc OpenFOAM-2.1.1/etc/bashrc --- OpenFOAM-2.1.1.ORIG/etc/bashrc 2012-05-24 16:51:32.000000000 +0200 +++ OpenFOAM-2.1.1/etc/bashrc 2014-07-07 11:48:54.265168442 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.0.patch index 81f21c62be..0df71cb648 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.0.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.0.patch @@ -1,3 +1,5 @@ +patch to avoid hardcoding of settings, so defaults can be set on the outside by defining environment variables +author: kenneth hoste (ghent university) diff -ru OpenFOAM-2.2.0.ORIG/etc/bashrc OpenFOAM-2.2.0/etc/bashrc --- OpenFOAM-2.2.0.ORIG/etc/bashrc 2013-01-14 09:48:51.000000000 +0100 +++ OpenFOAM-2.2.0/etc/bashrc 2014-07-07 16:36:36.784886564 +0200 diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch index b3cf4117c9..14ebe59f75 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch @@ -1,3 +1,5 @@ +patch to avoid hardcoding of settings, so defaults can be set on the outside by defining environment variables +author: Kenneth Hoste (Ghent University) diff -ru OpenFOAM-2.2.2.orig/etc/bashrc OpenFOAM-2.2.2/etc/bashrc --- OpenFOAM-2.2.2.orig/etc/bashrc 2013-10-03 12:28:16.000000000 +0200 +++ OpenFOAM-2.2.2/etc/bashrc 2015-03-03 10:39:07.817538712 +0100 diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.0.patch index 35356f2d17..d0ee62a153 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.0.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.0.patch @@ -1,3 +1,5 @@ +patch to avoid hardcoding of settings, so defaults can be set on the outside by defining environment variables +author: kenneth hoste (ghent university) diff -ru OpenFOAM-2.3.0.ORIG/etc/bashrc OpenFOAM-2.3.0/etc/bashrc --- OpenFOAM-2.3.0.ORIG/etc/bashrc 2014-02-11 12:59:42.000000000 +0100 +++ OpenFOAM-2.3.0/etc/bashrc 2014-07-07 19:13:12.383703455 +0200 diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb similarity index 82% rename from easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb rename to easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb index 04430d4385..9c8e465231 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb @@ -1,5 +1,5 @@ name = 'SCOTCH' -version = '6.0.0_esmumps' +version = '6.0.3' homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, @@ -8,7 +8,7 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34099/'] sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' -- GitLab From 92f94ebe277dba5279bbba5744edbe03f9e1ac30 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:06:25 +0100 Subject: [PATCH 335/911] Fix perl path --- .../easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch index 9f4ec23cf2..b096b7e51d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch @@ -170,4 +170,12 @@ diff --git a/doc/sphinxman/CMakeLists.txt b/doc/sphinxman/CMakeLists.txt - - endif(PERL_FOUND AND SPHINX_FOUND) +diff --git a/tests/psitest.pl b/tests/psitest.pl +--- a/tests/psitest.pl ++++ b/tests/psitest.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # + # Rules of use: -- GitLab From 00941ca65e1f7eff281424e6ce97f7c3687b4352 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:07:23 +0100 Subject: [PATCH 336/911] Fix patch --- easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch index b096b7e51d..2e48f50bf3 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150228-fix-cmake.patch @@ -170,6 +170,7 @@ diff --git a/doc/sphinxman/CMakeLists.txt b/doc/sphinxman/CMakeLists.txt - - endif(PERL_FOUND AND SPHINX_FOUND) + diff --git a/tests/psitest.pl b/tests/psitest.pl --- a/tests/psitest.pl +++ b/tests/psitest.pl -- GitLab From 043f333b0d915b478c106f09ee358b68845ebc8a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:26:32 +0100 Subject: [PATCH 337/911] New version of h5py --- .../h5py-2.4.0-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..8ec2679d1d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.4.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# make sure that MPI features are enabled (new in h5py v2.2) +buildopts = '--mpi' + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.14'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], +} + +moduleclass = 'data' -- GitLab From e45477e3819f0f65c9a2e017a6ad033fa478d95f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:33:55 +0100 Subject: [PATCH 338/911] Non-MPI build of h5py --- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb index 8ec2679d1d..12f811fc85 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb @@ -9,7 +9,7 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': False} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] @@ -19,12 +19,9 @@ pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled (new in h5py v2.2) -buildopts = '--mpi' - dependencies = [ (python, pythonver), - ('HDF5', '1.8.14'), + ('HDF5', '1.8.14', '-serial'), ] sanity_check_paths = { -- GitLab From 6d05d3199b44dd4a84124d00821e744972b9f8a8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:36:49 +0100 Subject: [PATCH 339/911] Add version suffix to h5py --- ...on-2.7.9.eb => h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/h/h5py/{h5py-2.4.0-intel-2015a-Python-2.7.9.eb => h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb} (97%) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb similarity index 97% rename from easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 12f811fc85..9d53acbd22 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -2,6 +2,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.4.0' +versionsuffix = '-serial' homepage = 'http://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, -- GitLab From 37651f54c76eded5caf4db91e2fbb1f608e7a550 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:44:09 +0100 Subject: [PATCH 340/911] Change sanity check to test for egg --- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 9d53acbd22..767e8fe838 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -26,8 +26,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'dirs': [], } moduleclass = 'data' -- GitLab From 25dc618065dbed8ee8e8df0b354c0bb44fe65020 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 3 Mar 2015 15:46:50 +0100 Subject: [PATCH 341/911] h5py: correct versionsuffix --- .../h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb index 767e8fe838..c839cbc2dd 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.4.0-intel-2015a-Python-2.7.9-serial.eb @@ -2,7 +2,6 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.4.0' -versionsuffix = '-serial' homepage = 'http://www.h5py.org/' description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, @@ -18,7 +17,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.9' pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +versionsuffix = '-%s-%s-serial' % (python, pythonver) dependencies = [ (python, pythonver), -- GitLab From 853959c04a0e3681250221a4c176a305b2585b4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Mar 2015 16:10:20 +0100 Subject: [PATCH 342/911] exclude Perl as dep for parallel built with ictce/4.0.6 --- .../p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb | 18 ------------------ .../parallel/parallel-20130122-ictce-4.0.6.eb | 6 +++--- 2 files changed, 3 insertions(+), 21 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb deleted file mode 100644 index 9e108b5b00..0000000000 --- a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-4.0.6-bare.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'Perl' -version = '5.16.3' -versionsuffix = "-bare" - -homepage = 'http://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language""" - -toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://www.cpan.org/src/5.0'] -sources = [SOURCELOWER_TAR_GZ] - -patches = ['exitcode_error.patch'] - -runtest = 'test' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb index df8ba6abaf..94c10ffced 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb @@ -23,9 +23,9 @@ toolchain = {'version': '4.0.6', 'name': 'ictce'} sources = [SOURCE_TAR_BZ2] source_urls = [GNU_SOURCE] -dependencies = [ - ('Perl', '5.16.3', '-bare'), -] +# Perl *should* be a dependency here (for pod2man and runtime), but building Perl 5.16.3 with ictce/4.0.6 fails +# it seems like the Intel compilers are miscompiling 'miniperl' which is used during the build procedure +#dependencies = [('Perl', '5.16.3', '-bare')] sanity_check_paths = { 'files': ['bin/parallel'], -- GitLab From ee0124850b08904cea2d698d9f2edbfb8956b22d Mon Sep 17 00:00:00 2001 From: Benjamin Roberts Date: Wed, 4 Mar 2015 11:29:11 +1300 Subject: [PATCH 343/911] New Easyconfig for ORCA 3.0.3 --- .../ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb new file mode 100644 index 0000000000..b63bd53de9 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64-OpenMPI-1.6.5.eb @@ -0,0 +1,35 @@ +easyblock = "PackedBinary" + +name = "ORCA" +version = '3_0_3-linux_x86-64' + +openmpiversion = '1.6.5' +versionsuffix = '-OpenMPI-%s' % openmpiversion + +homepage = 'http://cec.mpg.de/forum/' +description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry + with specific emphasis on spectroscopic properties of open-shell molecules. + It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- + and multireference correlated ab initio methods. + It can also treat environmental and relativistic effects.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] + +dependencies = [('OpenMPI', openmpiversion, '-GCC-4.7.2')] + +sanity_check_paths = { + 'files': ['orca_%s%s' % (x,y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', + 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', + 'rocis', 'scf', 'scfgrad', 'soc'] + for y in ["", "_mpi"]] + \ + ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', + 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', + 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', + 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + \ + ['orca', 'otool_cosmo'], + 'dirs': [], +} + +moduleclass = 'chem' -- GitLab From c5636a4329b120c617e98a89133610d93b4af795 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 4 Mar 2015 13:40:24 +0100 Subject: [PATCH 344/911] renamed blast easyconfigs --- ...b => BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb} | 2 +- ....4.10.eb => BLAST+-2.2.27-goolf-1.4.10.eb} | 2 +- ...-4.0.6.eb => BLAST+-2.2.27-ictce-4.0.6.eb} | 4 +- ....patch => BLAST+-2.2.27_ictce-fixes.patch} | 0 ...LAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb} | 2 +- ....4.10.eb => BLAST+-2.2.28-goolf-1.4.10.eb} | 2 +- ....1.13.eb => BLAST+-2.2.28-ictce-4.1.13.eb} | 2 +- ...BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb} | 2 +- ...-5.3.0.eb => BLAST+-2.2.28-ictce-5.3.0.eb} | 2 +- ....patch => BLAST+-2.2.28_ictce-fixes.patch} | 0 .../b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb | 41 +++++++++++++++++++ 11 files changed, 50 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.27-goalf-1.1.0-no-OFED.eb => BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.27-goolf-1.4.10.eb => BLAST+-2.2.27-goolf-1.4.10.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.27-ictce-4.0.6.eb => BLAST+-2.2.27-ictce-4.0.6.eb} (95%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.27_ictce-fixes.patch => BLAST+-2.2.27_ictce-fixes.patch} (100%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28-goolf-1.4.10-Python-2.7.3.eb => BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28-goolf-1.4.10.eb => BLAST+-2.2.28-goolf-1.4.10.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28-ictce-4.1.13.eb => BLAST+-2.2.28-ictce-4.1.13.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28-ictce-5.3.0-Python-2.7.3.eb => BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28-ictce-5.3.0.eb => BLAST+-2.2.28-ictce-5.3.0.eb} (98%) rename easybuild/easyconfigs/b/BLAST/{BLAST-2.2.28_ictce-fixes.patch => BLAST+-2.2.28_ictce-fixes.patch} (100%) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb index f4b3245692..d803c10c5d 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.27' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goolf-1.4.10.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goolf-1.4.10.eb index f1853407cc..28d49cf87c 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goolf-1.4.10.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.27' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-ictce-4.0.6.eb similarity index 95% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-ictce-4.0.6.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-ictce-4.0.6.eb index 5b8b658539..df27a457e4 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-ictce-4.0.6.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.27' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. @@ -27,7 +27,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['BLAST-2.2.27_ictce-fixes.patch'] +patches = ['BLAST+-2.2.27_ictce-fixes.patch'] dependencies = [('Boost', '1.51.0')] diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.27_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27_ictce-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.27_ictce-fixes.patch rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27_ictce-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10-Python-2.7.3.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb index f16f3445c0..92685d8e49 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.28' versionsuffix = '-Python-2.7.3' diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10.eb index d7a23abb92..798595e5d7 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.28' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-4.1.13.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-4.1.13.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-4.1.13.eb index 44ad40f2e4..ea4409e679 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-4.1.13.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.28' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0-Python-2.7.3.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb index 9ae9e7de68..6724f2f4a9 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.28' versionsuffix = '-Python-2.7.3' diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0.eb rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0.eb index 950edd8368..6d0b74f52a 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.28' altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.28_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28_ictce-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.28_ictce-fixes.patch rename to easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28_ictce-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb new file mode 100644 index 0000000000..1097f7c5b1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.2.30' +altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_ictce-fixes.patch'] + +dependencies = [('Boost', '1.51.0')] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] + } + +moduleclass = 'bio' -- GitLab From e192d64c70695f5fd0636e5d3c97b8137f47e02a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Mar 2015 18:42:10 +0100 Subject: [PATCH 345/911] disable running of tests for GAMESS-US on top of goolf/OpenMPI --- .../g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb index 5c7679d343..926bce3428 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1-goolf-1.5.14-no-OFED.eb @@ -24,4 +24,7 @@ patches = [ maxcpus = '1000' maxnodes = '100000' +# disable running of tests, since rungms needs patching in order to support running on top of OpenMPI +runtest = False + moduleclass = 'chem' -- GitLab From 41a0c87d3d72f4103f3ed75c934650086f4fb4d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Mar 2015 09:43:09 +0100 Subject: [PATCH 346/911] include comments in patches for GAMESS-US --- .../g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch | 2 ++ .../g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch index 3125b9d0be..a4ae8653c0 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_openblas.patch @@ -1,3 +1,5 @@ +include support for OpenBLAS in config and lked scripts +author: Kenneth Hoste (Ghent University) --- config.orig 2015-03-03 10:45:24.562802000 +0100 +++ config 2015-03-03 10:48:31.411157020 +0100 @@ -569,7 +569,7 @@ diff --git a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch index e93717f078..998b5ffd36 100644 --- a/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch +++ b/easybuild/easyconfigs/g/GAMESS-US/GAMESS-US-20130501-R1_recent-gcc.patch @@ -1,3 +1,5 @@ +include support for recent GCC versions in config and comp scripts +author: Kenneth Hoste (Ghent University) --- config.orig 2015-03-03 10:33:00.023695000 +0100 +++ config 2015-03-03 10:33:37.858993156 +0100 @@ -452,6 +452,8 @@ -- GitLab From 3e57469f087d653d75a48831192721ac8a1f4e93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Mar 2015 09:54:00 +0100 Subject: [PATCH 347/911] fix conflict detection by considering build deps separately from runtime deps --- test/easyconfigs/easyconfigs.py | 60 +++++++++++++++++++-------------- 1 file changed, 35 insertions(+), 25 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 20c3cab4f7..5d7ca77279 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -128,41 +128,51 @@ class EasyConfigTest(TestCase): def mk_dep_mod_name(spec): return tuple(ActiveMNS().det_full_module_name(spec).split(os.path.sep)) - # construct a dictionary: (name, installver) tuple to dependencies + # construct a dictionary: (name, installver) tuple to (build) dependencies depmap = {} for spec in self.ordered_specs: - builddeps = map(mk_dep_mod_name, spec['builddependencies']) + build_deps = map(mk_dep_mod_name, spec['builddependencies']) deps = map(mk_dep_mod_name, spec['unresolved_deps']) + # separate runtime deps from build deps + runtime_deps = [d for d in deps if d not in build_deps] key = tuple(spec['full_mod_name'].split(os.path.sep)) - depmap.update({key: [builddeps, deps]}) + depmap.update({key: [build_deps, runtime_deps]}) - # iteratively expand list of (non-build) dependencies until we reach the end (toolchain) + # iteratively expand list of dependencies depmap_last = None while depmap != depmap_last: depmap_last = copy.deepcopy(depmap) - for (spec, (builddependencies, dependencies)) in depmap_last.items(): - # extend dependencies with non-build dependencies of own (non-build) dependencies - for dep in dependencies: - if dep not in builddependencies: - depmap[spec][1].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) + for (spec, (build_deps, runtime_deps)) in depmap_last.items(): + # extend runtime dependencies with non-build dependencies of own runtime dependencies + for dep in runtime_deps: + depmap[spec][1].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) depmap[spec][1] = sorted(nub(depmap[spec][1])) - - # for each of the easyconfigs, check whether the dependencies contain any conflicts + # extend build dependencies with non-build dependencies of own build dependencies + for dep in build_deps: + depmap[spec][0].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) + depmap[spec][0] = sorted(nub(depmap[spec][0])) + + def check_conflict((name, installver), (name1, installver1), (name2, installver2)): + """Check whether dependencies with given name/(install) version conflict with each other.""" + # dependencies with the same name should have the exact same install version + # if not => CONFLICT! + if name1 == name2 and installver1 != installver2: + specname = '%s-%s' % (name, installver) + vs_msg = "%s-%s vs %s-%s" % (name1, installver1, name2, installver2) + print "Conflict found for dependencies of %s: %s" % (specname, vs_msg) + return True + else: + return False + + # for each of the easyconfigs, check whether the dependencies (incl. build deps) contain any conflicts conflicts = False - for ((name, installver), (builddependencies, dependencies)) in depmap.items(): - # only consider non-build dependencies - non_build_deps = [d for d in dependencies if d not in builddependencies] - for i in xrange(len(non_build_deps)): - (name_dep1, installver_dep1) = non_build_deps[i] - # also make sure that module for easyconfig doesn't conflict with any of its dependencies - for (name_dep2, installver_dep2) in [(name, installver)] + non_build_deps[i+1:]: - # dependencies with the same name should have the exact same install version - # if not => CONFLICT! - if name_dep1 == name_dep2 and installver_dep1 != installver_dep2: - specname = '%s-%s' % (name, installver) - vs_msg = "%s-%s vs %s-%s" % (name_dep1, installver_dep1, name_dep2, installver_dep2) - print "Conflict found for (non-build) dependencies of %s: %s" % (specname, vs_msg) - conflicts = True + for ((name, installver), (build_deps, runtime_deps)) in depmap.items(): + # also check whether module itself clashes with any of its dependencies + for i, dep1 in enumerate(build_deps + runtime_deps + [(name, installver)]): + for dep2 in (build_deps + runtime_deps)[i+1:]: + # don't worry about conflicts between module itself and any of its build deps + if dep1 != (name, installver) or dep2 not in build_deps: + conflicts |= check_conflict((name, installver), dep1, dep2) self.assertFalse(conflicts, "No conflicts detected") def test_sanity_check_paths(self): -- GitLab From de0c1d66a84648b00a598de513cdbf479f39d11a Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Mar 2015 09:59:35 +0100 Subject: [PATCH 348/911] removed unneded patch for BLAST+-2.2.30-goolf-1.4.10.eb --- easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb index 1097f7c5b1..8db7890786 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb @@ -27,8 +27,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['%(name)s-%(version)s_ictce-fixes.patch'] - dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' -- GitLab From b718b12750f51d8ae7a4bc21115171fc38e29b92 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Mar 2015 10:02:34 +0100 Subject: [PATCH 349/911] fixed dependencies in other easyconfigs --- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index 1919d75c76..646cbde1cd 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('ALLPATHS-LG', '46968'), ('AMOS', '3.1.0'), ('BFAST', '0.7.0a'), - ('BLAST', '2.2.28', '-Python-2.7.3'), + ('BLAST+', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('BamTools', '2.2.3'), ('BioPerl', '1.6.1', '-Perl-5.16.3'), diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index 07974e95af..279cbcaf0c 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ # ('ALLPATHS-LG', '46968'), ('AMOS', '3.1.0'), ('BFAST', '0.7.0a'), - ('BLAST', '2.2.28', '-Python-2.7.3'), + ('BLAST+', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('BamTools', '2.2.3'), ('BioPerl', '1.6.1', '-Perl-5.16.3'), diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index 105b0630d6..70d7373fbb 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # ie. build against the GNU # TODO: Vina, Dock dependencies = [ - ('BLAST', '2.2.28', '-Python-2.7.3'), + ('BLAST+', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('ClustalW2', '2.1'), ('GROMACS', '4.6.1', '-hybrid'), diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index 20fb4bbb29..49ed51d973 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # ie. build against the INTEL # TODO: Vina, Dock dependencies = [ - ('BLAST', '2.2.28', '-Python-2.7.3'), + ('BLAST+', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('ClustalW2', '2.1'), ('GROMACS', '4.6.1', '-hybrid'), -- GitLab From 4094b88cd4244df3dc19e2630dd0c58183a43e75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Mar 2015 10:11:24 +0100 Subject: [PATCH 350/911] fix Bison build dep in MVAPICH2 easyconfig --- .../b/Bison/Bison-2.7-iccifort-2011.13.367.eb | 22 ++++++++++++++++ .../m/M4/M4-1.4.16-iccifort-2011.13.367.eb | 25 +++++++++++++++++++ .../MVAPICH2-1.9-iccifort-2011.13.367.eb | 2 +- 3 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb new file mode 100644 index 0000000000..6f79524592 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'iccifort', 'version': '2011.13.367'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs':[], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb new file mode 100644 index 0000000000..00ab5d7de7 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-iccifort-2011.13.367.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.16' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'iccifort', 'version': '2011.13.367'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb index 51fd98fd16..f87ce5fafe 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb @@ -10,7 +10,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] sources = [SOURCELOWER_TGZ] -builddependencies = [('Bison', '2.7', '', ('ictce', '4.1.13'))] +builddependencies = [('Bison', '2.7')] # the hydra launcher start's before LD_LIBRARY_PATH is forwarded, so we provide this hint on where to find some libs preconfigopts = 'LDFLAGS="-Wl,-rpath,$EBROOTICC/compiler/lib/intel64 $LDFLAGS"' -- GitLab From 3bb79637fc7d209504812f8277677a8d21fdad75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Mar 2015 10:16:48 +0100 Subject: [PATCH 351/911] fix version for ORCA 3.0.0 easyconfig --- .../o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb index f4147dd3b8..3b66a977f7 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb @@ -1,10 +1,8 @@ easyblock = "PackedBinary" name = "ORCA" -version = '3_0_0-linux_x86-64' - openmpiversion = '1.6.5' -versionsuffix = '-OpenMPI-%s' % openmpiversion +version = '3_0_0-linux_x86-64_openmpi_%s' % ''.join(openmpiversion.split('.')) homepage = 'http://www.thch.uni-bonn.de/tc/orca/' description = """ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry -- GitLab From aa2cb94e8c056012bc1505327918f2e1d03222e3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 5 Mar 2015 10:26:22 +0100 Subject: [PATCH 352/911] Sanity check for Clang is in the easyblock --- easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 5be4ff6781..2e05deca3c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -36,11 +36,6 @@ dependencies = [ ('ISL', '0.14') ] -sanity_check_paths = { - 'files': ['bin/clang', 'bin/clang++', 'lib/libclang.so', 'lib/clang/%(version)s/include/stddef.h'], - 'dirs': [], -} - assertions = True usepolly = True -- GitLab From 85c2daf342ac09e4499c7a31fc149e91177681fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Mar 2015 10:32:25 +0100 Subject: [PATCH 353/911] correct filename for ORCA v3.0.0 --- ...64-OpenMPI-1.6.5.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/ORCA/{ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb => ORCA-3_0_0-linux_x86-64_openmpi_165.eb} (100%) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb similarity index 100% rename from easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64-OpenMPI-1.6.5.eb rename to easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb -- GitLab From b196f6ccba40f2fd1dd549c536845d682fad1086 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 5 Mar 2015 11:00:59 +0100 Subject: [PATCH 354/911] Added missing python build dep to Clang --- .../b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb | 15 ++++++++++ .../c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 9 ++++-- .../libreadline/libreadline-6.3-GCC-4.9.2.eb | 27 +++++++++++++++++ .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 29 +++++++++++++++++++ 4 files changed, 77 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb new file mode 100644 index 0000000000..c1e6796922 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 2e05deca3c..db38546ea9 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -29,13 +29,16 @@ sources = [ "polly-%(version)s.src.tar.xz", ] -builddependencies = [('CMake', '3.1.3')] - dependencies = [ ('GMP', '6.0.0'), - ('ISL', '0.14') + ('ISL', '0.14'), ] +builddependencies = [ + ('CMake', '3.1.3'), + ('Python', '2.7.9', '-bare'), +] + assertions = True usepolly = True diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb new file mode 100644 index 0000000000..718f40a355 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000..169427938d --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -0,0 +1,29 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' -- GitLab From 613f5f23a849fda495246e81d138a1c496675fa3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Mar 2015 12:41:47 +0100 Subject: [PATCH 355/911] added BLAST+ folder --- .../b/{BLAST => BLAST+}/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27-goolf-1.4.10.eb | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27-ictce-4.0.6.eb | 0 .../b/{BLAST => BLAST+}/BLAST+-2.2.27_ictce-fixes.patch | 0 .../{BLAST => BLAST+}/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-goolf-1.4.10.eb | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-4.1.13.eb | 0 .../b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-5.3.0.eb | 0 .../b/{BLAST => BLAST+}/BLAST+-2.2.28_ictce-fixes.patch | 0 .../easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.30-goolf-1.4.10.eb | 0 11 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27-ictce-4.0.6.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.27_ictce-fixes.patch (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-4.1.13.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28-ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.28_ictce-fixes.patch (100%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/BLAST+-2.2.30-goolf-1.4.10.eb (100%) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27-ictce-4.0.6.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27_ictce-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.27_ictce-fixes.patch rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27_ictce-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-4.1.13.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28-ictce-5.3.0.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28_ictce-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.28_ictce-fixes.patch rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28_ictce-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST+-2.2.30-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb -- GitLab From 7f660ea29654133c1d768543fe97067fc68439ba Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Mar 2015 12:45:51 +0100 Subject: [PATCH 356/911] cleanup --- .../b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb | 2 -- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb | 2 -- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb | 2 -- .../b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb | 5 ----- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb | 4 ---- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb | 2 -- .../b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb | 3 --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb | 2 -- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 -- 9 files changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb index d803c10c5d..8129083a06 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.27' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb index 28d49cf87c..e7772ac728 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-goolf-1.4.10.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.27' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb index df27a457e4..3800356ed9 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.27-ictce-4.0.6.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.27' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'ictce', 'version': '4.0.6'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb index 92685d8e49..f3f69270a5 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10-Python-2.7.3.eb @@ -16,8 +16,6 @@ name = 'BLAST+' version = '2.2.28' versionsuffix = '-Python-2.7.3' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. - homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid @@ -25,12 +23,9 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['%(name)s-%(version)s_ictce-fixes.patch'] - dependencies = [('Boost', '1.51.0', '-Python-2.7.3')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb index 798595e5d7..d52c0aba66 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-goolf-1.4.10.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.28' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,12 +22,9 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['%(name)s-%(version)s_ictce-fixes.patch'] - dependencies = [('Boost', '1.51.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb index ea4409e679..adcf957193 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-4.1.13.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.28' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'ictce', 'version': '4.1.13'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb index 6724f2f4a9..a4329e5cf5 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0-Python-2.7.3.eb @@ -16,8 +16,6 @@ name = 'BLAST+' version = '2.2.28' versionsuffix = '-Python-2.7.3' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. - homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid @@ -25,7 +23,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'ictce', 'version': '5.3.0'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb index 6d0b74f52a..a55a29ffe4 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.28-ictce-5.3.0.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.28' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'ictce', 'version': '5.3.0'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 8db7890786..8241cb4edd 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -14,7 +14,6 @@ easyblock = 'ConfigureMake' name = 'BLAST+' version = '2.2.30' -altversions = ['2.2.26', '2.2.27'] # Versions .18 & .23-25 are also important but seem not to build fine, yet. homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -23,7 +22,6 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -- GitLab From de9694f5a464b9e3e16145425daa870f7cc8de5b Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 5 Mar 2015 09:27:26 -0500 Subject: [PATCH 357/911] changed to BITBUCKET_SOURCE per note by @wpoely86 --- easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb index a2767dc205..9cca953ebc 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -8,7 +8,7 @@ description = """Eigen is a C++ template library for linear algebra: toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] moduleclass = 'math' -- GitLab From fc9be42ca55087a84a729719b5bc9cf5297b9dce Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 5 Mar 2015 21:28:29 +0100 Subject: [PATCH 358/911] removed 2.2.30 --- .../b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb deleted file mode 100644 index 8241cb4edd..0000000000 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'BLAST+' -version = '2.2.30' - -homepage = 'http://blast.ncbi.nlm.nih.gov/' -description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm - for comparing primary biological sequence information, such as the amino-acid - sequences of different proteins or the nucleotides of DNA sequences.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] - -dependencies = [('Boost', '1.51.0')] - -configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' - -sanity_check_paths = { - 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], - 'dirs': [] - } - -moduleclass = 'bio' -- GitLab From ae95523aefd991aecdce1bdc9d4f75156ab04ceb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 5 Mar 2015 21:40:35 +0100 Subject: [PATCH 359/911] Added libxml as build dep to Clang --- .../c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 1 + .../l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb | 23 +++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index db38546ea9..445ace0985 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -37,6 +37,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.1.3'), ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), ] assertions = True diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb new file mode 100644 index 0000000000..25967be117 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' -- GitLab From 862696e8492ff63f5c37dcf65064ef6503acf550 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:22:42 +0100 Subject: [PATCH 360/911] use new 'bundle' moduleclass for bundles --- .../easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb index 067ccdbe63..cd3235cdf1 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb @@ -14,4 +14,4 @@ dependencies = [ ('libtool', '2.4.5'), # 20150119 ] -moduleclass = 'devel' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index 6747f4c983..19dccf4c5a 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -70,4 +70,4 @@ dependencies = [ ('ViennaRNA', '2.0.7'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index e012ed1bb8..34dc4faa24 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -70,4 +70,4 @@ dependencies = [ ('ViennaRNA', '2.0.7'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 0b0682b5cc..209941c445 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -28,4 +28,4 @@ dependencies = [ ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index ac60d4668c..a6bd997119 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -34,4 +34,4 @@ dependencies = [ # ('Rosetta', '3.5'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index 7967a67baf..d129c36c59 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -34,4 +34,4 @@ dependencies = [ # ('Rosetta', '3.5'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb index f4b107240d..d31e22cb47 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb @@ -29,4 +29,4 @@ dependencies = [ ('GSL', '1.15'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb index 5a7e87852a..cdf41a29ac 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb @@ -30,4 +30,4 @@ dependencies = [ ('SPRNG', '2.0b'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb index 9eead1e8ea..ba99a2d9b6 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb @@ -28,4 +28,4 @@ dependencies = [ ('SPRNG', '2.0b'), ] -moduleclass = 'toolchain' +moduleclass = 'bundle' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index ae3956c8ea..5b73516d37 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -29,4 +29,4 @@ dependencies = [ ('binutils', '2.22'), # this one provides gprof ] -moduleclass = 'toolchain' +moduleclass = 'bundle' -- GitLab From 76a6b06a273dc6d556584fcc04f592aceab22126 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:25:11 +0100 Subject: [PATCH 361/911] fix name of google-sparsehash easyconfig --- .../google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{s/sparsehash/sparsehash-2.0.2-intel-2015a.eb => g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-intel-2015a.eb b/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-intel-2015a.eb rename to easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb -- GitLab From 77903fdc7e0638294baf1ed2d950d66e1dcb4e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:26:34 +0100 Subject: [PATCH 362/911] bump to v2.0.0 + update release notes --- RELEASE_NOTES | 37 +++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 36 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 01b1286c29..3563f389c6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,41 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,066 easyconfig files, for 551 different software packages -and 32 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 581 different software packages, +32 different (compiler) toolchains and 6 software bundles. + + +v2.0.0 (March 6th 2015) +----------------------- + +feature + bugfix release +- added example easyconfig files for 29 new software packages: + bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) +- added easyconfigs for new (common) toolchains + foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) +- added new bundles: Autotools (#1385) +- various other enhancements, including: + - don't define $LDSHARED in zlib easyconfigs (#1350) + - this fixes the long-standing "no version information available" issue with zlib + - see also https://github.com/hpcugent/easybuild-framework/issues/108 + - add unit test to check that all extra_options keys are defined in EasyConfig instance (#1378) + - add source MD5 checksums in all GCC easyconfigs (#1391) + - speeding up the unit tests by avoiding rereading of same easyconfig file (#1432) + - fix conflict detection in unit tests by considering build deps separately from runtime deps (#1447) + - fix toolchain for Bison build dep in MVAPICH2-1.9-iccifort-2011.13.367.eb easyconfig (#1448) + - use Bundle generic easyblock and 'bundle' moduleclass for software bundles (#1451) +- various bug fixes, including: + - revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144) + - added Java dependencies to EMBOSS easyconfigs (#1167) + - don't list 'lto' as a language in GCC easyconfigs (#1286) + - related to the fixes in the GCC easyblock, see hpcugent/easybuild-easyblocks#535 + - rename libint2 easyconfigs as Libint v2 easyconfigs (#1287) + - fix mpi4py source_urls in Python easyconfigs (#1306) + - consistently use CLooG 0.18.0 for GCC 4.8 series (#1392) + - rename GenomeAnalysisTk easyconfigs to GATK (#1399) + - include openssl-devel SLES11 OS dependency in cURL/MySQL/Python easyconfigs (#1422) + - add missing Perl dependency in parallel easyconfigs (#1430) + - correct name in BLAST+ easyconfigs (#1443) v1.16.1.0 (December 19th 2014) ------------------------------ diff --git a/setup.py b/setup.py index 6fdb0b240f..030d532e33 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "2.0.0.0dev" +VERSION = "2.0.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 273c9e69d52a40ed5fc6f6c3e2b81c70c0c618fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:34:26 +0100 Subject: [PATCH 363/911] fix moduleclass in HPCBIOS easyconfigs --- .../easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb | 2 +- .../HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb | 2 +- .../h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb | 2 +- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb index cd3235cdf1..067ccdbe63 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150119-GCC-4.9.2.eb @@ -14,4 +14,4 @@ dependencies = [ ('libtool', '2.4.5'), # 20150119 ] -moduleclass = 'bundle' +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb index 19dccf4c5a..b103b8110e 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-goolf-1.4.10.eb @@ -70,4 +70,4 @@ dependencies = [ ('ViennaRNA', '2.0.7'), ] -moduleclass = 'bundle' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb index 34dc4faa24..e1d3fd7aa1 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb @@ -70,4 +70,4 @@ dependencies = [ ('ViennaRNA', '2.0.7'), ] -moduleclass = 'bundle' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 209941c445..76836f3aed 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -28,4 +28,4 @@ dependencies = [ ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode ] -moduleclass = 'bundle' +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb index a6bd997119..3925d65933 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-goolf-1.4.10.eb @@ -34,4 +34,4 @@ dependencies = [ # ('Rosetta', '3.5'), ] -moduleclass = 'bundle' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb index d129c36c59..fc1b20fc8e 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_LifeSciences/HPCBIOS_LifeSciences-20130829-ictce-5.3.0.eb @@ -34,4 +34,4 @@ dependencies = [ # ('Rosetta', '3.5'), ] -moduleclass = 'bundle' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb index d31e22cb47..e86ac02683 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb @@ -29,4 +29,4 @@ dependencies = [ ('GSL', '1.15'), ] -moduleclass = 'bundle' +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb index cdf41a29ac..db4a026864 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goolf-1.4.10.eb @@ -30,4 +30,4 @@ dependencies = [ ('SPRNG', '2.0b'), ] -moduleclass = 'bundle' +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb index ba99a2d9b6..b2b1287193 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-ictce-5.3.0.eb @@ -28,4 +28,4 @@ dependencies = [ ('SPRNG', '2.0b'), ] -moduleclass = 'bundle' +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index 5b73516d37..7f92d9a951 100644 --- a/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -29,4 +29,4 @@ dependencies = [ ('binutils', '2.22'), # this one provides gprof ] -moduleclass = 'bundle' +moduleclass = 'perf' -- GitLab From 52c16302befaae6afbcf42eba058dd2a2993a218 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:38:15 +0100 Subject: [PATCH 364/911] fix name in google-sparsehash easyconfig --- .../g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb b/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb index e90039667a..07fe5cfe9d 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'sparsehash' +name = 'google-sparsehash' version = '2.0.2' homepage = 'https://code.google.com/p/sparsehash/' -- GitLab From 7243320abf9bcc3eefa39230a5c3b9deb22082e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:41:05 +0100 Subject: [PATCH 365/911] actually, the correct name is 'sparsehash'... --- .../sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb} | 2 +- .../sparsehash/sparsehash-goolf-1.4.10.eb} | 2 +- .../sparsehash/sparsehash-ictce-4.0.6.eb} | 2 +- .../sparsehash/sparsehash-ictce-5.3.0.eb} | 2 +- .../sparsehash/sparsehash-intel-2015a.eb} | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/{g/google-sparsehash/google-sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb => s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb} (97%) rename easybuild/easyconfigs/{g/google-sparsehash/google-sparsehash-2.0.2-goolf-1.4.10.eb => s/sparsehash/sparsehash-goolf-1.4.10.eb} (97%) rename easybuild/easyconfigs/{g/google-sparsehash/google-sparsehash-2.0.2-ictce-4.0.6.eb => s/sparsehash/sparsehash-ictce-4.0.6.eb} (97%) rename easybuild/easyconfigs/{g/google-sparsehash/google-sparsehash-2.0.2-ictce-5.3.0.eb => s/sparsehash/sparsehash-ictce-5.3.0.eb} (97%) rename easybuild/easyconfigs/{g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb => s/sparsehash/sparsehash-intel-2015a.eb} (95%) diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb similarity index 97% rename from easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb index f3f86925e6..c85808d4fd 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'google-sparsehash' +name = 'sparsehash' version = '2.0.2' homepage = 'http://code.google.com/p/google-sparsehash/' diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb similarity index 97% rename from easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goolf-1.4.10.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb index a0d26dcb60..3196f29d16 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'google-sparsehash' +name = 'sparsehash' version = '2.0.2' homepage = 'http://code.google.com/p/google-sparsehash/' diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb similarity index 97% rename from easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb index 8fa567fea4..11ae1d4125 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'google-sparsehash' +name = 'sparsehash' version = '2.0.2' homepage = 'http://code.google.com/p/google-sparsehash/' diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb similarity index 97% rename from easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-5.3.0.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb index 24f5fb8427..c01a0f11c0 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'google-sparsehash' +name = 'sparsehash' version = '2.0.2' homepage = 'http://code.google.com/p/google-sparsehash/' diff --git a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-intel-2015a.eb similarity index 95% rename from easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-intel-2015a.eb index 07fe5cfe9d..e90039667a 100644 --- a/easybuild/easyconfigs/g/google-sparsehash/google-sparsehash-2.0.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'google-sparsehash' +name = 'sparsehash' version = '2.0.2' homepage = 'https://code.google.com/p/sparsehash/' -- GitLab From e7881707d297158dc6a4bb46cb68aecb485595be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:43:25 +0100 Subject: [PATCH 366/911] include #1452 in release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3563f389c6..f5271cdbb6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -38,6 +38,7 @@ feature + bugfix release - include openssl-devel SLES11 OS dependency in cURL/MySQL/Python easyconfigs (#1422) - add missing Perl dependency in parallel easyconfigs (#1430) - correct name in BLAST+ easyconfigs (#1443) + - fix name for sparsehash easyconfigs (#1452) v1.16.1.0 (December 19th 2014) ------------------------------ -- GitLab From ca5240c0e6c41bd7684d9b01539fb366e1c2dfa9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 17:43:49 +0100 Subject: [PATCH 367/911] fix name of sparsehash dep in ABySS easyconfig --- .../a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb index 418f170236..cdc9d8c7ad 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] dependencies = [ - ('google-sparsehash', '2.0.2'), + ('sparsehash', '2.0.2'), ('Boost', '1.49.0', versionsuffix), ] -- GitLab From 4395afea302c4c99928e8bc51564bf4e4ed20f40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 18:15:50 +0100 Subject: [PATCH 368/911] fix 'sources' spec in sparsehash easyconfigs --- .../easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb | 3 +-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb index c85808d4fd..8f5d666a8c 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ description = """An extremely memory-efficient hash_map implementation. 2 bits/e toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} -sources = ['%s-%s.tar.gz' % (name.split('-')[1].lower(), version)] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] runtest = "check" diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb index 3196f29d16..2c1c772b75 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb @@ -6,10 +6,11 @@ version = '2.0.2' homepage = 'http://code.google.com/p/google-sparsehash/' description = """An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} -sources = ['%s-%s.tar.gz' % (name.split('-')[1].lower(), version)] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] runtest = "check" diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb index 11ae1d4125..0e8273491c 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb @@ -10,7 +10,7 @@ description = """An extremely memory-efficient hash_map implementation. 2 bits/e toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} -sources = ['%s-%s.tar.gz' % (name.split('-')[1].lower(), version)] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] #runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb index c01a0f11c0..ef04dcc09e 100644 --- a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb @@ -7,11 +7,10 @@ homepage = 'http://code.google.com/p/google-sparsehash/' description = """An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} -sources = ['%s-%s.tar.gz' % (name.split('-')[1].lower(), version)] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sparsehash.googlecode.com/files'] #runtest = "check" # 1/7 tests fails (hashtable_test), so disabling 'make check' for now -- GitLab From dec0b64b36042bebb84fa52cf8eb919db03b5b18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 18:33:27 +0100 Subject: [PATCH 369/911] fix filenames for sparsehash easyconfigs --- ...f-1.1.0-no-OFED.eb => sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb} | 0 ...parsehash-goolf-1.4.10.eb => sparsehash-2.0.2-goolf-1.4.10.eb} | 0 ...{sparsehash-ictce-4.0.6.eb => sparsehash-2.0.2-ictce-4.0.6.eb} | 0 ...{sparsehash-ictce-5.3.0.eb => sparsehash-2.0.2-ictce-5.3.0.eb} | 0 ...{sparsehash-intel-2015a.eb => sparsehash-2.0.2-intel-2015a.eb} | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/sparsehash/{sparsehash-goalf-1.1.0-no-OFED.eb => sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb} (100%) rename easybuild/easyconfigs/s/sparsehash/{sparsehash-goolf-1.4.10.eb => sparsehash-2.0.2-goolf-1.4.10.eb} (100%) rename easybuild/easyconfigs/s/sparsehash/{sparsehash-ictce-4.0.6.eb => sparsehash-2.0.2-ictce-4.0.6.eb} (100%) rename easybuild/easyconfigs/s/sparsehash/{sparsehash-ictce-5.3.0.eb => sparsehash-2.0.2-ictce-5.3.0.eb} (100%) rename easybuild/easyconfigs/s/sparsehash/{sparsehash-intel-2015a.eb => sparsehash-2.0.2-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-goolf-1.4.10.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-4.0.6.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-ictce-5.3.0.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-intel-2015a.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/s/sparsehash/sparsehash-intel-2015a.eb rename to easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.2-intel-2015a.eb -- GitLab From 3a81d454733709a07dd1a450d6313d3d0d0f3fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 18:50:21 +0100 Subject: [PATCH 370/911] minor fixes in release notes --- RELEASE_NOTES | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f5271cdbb6..133fd064f1 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -15,7 +15,7 @@ feature + bugfix release bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) - added easyconfigs for new (common) toolchains foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) -- added new bundles: Autotools (#1385) +- added new software bundle: Autotools (#1385) - various other enhancements, including: - don't define $LDSHARED in zlib easyconfigs (#1350) - this fixes the long-standing "no version information available" issue with zlib @@ -25,7 +25,7 @@ feature + bugfix release - speeding up the unit tests by avoiding rereading of same easyconfig file (#1432) - fix conflict detection in unit tests by considering build deps separately from runtime deps (#1447) - fix toolchain for Bison build dep in MVAPICH2-1.9-iccifort-2011.13.367.eb easyconfig (#1448) - - use Bundle generic easyblock and 'bundle' moduleclass for software bundles (#1451) + - use Bundle generic easyblock for HPCBIOS bundles and fix moduleclass (#1451) - various bug fixes, including: - revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144) - added Java dependencies to EMBOSS easyconfigs (#1167) -- GitLab From ae204ecf1c07f3ad9f67eeeda3ac287ed1d1dae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 20:47:04 +0100 Subject: [PATCH 371/911] add easyconfig file for EasyBuild v1.16.2 --- .../e/EasyBuild/EasyBuild-1.16.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb new file mode 100644 index 0000000000..8f07608f03 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "1.16.2" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.0.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 28fcb4ccff4cecf3adfae89875b9b911b805fc8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 20:47:29 +0100 Subject: [PATCH 372/911] add easyconfig file for EasyBuild v2.0.0 --- .../e/EasyBuild/EasyBuild-2.0.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb new file mode 100644 index 0000000000..c0ecf89fd6 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.0.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.0.3.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From fc1a90acbc5d9b86a71c069f69ff2f66d92372dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Mar 2015 21:06:57 +0100 Subject: [PATCH 373/911] bump version to v1.16.2.0, update release notes --- RELEASE_NOTES | 5 +++++ setup.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 01b1286c29..025b011209 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,11 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 3,066 easyconfig files, for 551 different software packages and 32 different (compiler) toolchains. +v1.16.2.0 (March 6th 2015) +-------------------------- + +(no changes compared to v1.16.1.0, simple version bump to stay in sync with easybuild-easyblocks) + v1.16.1.0 (December 19th 2014) ------------------------------ diff --git a/setup.py b/setup.py index a37161620a..99ab5ad312 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "1.16.1.0" +VERSION = "1.16.2.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 1214db6356a0d4ec9c55f393cec15de8523c2618 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Mar 2015 18:55:17 +0100 Subject: [PATCH 374/911] bump version to v2.1.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 030d532e33..e23ed2d782 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "2.0.0" +VERSION = "2.1.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From c554949dd37aec86ae4ce8112bc2440a5bc65641 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Mar 2015 11:30:59 +0100 Subject: [PATCH 375/911] bump vsc-base dep for v2.0.4 --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index c0ecf89fd6..2528629319 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -18,7 +18,7 @@ source_urls = [ ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ - 'vsc-base-2.0.3.tar.gz', + 'vsc-base-2.0.4.tar.gz', 'easybuild-framework-%(version)s.tar.gz', 'easybuild-easyblocks-%(version)s.tar.gz', 'easybuild-easyconfigs-%(version)s.tar.gz', -- GitLab From d6df555ece4aa4a319de43d2c851515ca585252a Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 12:01:07 -0500 Subject: [PATCH 376/911] adding the foss-2015a with fpm easyconfig --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb new file mode 100644 index 0000000000..f53f7ccb61 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + + +exts_list = [ + ('fpm', '1.3.3', { + 'source_tmpl': 'fpm-1.3.3.gem', + 'source_urls': ['http://rubygems.org/downloads/'], + }), + +] -- GitLab From c3c8683809ff1c8bdf8e6cb3c07cd452922d5c7e Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 15:14:34 -0500 Subject: [PATCH 377/911] moving fpm to bundle separate from the base ruby install --- .../Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 31 +++++++++++++++++++ .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 8 ----- 2 files changed, 31 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb new file mode 100644 index 0000000000..e9351e062d --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'Bundle' + +name = 'Ruby-FPM' +rubyver = '2.1.5' +version = '%s-1.0.0' % rubyver + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# these are extensions for Ruby +exts_defaultclass = 'RubyGem' +exts_filter = ("gem list %(ext_name)s -i", "") + +dependencies = [ + ('Ruby', rubyver), +] + +name_tmpl = '%(name)s-%(version)s.gem' +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} +exts_list = [ + ('fpm', '1.3.3', ext_options), +] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb index f53f7ccb61..c585ab1d31 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -31,11 +31,3 @@ configopts = "--disable-install-doc --enable-shared" moduleclass = 'lang' - -exts_list = [ - ('fpm', '1.3.3', { - 'source_tmpl': 'fpm-1.3.3.gem', - 'source_urls': ['http://rubygems.org/downloads/'], - }), - -] -- GitLab From 52eed5d1cc5b7a1e5babfb57488ef725532f066f Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 21:42:57 -0500 Subject: [PATCH 378/911] adding dependency gems --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index e9351e062d..d664b9bdb3 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -27,5 +27,11 @@ ext_options = { 'source_tmpl': name_tmpl, } exts_list = [ - ('fpm', '1.3.3', ext_options), + ('fpm', '1.3.3', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('ffi', '1.9.6', ext_options), ] -- GitLab From 720160c0eb33b58802856a76ba723af6185f00e2 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Tue, 3 Mar 2015 21:57:58 -0500 Subject: [PATCH 379/911] missed childprocess dep --- .../easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index d664b9bdb3..c4f32ff0e9 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -34,4 +34,5 @@ exts_list = [ ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), ] -- GitLab From 6f768482ad7e828f631cf3cf98dc6a04e732e5db Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Wed, 4 Mar 2015 10:15:32 -0500 Subject: [PATCH 380/911] reorder dependencies to work with local only gem installer --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb index c4f32ff0e9..1aa58a2ac6 100644 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb @@ -27,12 +27,12 @@ ext_options = { 'source_tmpl': name_tmpl, } exts_list = [ - ('fpm', '1.3.3', ext_options), + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), ('json', '1.8.2', ext_options), ('cabin', '0.7.1', ext_options), ('backports', '3.6.4', ext_options), ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), + ('fpm', '1.3.3', ext_options), ] -- GitLab From 7ea5926e46c0e53ed04d704f91c17ade7ed7847f Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 10 Mar 2015 15:53:19 +0100 Subject: [PATCH 381/911] blast+ 2.2.30 and patch --- .../b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb | 38 +++++++++++++++++++ .../easyconfigs/b/BLAST/blast-2.2.30+.patch | 12 ++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb new file mode 100644 index 0000000000..1445f24f31 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'BLAST' +version = "2.2.30" + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['blast-2.2.30+.patch'] + +dependencies = [('Boost', '1.51.0')] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch b/easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch new file mode 100644 index 0000000000..72a5eeeecc --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch @@ -0,0 +1,12 @@ +diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top +--- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top 2014-08-01 20:43:59.000000000 +0200 ++++ ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top 2015-03-10 15:11:09.140548221 +0100 +@@ -46,7 +46,7 @@ + -rm -f $(libdir)/lib*-static.a + cd $(libdir) && \ + for x in *.a; do \ +- $(LN_S) "$$x" "`/usr/bin/basename \"$$x\" .a`-static.a"; \ ++ $(LN_S) "$$x" "`basename \"$$x\" .a`-static.a"; \ + done + cd $(includedir0) && find * -name CVS -prune -o -print |\ + cpio -pd $(pincludedir) -- GitLab From c4aef62dc56c7d908b34ae09442013061e844296 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 10:57:13 +0100 Subject: [PATCH 382/911] moved easyconfigs to BLAST+ folder --- .../BLAST+-2.2.30-goolf-1.4.10.eb} | 2 +- easybuild/easyconfigs/b/{BLAST => BLAST+}/blast-2.2.30+.patch | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/{BLAST/BLAST-2.2.30-goolf-1.4.10.eb => BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb} (98%) rename easybuild/easyconfigs/b/{BLAST => BLAST+}/blast-2.2.30+.patch (100%) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 1445f24f31..18f254d821 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## -name = 'BLAST' +name = 'BLAST+' version = "2.2.30" homepage = 'http://blast.ncbi.nlm.nih.gov/' diff --git a/easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch b/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/blast-2.2.30+.patch rename to easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch -- GitLab From 6a684729ace61acba4886e469c161522a11f4d26 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 10:59:34 +0100 Subject: [PATCH 383/911] added easyblock=configuremake --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 18f254d821..e4849b66af 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -10,6 +10,8 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## +easyblock = 'ConfigureMake' + name = 'BLAST+' version = "2.2.30" -- GitLab From 687239def20791c6b071ef734e6793b85c255389 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Mar 2015 12:45:47 +0100 Subject: [PATCH 384/911] Disable makeinfo for GDB --- easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb index a1ba41f0f4..f862997251 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('ncurses', '5.9')] +configopts = 'MAKEINFO=false' parallel = 1 sanity_check_paths = { -- GitLab From 135e87c38807b71c94d6a8fb8e2aba8d97572ae9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Mar 2015 13:46:09 +0100 Subject: [PATCH 385/911] Another try for makeinfo --- easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb index f862997251..5b0f7725b7 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('ncurses', '5.9')] -configopts = 'MAKEINFO=false' +configopts = 'MAKEINFO=true' parallel = 1 sanity_check_paths = { -- GitLab From 8052b79ff25cfeef59f1d949e3abab732a2e62fe Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 13:58:39 +0100 Subject: [PATCH 386/911] added comment to patch file --- easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch b/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch index 72a5eeeecc..b4d018091b 100644 --- a/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch +++ b/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch @@ -1,3 +1,5 @@ +/* don't hardcode path to basename - Pablo Escobar (sciCORE, SIB, UniBAS) */ + diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top --- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top 2014-08-01 20:43:59.000000000 +0200 +++ ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top 2015-03-10 15:11:09.140548221 +0100 -- GitLab From 8d702807a85cd8ff96789f662b6f4a074c01032a Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 14:07:17 +0100 Subject: [PATCH 387/911] updated patch comment --- easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch b/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch index b4d018091b..ee0c779bf9 100644 --- a/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch +++ b/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch @@ -1,4 +1,4 @@ -/* don't hardcode path to basename - Pablo Escobar (sciCORE, SIB, UniBAS) */ +don't hardcode path to basename - Pablo Escobar (sciCORE, SIB, UniBAS) diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top --- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top 2014-08-01 20:43:59.000000000 +0200 -- GitLab From 21c21fbec35b41aef3e069522a80b79c7c6f5336 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 14:21:08 +0100 Subject: [PATCH 388/911] changed patch name updated easyconfig --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 +- .../b/BLAST+/{blast-2.2.30+.patch => blast+_2.2.30.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/BLAST+/{blast-2.2.30+.patch => blast+_2.2.30.patch} (100%) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index e4849b66af..ef50a95d00 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -25,7 +25,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -patches = ['blast-2.2.30+.patch'] +patches = ['blast+_%(version)s.patch'] dependencies = [('Boost', '1.51.0')] diff --git a/easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch b/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST+/blast-2.2.30+.patch rename to easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch -- GitLab From 499648742fd8267915e29358da2ab07f967922b5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Mar 2015 14:24:15 +0100 Subject: [PATCH 389/911] Final fix? for missing makeinfo --- easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb | 3 ++- .../g/GDB/GDB-7.9-missing-makeinfo.patch | 13 +++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb index 5b0f7725b7..cfd83fc09a 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-GCC-4.9.2.eb @@ -13,7 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('ncurses', '5.9')] -configopts = 'MAKEINFO=true' +patches = ['GDB-%(version)s-missing-makeinfo.patch'] + parallel = 1 sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch new file mode 100644 index 0000000000..6f22a427df --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch @@ -0,0 +1,13 @@ +# Don't let the make fail when makeinfo is not found +diff -ur gdb-7.9.orig/missing gdb-7.9/missing +--- gdb-7.9.orig/missing 2015-02-19 12:58:08.000000000 +0100 ++++ gdb-7.9/missing 2015-03-11 14:22:52.000000000 +0100 +@@ -204,7 +204,7 @@ + + # Propagate the correct exit status (expected to be 127 for a program + # not found, 63 for a program that failed due to version mismatch). +-exit $st ++exit 0 + + # Local variables: + # eval: (add-hook 'write-file-hooks 'time-stamp) -- GitLab From 393442a5357700ecde7d19cbf89c3f5f801a2876 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 15:29:49 +0100 Subject: [PATCH 390/911] added comment about the patch --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index ef50a95d00..f306341fc4 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -25,6 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +# patch not needed in BLAST+ 2.2.31 or higher +# http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 patches = ['blast+_%(version)s.patch'] dependencies = [('Boost', '1.51.0')] diff --git a/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch b/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch index ee0c779bf9..d5d2d3b8b7 100644 --- a/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch +++ b/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch @@ -1,4 +1,6 @@ don't hardcode path to basename - Pablo Escobar (sciCORE, SIB, UniBAS) +This patch is not needed in BLAST+ version 2.2.31 or higher +http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top --- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top 2014-08-01 20:43:59.000000000 +0200 -- GitLab From 87ffeb251547e84febfef08a4b15bd8094a5e34c Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 11 Mar 2015 15:46:22 +0100 Subject: [PATCH 391/911] switched to http download url --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index f306341fc4..3fd6b2b7dd 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -23,7 +23,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] # patch not needed in BLAST+ 2.2.31 or higher # http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 -- GitLab From aae9e84586e55b47a7dbe0a047c4036b1c1d247c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Mar 2015 17:40:41 +0100 Subject: [PATCH 392/911] Extend comments in patch --- easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch index 6f22a427df..2e1e633cca 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch @@ -1,4 +1,9 @@ -# Don't let the make fail when makeinfo is not found +# Don't let the make fail when makeinfo is not found. +# The missing script is supposed to handle missing deps for the build, +# but by return the actual exit code, the build will still fail. +# In GDB 7.8, they always return 0 as exit code. This patch does the +# same. +# Bug report at https://sourceware.org/bugzilla/show_bug.cgi?id=18113 diff -ur gdb-7.9.orig/missing gdb-7.9/missing --- gdb-7.9.orig/missing 2015-02-19 12:58:08.000000000 +0100 +++ gdb-7.9/missing 2015-03-11 14:22:52.000000000 +0100 -- GitLab From a19b1f5ac2222ae1c1e9df1ecc58ca8160bd2cbd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Mar 2015 17:43:50 +0100 Subject: [PATCH 393/911] Fix typo --- easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch index 2e1e633cca..68ed99f5bb 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch +++ b/easybuild/easyconfigs/g/GDB/GDB-7.9-missing-makeinfo.patch @@ -1,6 +1,6 @@ # Don't let the make fail when makeinfo is not found. # The missing script is supposed to handle missing deps for the build, -# but by return the actual exit code, the build will still fail. +# but by returning the actual exit code, the build will still fail. # In GDB 7.8, they always return 0 as exit code. This patch does the # same. # Bug report at https://sourceware.org/bugzilla/show_bug.cgi?id=18113 -- GitLab From 0315cb76b9039b530c7052ea9d12a2a446a9c119 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 Mar 2015 21:30:05 +0100 Subject: [PATCH 394/911] Dummy --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From 55c7f0c38dd71ea9e5ea4a552350e4071db64dd2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 Mar 2015 21:50:00 +0100 Subject: [PATCH 395/911] METIS 5.1.0 with foss-2015a --- .../c/CMake/CMake-3.1.3-foss-2015a.eb | 22 +++++++++++++++++++ .../m/METIS/METIS-5.1.0-foss-2015a.eb | 21 +++++++++++++++++- 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-foss-2015a.eb new file mode 100644 index 0000000000..543c9cc79f --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.1.3' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb index 421376db9e..f49db11981 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-foss-2015a.eb @@ -1 +1,20 @@ -dummy +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, + and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the + multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +builddependencies = [('CMake', '3.1.3')] + +moduleclass = 'math' -- GitLab From be5769137332cb9a52ceba26a93dbebcbade5bad Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 Mar 2015 22:05:25 +0100 Subject: [PATCH 396/911] Dummy --- .../easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From 267de71bffdb02e149df2cdfd6201a93469ebbf2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 Mar 2015 22:56:42 +0100 Subject: [PATCH 397/911] beagle-lib 20141202 aka r1261 with intel-2015a --- .../beagle-lib-20141202-intel-2015a.eb | 37 ++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 421376db9e..6958ac7224 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -1 +1,36 @@ -dummy +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +#revision r1261 +version = '20141202' + +homepage = 'http://code.google.com/p/beagle-lib/' +description = """beagle-lib is a high-performance library that can perform the core + calculations at the heart of most Bayesian and Maximum Likelihood + phylogenetics packages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# there is no tarball provided, only SVN checkout through: +# svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib +sources = [SOURCE_TGZ] + +dependencies = [ + ('Java', '1.8.0_31', '', True), + ('Autoconf', '2.69') +] + +preconfigopts = './autogen.sh && ' + +# parallel build does not work +parallel = 1 + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni" ,""]], + 'dirs' : [] +} + +moduleclass = 'numlib' -- GitLab From 1c37e81e008046dd3187a6bfda113e924063485a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 12 Mar 2015 11:12:39 +0100 Subject: [PATCH 399/911] remove more whitespace --- easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb index 7e01fd3fc1..785c4e7264 100644 --- a/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb +++ b/easybuild/easyconfigs/g/gtest/gtest-1.6.0-intel-2014b.eb @@ -13,7 +13,6 @@ source_urls = ['https://googletest.googlecode.com/files'] with_configure = True - files_to_copy = ['lib', 'include'] sanity_check_paths={ -- GitLab From 2f3137a843dc1fba6b210697efbb01911af576f7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 Mar 2015 12:24:23 +0100 Subject: [PATCH 400/911] Lockfile needs pbr --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index ee34812203..551b551518 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -55,6 +55,9 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), + ('pbr', '0.10.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 51b20dc349..476f839933 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -55,6 +55,9 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), + ('pbr', '0.10.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 9107501405..70fcbf0f5a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -58,6 +58,9 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), + ('pbr', '0.10.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), -- GitLab From 145a8d36f0e0b5a9d1e70abeb9c9a37d74b8151d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 Mar 2015 12:29:10 +0100 Subject: [PATCH 401/911] dummy --- .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1 @@ +dummy -- GitLab From 95fea9259170e69655d68e0774868a690e210048 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 Mar 2015 14:08:54 +0100 Subject: [PATCH 402/911] Matplotlib 1.4.3-Python-2.7.9 with deps --- .../f/freetype/freetype-2.5.5-foss-2015a.eb | 21 ++++++++++ .../f/freetype/freetype-2.5.5-intel-2015a.eb | 21 ++++++++++ .../m/matplotlib/Qhull-intel-fix.patch | 22 ++++++++++ ...atplotlib-1.4.3-foss-2015a-Python-2.7.9.eb | 39 +++++++++++++++++ ...tplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 42 ++++++++++++++++++- .../mock-1.0.1-foss-2015a-Python-2.7.9.eb | 35 ++++++++++++++++ .../mock-1.0.1-intel-2015a-Python-2.7.9.eb | 35 ++++++++++++++++ .../pytz-2014.10-foss-2015a-Python-2.7.9.eb | 31 ++++++++++++++ .../pytz-2014.10-intel-2015a-Python-2.7.9.eb | 31 ++++++++++++++ 9 files changed, 276 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb new file mode 100644 index 0000000000..a62c8bab17 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb new file mode 100644 index 0000000000..3f93bd6070 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch b/easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch new file mode 100644 index 0000000000..d0e795131e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch @@ -0,0 +1,22 @@ +# they use some weird template thing in pure C code to avoid +# warnings, I think, but only for intel compilers +# We remove the special case for intel and use the general one +# Ward Poelmans +--- matplotlib-1.4.3/extern/qhull/qhull_a.h.org 2012-01-26 04:32:07.000000000 +0100 ++++ matplotlib-1.4.3/extern/qhull/qhull_a.h 2014-10-01 11:49:18.000000000 +0200 +@@ -102,13 +102,8 @@ + #elif defined(__MWERKS__) && defined(__INTEL__) + # define QHULL_OS_WIN + #endif +-#if defined(__INTEL_COMPILER) && !defined(QHULL_OS_WIN) +-template +-inline void qhullUnused(T &x) { (void)x; } +-# define QHULL_UNUSED(x) qhullUnused(x); +-#else +-# define QHULL_UNUSED(x) (void)x; +-#endif ++ ++#define QHULL_UNUSED(x) (void)x; + + /***** -libqhull.c prototypes (alphabetical after qhull) ********************/ + diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2a6d8ee18f --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('mock', '1.0.1', versionsuffix), + ('pytz', '2014.10', versionsuffix), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 421376db9e..5c56e9a7ef 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -1 +1,41 @@ -dummy +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('mock', '1.0.1', versionsuffix), + ('pytz', '2014.10', versionsuffix), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..baada2e6cf --- /dev/null +++ b/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'mock' +version = '1.0.1' + +homepage = 'https://pypi.python.org/pypi/mock' +description = """A Python Mocking and Patching Library for Testing. + mock is a library for testing in Python. + It allows you to replace parts of your system under test + with mock objects and make assertions about how they have been used.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +#mock is part of Python 3.3 +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..afc6e7f4bc --- /dev/null +++ b/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'mock' +version = '1.0.1' + +homepage = 'https://pypi.python.org/pypi/mock' +description = """A Python Mocking and Patching Library for Testing. + mock is a library for testing in Python. + It allows you to replace parts of your system under test + with mock objects and make assertions about how they have been used.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +#mock is part of Python 3.3 +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2362eab77c --- /dev/null +++ b/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'pytz' +version = '2014.10' + +homepage = 'https://pypi.python.org/pypi/pytz' +description = """World timezone definitions, modern and historical.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..37fedc7a5b --- /dev/null +++ b/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'pytz' +version = '2014.10' + +homepage = 'https://pypi.python.org/pypi/pytz' +description = """World timezone definitions, modern and historical.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'system' -- GitLab From 954367dbabde8e71950c96308f3fc11009afabbc Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 12 Mar 2015 14:15:15 +0100 Subject: [PATCH 403/911] bump to boost-1.57.0 --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 3fd6b2b7dd..54dfbd50cc 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s # http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 patches = ['blast+_%(version)s.patch'] -dependencies = [('Boost', '1.51.0')] +dependencies = [('Boost', '1.57.0')] configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' -- GitLab From d906ad3459bc3f62f94fb1307083dabde3c23a9f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 12 Mar 2015 14:26:26 +0100 Subject: [PATCH 404/911] Deps moved from another PR (plus some extra) --- .../a/Autoconf/Autoconf-2.69-intel-2015a.eb | 25 ++++++++++++++ .../a/Automake/Automake-1.15-intel-2015a.eb | 33 +++++++++++++++++++ .../makedepend-1.0.5-intel-2015a.eb | 20 +++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb new file mode 100644 index 0000000000..a3c280daab --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically + configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like + systems without manual user intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb new file mode 100644 index 0000000000..3a528809f4 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2015a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnu.org/gnu/automake'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb new file mode 100644 index 0000000000..0b36b37c50 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.5' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/releases/individual/util'] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 3c68831530aa8a1d3045a530f648ad4db09b98f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Mar 2015 15:05:24 +0100 Subject: [PATCH 405/911] {devel}[goolf/1.4.10] Boost 1.57.0 (REVIEW) --- .../b/Boost/Boost-1.57.0-goolf-1.4.10.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.57.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.57.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..d038bec2b5 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.57.0-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.57.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3890f73cfc0a9de5834792649c7e43352670b2e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Mar 2015 16:17:18 +0100 Subject: [PATCH 406/911] add easyconfig file for TINKER v7.1.2 with intel/2015a --- .../t/TINKER/TINKER-7.1.2-intel-2015a.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb new file mode 100644 index 0000000000..d61fb49b07 --- /dev/null +++ b/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb @@ -0,0 +1,15 @@ +name = 'TINKER' +version = '7.1.2' + +homepage = 'http://dasher.wustl.edu/tinker' +description = """The TINKER molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +runtest = True + +moduleclass = 'chem' -- GitLab From 4f5a6c0914ed9adea45d845d6d45a28224b60e0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Mar 2015 17:07:42 +0100 Subject: [PATCH 407/911] add FFTW dep to TINKER easyconfig --- .../f/FFTW/FFTW-3.3.4-intel-2015a.eb | 34 +++++++++++++++++++ .../t/TINKER/TINKER-7.1.2-intel-2015a.eb | 2 ++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb new file mode 100644 index 0000000000..ce8a9b16ca --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +# see also http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb index d61fb49b07..814e32e34a 100644 --- a/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/t/TINKER/TINKER-7.1.2-intel-2015a.eb @@ -10,6 +10,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://dasher.wustl.edu/tinker/downloads/'] sources = [SOURCELOWER_TAR_GZ] +dependencies = [('FFTW', '3.3.4')] + runtest = True moduleclass = 'chem' -- GitLab From ff730443688b2bfd3574ab0865db440120849c30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 11:41:26 +0100 Subject: [PATCH 408/911] add missing extensions in Python 2.7.8 goolf/1.5.14 easyconfig --- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index df184b1c3e..9be6d7955c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -25,10 +25,9 @@ dependencies = [ # ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! -# Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], @@ -48,8 +47,11 @@ exts_list = [ ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), - ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + ('bdist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/bdist/'], + }), + ('six', '1.7.3', { + 'source_urls': ['http://pypi.python.org/packages/source/s/six/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], @@ -84,12 +86,19 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), ('pyparsing', '2.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], }), + ('pygments', '1.6', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'source_tmpl': 'Pygments-%(version)s.tar.gz', + }), ] moduleclass = 'lang' -- GitLab From 5627067f6235a9cadfbec358476bce98686383cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 11:59:32 +0100 Subject: [PATCH 409/911] fix typo: bdist -> blist --- easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 9be6d7955c..2dd2282def 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -47,8 +47,8 @@ exts_list = [ ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), - ('bdist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/bdist/'], + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), ('six', '1.7.3', { 'source_urls': ['http://pypi.python.org/packages/source/s/six/'], -- GitLab From 2cb09b0dc209e8861da69e9d19dd244adc549a98 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 12:03:33 +0100 Subject: [PATCH 410/911] added sqlite as dependency for python 2.7.9 --- .../easyconfigs/p/.ropeproject/config.py | 85 +++++++++++++++++++ .../easyconfigs/p/.ropeproject/globalnames | 1 + easybuild/easyconfigs/p/.ropeproject/history | 1 + easybuild/easyconfigs/p/.ropeproject/objectdb | 1 + .../p/Python/.ropeproject/config.py | 85 +++++++++++++++++++ .../p/Python/.ropeproject/globalnames | 1 + .../easyconfigs/p/Python/.ropeproject/history | 1 + .../p/Python/.ropeproject/objectdb | 1 + .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 + .../p/Python/Python-2.7.9-foss-2015a.eb | 2 + .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 4 +- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 + .../p/Python/Python-2.7.9-intel-2015a.eb | 2 + .../s/SQLite/SQLite-3.8.8.1-foss-2015a.eb | 38 +++++++++ 16 files changed, 227 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/.ropeproject/config.py create mode 100644 easybuild/easyconfigs/p/.ropeproject/globalnames create mode 100644 easybuild/easyconfigs/p/.ropeproject/history create mode 100644 easybuild/easyconfigs/p/.ropeproject/objectdb create mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/config.py create mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/globalnames create mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/history create mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/objectdb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/.ropeproject/config.py b/easybuild/easyconfigs/p/.ropeproject/config.py new file mode 100644 index 0000000000..ffebcd4fc3 --- /dev/null +++ b/easybuild/easyconfigs/p/.ropeproject/config.py @@ -0,0 +1,85 @@ +# The default ``config.py`` + + +def set_prefs(prefs): + """This function is called before opening the project""" + + # Specify which files and folders to ignore in the project. + # Changes to ignored resources are not added to the history and + # VCSs. Also they are not returned in `Project.get_files()`. + # Note that ``?`` and ``*`` match all characters but slashes. + # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc' + # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc' + # '.svn': matches 'pkg/.svn' and all of its children + # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o' + # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o' + prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject', + '.hg', '.svn', '_svn', '.git'] + + # Specifies which files should be considered python files. It is + # useful when you have scripts inside your project. Only files + # ending with ``.py`` are considered to be python files by + # default. + #prefs['python_files'] = ['*.py'] + + # Custom source folders: By default rope searches the project + # for finding source folders (folders that should be searched + # for finding modules). You can add paths to that list. Note + # that rope guesses project source folders correctly most of the + # time; use this if you have any problems. + # The folders should be relative to project root and use '/' for + # separating folders regardless of the platform rope is running on. + # 'src/my_source_folder' for instance. + #prefs.add('source_folders', 'src') + + # You can extend python path for looking up modules + #prefs.add('python_path', '~/python/') + + # Should rope save object information or not. + prefs['save_objectdb'] = True + prefs['compress_objectdb'] = False + + # If `True`, rope analyzes each module when it is being saved. + prefs['automatic_soa'] = True + # The depth of calls to follow in static object analysis + prefs['soa_followed_calls'] = 0 + + # If `False` when running modules or unit tests "dynamic object + # analysis" is turned off. This makes them much faster. + prefs['perform_doa'] = True + + # Rope can check the validity of its object DB when running. + prefs['validate_objectdb'] = True + + # How many undos to hold? + prefs['max_history_items'] = 32 + + # Shows whether to save history across sessions. + prefs['save_history'] = True + prefs['compress_history'] = False + + # Set the number spaces used for indenting. According to + # :PEP:`8`, it is best to use 4 spaces. Since most of rope's + # unit-tests use 4 spaces it is more reliable, too. + prefs['indent_size'] = 4 + + # Builtin and c-extension modules that are allowed to be imported + # and inspected by rope. + prefs['extension_modules'] = [] + + # Add all standard c-extensions to extension_modules list. + prefs['import_dynload_stdmods'] = True + + # If `True` modules with syntax errors are considered to be empty. + # The default value is `False`; When `False` syntax errors raise + # `rope.base.exceptions.ModuleSyntaxError` exception. + prefs['ignore_syntax_errors'] = False + + # If `True`, rope ignores unresolvable imports. Otherwise, they + # appear in the importing namespace. + prefs['ignore_bad_imports'] = False + + +def project_opened(project): + """This function is called after opening the project""" + # Do whatever you like here! diff --git a/easybuild/easyconfigs/p/.ropeproject/globalnames b/easybuild/easyconfigs/p/.ropeproject/globalnames new file mode 100644 index 0000000000..29c40cda94 --- /dev/null +++ b/easybuild/easyconfigs/p/.ropeproject/globalnames @@ -0,0 +1 @@ +€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/.ropeproject/history b/easybuild/easyconfigs/p/.ropeproject/history new file mode 100644 index 0000000000..fcd9c963ca --- /dev/null +++ b/easybuild/easyconfigs/p/.ropeproject/history @@ -0,0 +1 @@ +€]q(]q]qe. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/.ropeproject/objectdb b/easybuild/easyconfigs/p/.ropeproject/objectdb new file mode 100644 index 0000000000..29c40cda94 --- /dev/null +++ b/easybuild/easyconfigs/p/.ropeproject/objectdb @@ -0,0 +1 @@ +€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/config.py b/easybuild/easyconfigs/p/Python/.ropeproject/config.py new file mode 100644 index 0000000000..ffebcd4fc3 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/.ropeproject/config.py @@ -0,0 +1,85 @@ +# The default ``config.py`` + + +def set_prefs(prefs): + """This function is called before opening the project""" + + # Specify which files and folders to ignore in the project. + # Changes to ignored resources are not added to the history and + # VCSs. Also they are not returned in `Project.get_files()`. + # Note that ``?`` and ``*`` match all characters but slashes. + # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc' + # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc' + # '.svn': matches 'pkg/.svn' and all of its children + # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o' + # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o' + prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject', + '.hg', '.svn', '_svn', '.git'] + + # Specifies which files should be considered python files. It is + # useful when you have scripts inside your project. Only files + # ending with ``.py`` are considered to be python files by + # default. + #prefs['python_files'] = ['*.py'] + + # Custom source folders: By default rope searches the project + # for finding source folders (folders that should be searched + # for finding modules). You can add paths to that list. Note + # that rope guesses project source folders correctly most of the + # time; use this if you have any problems. + # The folders should be relative to project root and use '/' for + # separating folders regardless of the platform rope is running on. + # 'src/my_source_folder' for instance. + #prefs.add('source_folders', 'src') + + # You can extend python path for looking up modules + #prefs.add('python_path', '~/python/') + + # Should rope save object information or not. + prefs['save_objectdb'] = True + prefs['compress_objectdb'] = False + + # If `True`, rope analyzes each module when it is being saved. + prefs['automatic_soa'] = True + # The depth of calls to follow in static object analysis + prefs['soa_followed_calls'] = 0 + + # If `False` when running modules or unit tests "dynamic object + # analysis" is turned off. This makes them much faster. + prefs['perform_doa'] = True + + # Rope can check the validity of its object DB when running. + prefs['validate_objectdb'] = True + + # How many undos to hold? + prefs['max_history_items'] = 32 + + # Shows whether to save history across sessions. + prefs['save_history'] = True + prefs['compress_history'] = False + + # Set the number spaces used for indenting. According to + # :PEP:`8`, it is best to use 4 spaces. Since most of rope's + # unit-tests use 4 spaces it is more reliable, too. + prefs['indent_size'] = 4 + + # Builtin and c-extension modules that are allowed to be imported + # and inspected by rope. + prefs['extension_modules'] = [] + + # Add all standard c-extensions to extension_modules list. + prefs['import_dynload_stdmods'] = True + + # If `True` modules with syntax errors are considered to be empty. + # The default value is `False`; When `False` syntax errors raise + # `rope.base.exceptions.ModuleSyntaxError` exception. + prefs['ignore_syntax_errors'] = False + + # If `True`, rope ignores unresolvable imports. Otherwise, they + # appear in the importing namespace. + prefs['ignore_bad_imports'] = False + + +def project_opened(project): + """This function is called after opening the project""" + # Do whatever you like here! diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/globalnames b/easybuild/easyconfigs/p/Python/.ropeproject/globalnames new file mode 100644 index 0000000000..29c40cda94 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/.ropeproject/globalnames @@ -0,0 +1 @@ +€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/history b/easybuild/easyconfigs/p/Python/.ropeproject/history new file mode 100644 index 0000000000..fcd9c963ca --- /dev/null +++ b/easybuild/easyconfigs/p/Python/.ropeproject/history @@ -0,0 +1 @@ +€]q(]q]qe. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/objectdb b/easybuild/easyconfigs/p/Python/.ropeproject/objectdb new file mode 100644 index 0000000000..29c40cda94 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/.ropeproject/objectdb @@ -0,0 +1 @@ +€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 169427938d..3974b6e842 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -17,6 +17,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 030f78c75d..669c54c38d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,6 +18,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 921ed3e70b..d8da5a3446 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 2d2b758eb9..e206b78e22 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -16,7 +16,9 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons + ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 51b20dc349..177fc2a8fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 2ff0414bd6..d2c02867a9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,6 +18,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 45b0a6d5db..540281c3ab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons ] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb new file mode 100644 index 0000000000..a8d05d1f18 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 99d31ad04400ad217a0833d4fbe9a29fc0ca83d1 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 12:05:28 +0100 Subject: [PATCH 411/911] removed unwanted ropeproject folder --- .gitignore | 1 + .../easyconfigs/p/.ropeproject/config.py | 85 ------------------- .../easyconfigs/p/.ropeproject/globalnames | 1 - easybuild/easyconfigs/p/.ropeproject/history | 1 - easybuild/easyconfigs/p/.ropeproject/objectdb | 1 - .../p/Python/.ropeproject/config.py | 85 ------------------- .../p/Python/.ropeproject/globalnames | 1 - .../easyconfigs/p/Python/.ropeproject/history | 1 - .../p/Python/.ropeproject/objectdb | 1 - 9 files changed, 1 insertion(+), 176 deletions(-) delete mode 100644 easybuild/easyconfigs/p/.ropeproject/config.py delete mode 100644 easybuild/easyconfigs/p/.ropeproject/globalnames delete mode 100644 easybuild/easyconfigs/p/.ropeproject/history delete mode 100644 easybuild/easyconfigs/p/.ropeproject/objectdb delete mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/config.py delete mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/globalnames delete mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/history delete mode 100644 easybuild/easyconfigs/p/Python/.ropeproject/objectdb diff --git a/.gitignore b/.gitignore index c6bb2c7fdd..8179a745b4 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ build/ dist/ *egg-info/ *.swp +*.ropeproject/ diff --git a/easybuild/easyconfigs/p/.ropeproject/config.py b/easybuild/easyconfigs/p/.ropeproject/config.py deleted file mode 100644 index ffebcd4fc3..0000000000 --- a/easybuild/easyconfigs/p/.ropeproject/config.py +++ /dev/null @@ -1,85 +0,0 @@ -# The default ``config.py`` - - -def set_prefs(prefs): - """This function is called before opening the project""" - - # Specify which files and folders to ignore in the project. - # Changes to ignored resources are not added to the history and - # VCSs. Also they are not returned in `Project.get_files()`. - # Note that ``?`` and ``*`` match all characters but slashes. - # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc' - # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc' - # '.svn': matches 'pkg/.svn' and all of its children - # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o' - # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o' - prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject', - '.hg', '.svn', '_svn', '.git'] - - # Specifies which files should be considered python files. It is - # useful when you have scripts inside your project. Only files - # ending with ``.py`` are considered to be python files by - # default. - #prefs['python_files'] = ['*.py'] - - # Custom source folders: By default rope searches the project - # for finding source folders (folders that should be searched - # for finding modules). You can add paths to that list. Note - # that rope guesses project source folders correctly most of the - # time; use this if you have any problems. - # The folders should be relative to project root and use '/' for - # separating folders regardless of the platform rope is running on. - # 'src/my_source_folder' for instance. - #prefs.add('source_folders', 'src') - - # You can extend python path for looking up modules - #prefs.add('python_path', '~/python/') - - # Should rope save object information or not. - prefs['save_objectdb'] = True - prefs['compress_objectdb'] = False - - # If `True`, rope analyzes each module when it is being saved. - prefs['automatic_soa'] = True - # The depth of calls to follow in static object analysis - prefs['soa_followed_calls'] = 0 - - # If `False` when running modules or unit tests "dynamic object - # analysis" is turned off. This makes them much faster. - prefs['perform_doa'] = True - - # Rope can check the validity of its object DB when running. - prefs['validate_objectdb'] = True - - # How many undos to hold? - prefs['max_history_items'] = 32 - - # Shows whether to save history across sessions. - prefs['save_history'] = True - prefs['compress_history'] = False - - # Set the number spaces used for indenting. According to - # :PEP:`8`, it is best to use 4 spaces. Since most of rope's - # unit-tests use 4 spaces it is more reliable, too. - prefs['indent_size'] = 4 - - # Builtin and c-extension modules that are allowed to be imported - # and inspected by rope. - prefs['extension_modules'] = [] - - # Add all standard c-extensions to extension_modules list. - prefs['import_dynload_stdmods'] = True - - # If `True` modules with syntax errors are considered to be empty. - # The default value is `False`; When `False` syntax errors raise - # `rope.base.exceptions.ModuleSyntaxError` exception. - prefs['ignore_syntax_errors'] = False - - # If `True`, rope ignores unresolvable imports. Otherwise, they - # appear in the importing namespace. - prefs['ignore_bad_imports'] = False - - -def project_opened(project): - """This function is called after opening the project""" - # Do whatever you like here! diff --git a/easybuild/easyconfigs/p/.ropeproject/globalnames b/easybuild/easyconfigs/p/.ropeproject/globalnames deleted file mode 100644 index 29c40cda94..0000000000 --- a/easybuild/easyconfigs/p/.ropeproject/globalnames +++ /dev/null @@ -1 +0,0 @@ -€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/.ropeproject/history b/easybuild/easyconfigs/p/.ropeproject/history deleted file mode 100644 index fcd9c963ca..0000000000 --- a/easybuild/easyconfigs/p/.ropeproject/history +++ /dev/null @@ -1 +0,0 @@ -€]q(]q]qe. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/.ropeproject/objectdb b/easybuild/easyconfigs/p/.ropeproject/objectdb deleted file mode 100644 index 29c40cda94..0000000000 --- a/easybuild/easyconfigs/p/.ropeproject/objectdb +++ /dev/null @@ -1 +0,0 @@ -€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/config.py b/easybuild/easyconfigs/p/Python/.ropeproject/config.py deleted file mode 100644 index ffebcd4fc3..0000000000 --- a/easybuild/easyconfigs/p/Python/.ropeproject/config.py +++ /dev/null @@ -1,85 +0,0 @@ -# The default ``config.py`` - - -def set_prefs(prefs): - """This function is called before opening the project""" - - # Specify which files and folders to ignore in the project. - # Changes to ignored resources are not added to the history and - # VCSs. Also they are not returned in `Project.get_files()`. - # Note that ``?`` and ``*`` match all characters but slashes. - # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc' - # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc' - # '.svn': matches 'pkg/.svn' and all of its children - # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o' - # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o' - prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject', - '.hg', '.svn', '_svn', '.git'] - - # Specifies which files should be considered python files. It is - # useful when you have scripts inside your project. Only files - # ending with ``.py`` are considered to be python files by - # default. - #prefs['python_files'] = ['*.py'] - - # Custom source folders: By default rope searches the project - # for finding source folders (folders that should be searched - # for finding modules). You can add paths to that list. Note - # that rope guesses project source folders correctly most of the - # time; use this if you have any problems. - # The folders should be relative to project root and use '/' for - # separating folders regardless of the platform rope is running on. - # 'src/my_source_folder' for instance. - #prefs.add('source_folders', 'src') - - # You can extend python path for looking up modules - #prefs.add('python_path', '~/python/') - - # Should rope save object information or not. - prefs['save_objectdb'] = True - prefs['compress_objectdb'] = False - - # If `True`, rope analyzes each module when it is being saved. - prefs['automatic_soa'] = True - # The depth of calls to follow in static object analysis - prefs['soa_followed_calls'] = 0 - - # If `False` when running modules or unit tests "dynamic object - # analysis" is turned off. This makes them much faster. - prefs['perform_doa'] = True - - # Rope can check the validity of its object DB when running. - prefs['validate_objectdb'] = True - - # How many undos to hold? - prefs['max_history_items'] = 32 - - # Shows whether to save history across sessions. - prefs['save_history'] = True - prefs['compress_history'] = False - - # Set the number spaces used for indenting. According to - # :PEP:`8`, it is best to use 4 spaces. Since most of rope's - # unit-tests use 4 spaces it is more reliable, too. - prefs['indent_size'] = 4 - - # Builtin and c-extension modules that are allowed to be imported - # and inspected by rope. - prefs['extension_modules'] = [] - - # Add all standard c-extensions to extension_modules list. - prefs['import_dynload_stdmods'] = True - - # If `True` modules with syntax errors are considered to be empty. - # The default value is `False`; When `False` syntax errors raise - # `rope.base.exceptions.ModuleSyntaxError` exception. - prefs['ignore_syntax_errors'] = False - - # If `True`, rope ignores unresolvable imports. Otherwise, they - # appear in the importing namespace. - prefs['ignore_bad_imports'] = False - - -def project_opened(project): - """This function is called after opening the project""" - # Do whatever you like here! diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/globalnames b/easybuild/easyconfigs/p/Python/.ropeproject/globalnames deleted file mode 100644 index 29c40cda94..0000000000 --- a/easybuild/easyconfigs/p/Python/.ropeproject/globalnames +++ /dev/null @@ -1 +0,0 @@ -€}q. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/history b/easybuild/easyconfigs/p/Python/.ropeproject/history deleted file mode 100644 index fcd9c963ca..0000000000 --- a/easybuild/easyconfigs/p/Python/.ropeproject/history +++ /dev/null @@ -1 +0,0 @@ -€]q(]q]qe. \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python/.ropeproject/objectdb b/easybuild/easyconfigs/p/Python/.ropeproject/objectdb deleted file mode 100644 index 29c40cda94..0000000000 --- a/easybuild/easyconfigs/p/Python/.ropeproject/objectdb +++ /dev/null @@ -1 +0,0 @@ -€}q. \ No newline at end of file -- GitLab From 71de145001f3acb4fe14b717322a57fceaf12472 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 12:18:41 +0100 Subject: [PATCH 412/911] added more dependencies --- .../s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb | 38 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb | 38 +++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb | 38 +++++++++++++++++++ .../easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb | 21 ++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..ed00f7b981 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-GCC-4.9.2.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb new file mode 100644 index 0000000000..d4af19e4fa --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-gompi-1.5.16.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb new file mode 100644 index 0000000000..474be8f629 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.4.14'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb new file mode 100644 index 0000000000..391e0178fc --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From f7980545904f87c7b070493f30f766afebfaf072 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 12:20:36 +0100 Subject: [PATCH 413/911] fixed typo --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb index 474be8f629..763de183e3 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.5.14.eb @@ -18,7 +18,7 @@ version = '3.8.8.1' homepage = 'http://www.sqlite.org/' description = 'SQLite: SQL Database Engine in a C Library' -toolchain = {'name': 'goolf', 'version': '1.4.14'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} # eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz source_urls = ['http://www.sqlite.org/2015/'] -- GitLab From 04c57306644255f4b57ef8ea23b37f7e7ed68541 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 12:24:12 +0100 Subject: [PATCH 414/911] added more dependencies (tcl) --- .../easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb | 21 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb | 21 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb | 21 +++++++++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb new file mode 100644 index 0000000000..7affc5dcb2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb new file mode 100644 index 0000000000..b13013fafe --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb new file mode 100644 index 0000000000..dbe7dcaaa1 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From 3ff2f80f08dfc1c85b2e1973888610b058dac136 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:26:13 +0100 Subject: [PATCH 415/911] Create CP2K-2.6.0-intel-para-2014.11.eb To be used in conjunction with a proposed easyblock that supports MPICH mpi families. ```runtest = "False"``` is required because our system does not support mpirun (but can be omitted for most others) --- .../c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb new file mode 100644 index 0000000000..0d6858f5a7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb @@ -0,0 +1,40 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel-para', 'version': '2014.11'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' + +runtest = "False" -- GitLab From 53f64284ab26a809d2f6732118dca11b0c01a2f7 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:40:38 +0100 Subject: [PATCH 416/911] Use toolchain in repo --- ...0-intel-para-2014.11.eb => CP2K-2.6.0-intel-para-2014.12.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/CP2K/{CP2K-2.6.0-intel-para-2014.11.eb => CP2K-2.6.0-intel-para-2014.12.eb} (94%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb similarity index 94% rename from easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb rename to easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb index 0d6858f5a7..078ff065ca 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.11.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb @@ -7,7 +7,7 @@ description = """CP2K is a freely available (GPL) program, written in Fortran 95 methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. """ -toolchain = {'name': 'intel-para', 'version': '2014.11'} +toolchain = {'name': 'intel-para', 'version': '2014.12'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_BZ2] -- GitLab From 83b1a2669a4fd0af2957fa8aeca6dc20ff81920d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 12:44:21 +0100 Subject: [PATCH 417/911] include setting of LD_PRELOAD in Haord/jemalloc easyconfigs --- easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb | 2 ++ .../easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb | 4 +++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb index 38e2d6db59..229cf3a9ba 100644 --- a/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb +++ b/easybuild/easyconfigs/h/Hoard/Hoard-3.10-intel-2015a.eb @@ -24,4 +24,6 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = {'LD_PRELOAD': ['lib/libhoard.so']} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb index ac8c2523c3..f80ef5fcba 100644 --- a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-intel-2015a.eb @@ -14,8 +14,10 @@ sources = [SOURCE_TAR_BZ2] sanity_check_paths = { 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.so', - 'include/jemalloc/jemalloc.h'], + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], 'dirs': ['share'], } +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + moduleclass = 'lib' -- GitLab From 90af247f97a8cc88a5be6332aaeff0d570a3dc68 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:47:34 +0100 Subject: [PATCH 418/911] Create Libint-1.1.4-intel-para-2014.12.eb --- .../Libint/Libint-1.1.4-intel-para-2014.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb new file mode 100644 index 0000000000..4cc465b70d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb @@ -0,0 +1,22 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'http://www.files.chem.vt.edu/chem-dept/valeev/software/libint/libint.html' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" +toolchain = {'name': 'intel-para', 'version': '2014.12'} +toolchainopts = {'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--with-pic --enable-shared --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ["include/lib%(x)s/lib%(x)s.h" % {'x': x} for x in ["deriv", "int", "r12"]] + + ["include/libint/hrr_header.h", "include/libint/vrr_header.h"] + + ["lib/lib%s.a" % x for x in ["deriv", "int", "r12"]], + 'dirs':[], +} + +moduleclass = 'chem' -- GitLab From 967ca07203b993ccb22cad9006e19a98a84bf78e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:53:42 +0100 Subject: [PATCH 419/911] Create libxc-2.2.1-intel-para-2014.12.eb Added command to build fortran support (required for ABINIT) --- .../l/libxc/libxc-2.2.1-intel-para-2014.12.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb new file mode 100644 index 0000000000..4588f32bf0 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = "2.2.1" + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +toolchain = {'name': 'intel-para', 'version': '2014.12'} +toolchainopts = {'opt': True} + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so', 'lib/lixcf90.a', 'lib/lixcf90.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From f54da75aca28b8c7b6bea6e87e15bb42b45e2bc3 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:54:45 +0100 Subject: [PATCH 420/911] Update libxc-2.0.2-ictce-5.3.0.eb Added support for fortran, required by ABINIT --- easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb index d4a9249a7f..b055ba4333 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True} -configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' # From the libxc mailing list # To summarize: expect less tests to fail in libxc 2.0.2, but don't expect -- GitLab From ed1227280f9c7864f35d83424dab6346ccd9df33 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 12:58:48 +0100 Subject: [PATCH 421/911] Create flex-2.5.39-intel-para-2014.12.eb --- .../f/flex/flex-2.5.39-intel-para-2014.12.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb new file mode 100644 index 0000000000..302f7d657a --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb @@ -0,0 +1,13 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" +toolchain = {'name': 'intel-para', 'version': '2014.12'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From fe2aa32b0a030b4243fb01d1fa8d5afe91393b09 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 13:01:36 +0100 Subject: [PATCH 422/911] Create Bison-3.0.2-intel-2014.12.eb --- .../b/Bison/Bison-3.0.2-intel-2014.12.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb new file mode 100644 index 0000000000..3375224689 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" +toolchain = {'name': 'intel', 'version': '2014.12'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 1e980b0b758972cd6501dddd1f72f4bfdfbcb405 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 13:05:33 +0100 Subject: [PATCH 423/911] Create M4-1.4.17-intel-para-2014.12.eb --- .../m/M4/M4-1.4.17-intel-para-2014.12.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb new file mode 100644 index 0000000000..ef9457f93b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" +toolchain = {'name': 'intel-para', 'version': '2014.12'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 8b34e00d7fe06dd0908965d7dad4040b4276b279 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 13:18:26 +0100 Subject: [PATCH 424/911] add easyconfig for FLUENT 16.0 --- easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb new file mode 100644 index 0000000000..d8a60604df --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '16.0' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDS_160_LINX64.tar'] + +moduleclass = 'cae' -- GitLab From fb2780506ff4fc83a086332e470b50f3c0440814 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 13:20:24 +0100 Subject: [PATCH 425/911] fix FLUENT homepage --- easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb | 2 +- easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb | 2 +- easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb index a883c12df3..a981a478ad 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb @@ -1,7 +1,7 @@ name = 'FLUENT' version = '14.5' -homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT' +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb index ffe31e9891..0079337b80 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb @@ -1,7 +1,7 @@ name = 'FLUENT' version = '15.0.7' -homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT' +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb index d8a60604df..0d42136505 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb @@ -1,7 +1,7 @@ name = 'FLUENT' version = '16.0' -homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT' +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, -- GitLab From 5efac5d22df02c866887e6b3ebf4a426bf09e704 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 14:12:40 +0100 Subject: [PATCH 426/911] Update and rename Bison-3.0.2-intel-2014.12.eb to Bison-3.0.2-intel-para-2014.12.eb --- ...3.0.2-intel-2014.12.eb => Bison-3.0.2-intel-para-2014.12.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/Bison/{Bison-3.0.2-intel-2014.12.eb => Bison-3.0.2-intel-para-2014.12.eb} (90%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb similarity index 90% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb index 3375224689..19b016a0fc 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-2014.12.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb @@ -6,7 +6,7 @@ version = '3.0.2' homepage = 'http://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" -toolchain = {'name': 'intel', 'version': '2014.12'} +toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -- GitLab From 30759cd5e3239078cd93100db910a1e6e88d5d83 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 14:13:31 +0100 Subject: [PATCH 427/911] Update Bison-3.0.2-intel-para-2014.12.eb --- easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb index 19b016a0fc..1b7cd1f48f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb @@ -6,6 +6,7 @@ version = '3.0.2' homepage = 'http://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 91fe398247da33ad9af8dd357fb5f62e3467551d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 14:13:49 +0100 Subject: [PATCH 428/911] Update flex-2.5.39-intel-para-2014.12.eb --- easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb index 302f7d657a..469e32f3d7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-para-2014.12.eb @@ -4,6 +4,7 @@ version = '2.5.39' homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + toolchain = {'name': 'intel-para', 'version': '2014.12'} toolchainopts = {'pic': True} -- GitLab From 36a497286fb694f837dbb6746b426286fe938264 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 14:14:11 +0100 Subject: [PATCH 429/911] Update Libint-1.1.4-intel-para-2014.12.eb --- .../easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb index 4cc465b70d..131e4988f1 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb @@ -4,6 +4,7 @@ version = '1.1.4' homepage = 'http://www.files.chem.vt.edu/chem-dept/valeev/software/libint/libint.html' description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + toolchain = {'name': 'intel-para', 'version': '2014.12'} toolchainopts = {'opt': True, 'optarch': True} -- GitLab From fad7ba29390df22f266d9da7da3bfe47bfc56942 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 15:17:16 +0100 Subject: [PATCH 430/911] moved new BLAST versions to BLAST+ --- .../BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb} | 2 +- .../BLAST+-2.2.30_basename-fixes.patch} | 0 .../BLAST+-2.2.30_ictce-fixes.patch} | 0 3 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/{BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb => BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb} (98%) rename easybuild/easyconfigs/b/{BLAST/BLAST-2.2.30_basename-fixes.patch => BLAST+/BLAST+-2.2.30_basename-fixes.patch} (100%) rename easybuild/easyconfigs/b/{BLAST/BLAST-2.2.30_ictce-fixes.patch => BLAST+/BLAST+-2.2.30_ictce-fixes.patch} (100%) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb similarity index 98% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb index 66879c0ee8..ccc52c6df7 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' -name = 'BLAST' +name = 'BLAST+' version = '2.2.30' versionsuffix = '-Python-2.7.9' diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30_basename-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_basename-fixes.patch rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30_basename-fixes.patch diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30_ictce-fixes.patch similarity index 100% rename from easybuild/easyconfigs/b/BLAST/BLAST-2.2.30_ictce-fixes.patch rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30_ictce-fixes.patch -- GitLab From 9bf1062a962ecbed9958b8490acd76e106d81948 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 15:17:54 +0100 Subject: [PATCH 431/911] Update M4-1.4.17-intel-para-2014.12.eb --- easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb index ef9457f93b..37a6837b2b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-para-2014.12.eb @@ -7,6 +7,7 @@ homepage = 'http://www.gnu.org/software/m4/m4.html' description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + toolchain = {'name': 'intel-para', 'version': '2014.12'} sources = [SOURCELOWER_TAR_GZ] -- GitLab From 5e8258f7fa091d4d362dc51a4699e64d3ef4fa9c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 15:20:31 +0100 Subject: [PATCH 432/911] Update CP2K-2.6.0-intel-para-2014.12.eb --- easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb index 078ff065ca..12c7a36d02 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb @@ -37,4 +37,5 @@ ignore_regtest_fails = True moduleclass = 'chem' -runtest = "False" +# If you do not want to run tests uncomment this line +# runtest = "False" -- GitLab From 6a79db9bb276ecb5e7e6396fdd0ed991724cbf60 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 13 Mar 2015 15:21:36 +0100 Subject: [PATCH 433/911] prefer http over ftp --- .../b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb index ccc52c6df7..87e25ede69 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-intel-2015a-Python-2.7.9.eb @@ -25,7 +25,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # eg. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] patches = [ '%(name)s-%(version)s_ictce-fixes.patch', -- GitLab From 8fcdb64d3508e73e88862b379125102044910b93 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 15:23:53 +0100 Subject: [PATCH 434/911] Update CP2K-2.6.0-intel-para-2014.12.eb --- easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb index 12c7a36d02..3579b5cbb6 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-intel-para-2014.12.eb @@ -35,7 +35,7 @@ parallel = 1 # regression test reports failures ignore_regtest_fails = True -moduleclass = 'chem' - # If you do not want to run tests uncomment this line # runtest = "False" + +moduleclass = 'chem' -- GitLab From 80fdd93c414ebe4890105ea6d817f165614e94ce Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 13 Mar 2015 16:45:51 +0100 Subject: [PATCH 435/911] Update libxc-2.2.1-intel-para-2014.12.eb --- easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb index 4588f32bf0..8ba57e35c5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb @@ -23,7 +23,7 @@ configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' #runtest = 'check' sanity_check_paths = { - 'files': ['lib/libxc.a', 'lib/libxc.so', 'lib/lixcf90.a', 'lib/lixcf90.so'], + 'files': ['lib/libxc.a', 'lib/libxc.so', 'lib/libxcf90.a', 'lib/libxcf90.so'], 'dirs': ['include'], } -- GitLab From 4570f473b0891ad54ef7114f4e3c13f7923c3fa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Mar 2015 17:40:34 +0100 Subject: [PATCH 436/911] one patch suffices to fix basename issue --- .../b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb | 4 +--- .../easyconfigs/b/BLAST+/blast+_2.2.30.patch | 16 ---------------- 2 files changed, 1 insertion(+), 19 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb index 54dfbd50cc..505c849588 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-goolf-1.4.10.eb @@ -25,9 +25,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] -# patch not needed in BLAST+ 2.2.31 or higher -# http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 -patches = ['blast+_%(version)s.patch'] +patches = ['%(name)s-%(version)s_basename-fixes.patch'] dependencies = [('Boost', '1.57.0')] diff --git a/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch b/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch deleted file mode 100644 index d5d2d3b8b7..0000000000 --- a/easybuild/easyconfigs/b/BLAST+/blast+_2.2.30.patch +++ /dev/null @@ -1,16 +0,0 @@ -don't hardcode path to basename - Pablo Escobar (sciCORE, SIB, UniBAS) -This patch is not needed in BLAST+ version 2.2.31 or higher -http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=65204 - -diff -ru ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top ---- ncbi-blast-2.2.30+-src.orig/c++/src/build-system/Makefile.in.top 2014-08-01 20:43:59.000000000 +0200 -+++ ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top 2015-03-10 15:11:09.140548221 +0100 -@@ -46,7 +46,7 @@ - -rm -f $(libdir)/lib*-static.a - cd $(libdir) && \ - for x in *.a; do \ -- $(LN_S) "$$x" "`/usr/bin/basename \"$$x\" .a`-static.a"; \ -+ $(LN_S) "$$x" "`basename \"$$x\" .a`-static.a"; \ - done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- GitLab From 318f1e8a1d7d9d088435a95242cae87f0089ffba Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 16 Mar 2015 08:55:10 +0100 Subject: [PATCH 437/911] added zlib easyconfig for goolf-1.7.20 --- .../z/zlib/zlib-1.2.8-goolf-1.7.20.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb new file mode 100644 index 0000000000..2e006a7aca --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 0074628c2c4ea21b7b28e352ec671192a97d58b7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 16 Mar 2015 12:05:31 +0100 Subject: [PATCH 438/911] Version update of pbr plus mock and pytz packages --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 8 +++++++- .../easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 8 +++++++- .../easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 8 +++++++- 3 files changed, 21 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 551b551518..bb3f4f62c6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -55,7 +55,7 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.7', { + ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { @@ -100,6 +100,12 @@ exts_list = [ ('netaddr', '0.7.13', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 476f839933..08d18ce9ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -55,7 +55,7 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.7', { + ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { @@ -100,6 +100,12 @@ exts_list = [ ('netaddr', '0.7.13', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 70fcbf0f5a..640c607060 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -58,7 +58,7 @@ exts_list = [ ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.7', { + ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { @@ -103,6 +103,12 @@ exts_list = [ ('netaddr', '0.7.13', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), ] moduleclass = 'lang' -- GitLab From a4c38e951f35abdfbd77b8f7890ddf93e6ab0941 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 16 Mar 2015 12:18:29 +0100 Subject: [PATCH 439/911] python deps moved to python, qhull patch renamed --- ...atplotlib-1.4.3-foss-2015a-Python-2.7.9.eb | 2 -- ...tplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 4 +-- ...=> matplotlib-1.4.3_Qhull-intel-fix.patch} | 0 .../mock-1.0.1-foss-2015a-Python-2.7.9.eb | 35 ------------------- .../mock-1.0.1-intel-2015a-Python-2.7.9.eb | 35 ------------------- .../pytz-2014.10-foss-2015a-Python-2.7.9.eb | 31 ---------------- .../pytz-2014.10-intel-2015a-Python-2.7.9.eb | 31 ---------------- 7 files changed, 1 insertion(+), 137 deletions(-) rename easybuild/easyconfigs/m/matplotlib/{Qhull-intel-fix.patch => matplotlib-1.4.3_Qhull-intel-fix.patch} (100%) delete mode 100644 easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb delete mode 100644 easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb index 2a6d8ee18f..b1aa689258 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -21,8 +21,6 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('mock', '1.0.1', versionsuffix), - ('pytz', '2014.10', versionsuffix), ('zlib', '1.2.8'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 5c56e9a7ef..38e482b680 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = [('Qhull-intel-fix.patch')] +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] python = "Python" pythonversion = '2.7.9' @@ -23,8 +23,6 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('mock', '1.0.1', versionsuffix), - ('pytz', '2014.10', versionsuffix), ('zlib', '1.2.8'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), diff --git a/easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3_Qhull-intel-fix.patch similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/Qhull-intel-fix.patch rename to easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3_Qhull-intel-fix.patch diff --git a/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb deleted file mode 100644 index baada2e6cf..0000000000 --- a/easybuild/easyconfigs/m/mock/mock-1.0.1-foss-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = "PythonPackage" - -name = 'mock' -version = '1.0.1' - -homepage = 'https://pypi.python.org/pypi/mock' -description = """A Python Mocking and Patching Library for Testing. - mock is a library for testing in Python. - It allows you to replace parts of your system under test - with mock objects and make assertions about how they have been used.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] -sources = [SOURCE_TAR_GZ] - -python = "Python" -pythonversion = '2.7.9' -#mock is part of Python 3.3 -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), -] - -pyprefix = 'lib/python%s/site-packages' % pyshortver -eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver -sanity_check_paths = { - 'files': [], - 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb deleted file mode 100644 index afc6e7f4bc..0000000000 --- a/easybuild/easyconfigs/m/mock/mock-1.0.1-intel-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = "PythonPackage" - -name = 'mock' -version = '1.0.1' - -homepage = 'https://pypi.python.org/pypi/mock' -description = """A Python Mocking and Patching Library for Testing. - mock is a library for testing in Python. - It allows you to replace parts of your system under test - with mock objects and make assertions about how they have been used.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] -sources = [SOURCE_TAR_GZ] - -python = "Python" -pythonversion = '2.7.9' -#mock is part of Python 3.3 -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), -] - -pyprefix = 'lib/python%s/site-packages' % pyshortver -eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver -sanity_check_paths = { - 'files': [], - 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb deleted file mode 100644 index 2362eab77c..0000000000 --- a/easybuild/easyconfigs/p/pytz/pytz-2014.10-foss-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pytz' -version = '2014.10' - -homepage = 'https://pypi.python.org/pypi/pytz' -description = """World timezone definitions, modern and historical.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] -sources = [SOURCE_TAR_GZ] - -python = "Python" -pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), -] - -pyprefix = 'lib/python%s/site-packages' % pyshortver -eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver -sanity_check_paths = { - 'files': [], - 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb deleted file mode 100644 index 37fedc7a5b..0000000000 --- a/easybuild/easyconfigs/p/pytz/pytz-2014.10-intel-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pytz' -version = '2014.10' - -homepage = 'https://pypi.python.org/pypi/pytz' -description = """World timezone definitions, modern and historical.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ['http://pypi.python.org/packages/source/%s/%s/' % (name[0],name)] -sources = [SOURCE_TAR_GZ] - -python = "Python" -pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), -] - -pyprefix = 'lib/python%s/site-packages' % pyshortver -eggname = '%%(name)s-%%(version)s-py%s.egg' % pyshortver -sanity_check_paths = { - 'files': [], - 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], -} - -moduleclass = 'system' -- GitLab From 8b31ede2b9a500f8d3b73b66a543b42331a42272 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 16 Mar 2015 14:24:45 +0100 Subject: [PATCH 440/911] implicit zlib dep removed --- .../m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb index b1aa689258..da06531921 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -21,7 +21,6 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('zlib', '1.2.8'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 38e482b680..3a24c2da81 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -23,7 +23,6 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('zlib', '1.2.8'), ('freetype', '2.5.5'), ('libpng', '1.6.16'), ] -- GitLab From b3a37fdab5163d030b18d81a977cc0893e0c23dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Mar 2015 10:52:46 +0100 Subject: [PATCH 441/911] fix SCOTCH homepage --- .../s/SCOTCH/SCOTCH-5.1.12b_esmumps-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.0.6.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.1.13.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-4.1.13.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb | 2 +- .../easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb | 2 +- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goalf-1.1.0-no-OFED.eb index 4f5ffc4906..616ce83405 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goalf-1.1.0-no-OFED.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '5.1.12b_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb index 8e74d1333e..f7e1fa75af 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-goolf-1.4.10.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '5.1.12b_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.0.6.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.0.6.eb index 8cef85de4d..7fa9486295 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.0.6.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '5.1.12b_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.1.13.eb index 03a76886ef..89be85ee36 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-4.1.13.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '5.1.12b_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb index beb56ccffe..63e54d60a9 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-5.1.12b_esmumps-ictce-5.3.0.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '5.1.12b_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb index fbe9ad703d..c0f61c056b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-gmpolf-1.4.8.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb index f88cac060b..adc2bceafc 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-goolf-1.4.10.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-4.1.13.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-4.1.13.eb index 96753b8111..ea32ffc384 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-4.1.13.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb index 7bad11e6da..8e693c1ca4 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb index 80933ffd85..b0d4836a13 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.5.0.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb index 787bd5cae8..b9f29b45c5 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-6.2.5.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb index c3124c78ca..89020e5a6b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-intel-2014b.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb index 14850741f6..3511ad489c 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-iqacml-4.4.13.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.0_esmumps' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb index 9c8e465231..f4c56ce013 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.3-intel-2015a.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.0.3' -homepage = 'http://www.labri.fr/perso/pelegrin/scotch/' +homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" -- GitLab From 381a35ceccf1174455c585b8738798dc99cebcde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Mar 2015 13:42:53 +0100 Subject: [PATCH 442/911] add easyconfig for OpenFOAM 2.3.1 with intel/2015a --- .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb | 32 +++ .../o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch | 235 ++++++++++++++++++ .../o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch | 55 ++++ .../s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb | 14 ++ 4 files changed, 336 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb new file mode 100644 index 0000000000..06ceafc8c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb @@ -0,0 +1,32 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch new file mode 100644 index 0000000000..9b7f790198 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch @@ -0,0 +1,235 @@ +diff -ru OpenFOAM-2.3.1.orig/etc/bashrc OpenFOAM-2.3.1/etc/bashrc +--- OpenFOAM-2.3.1.orig/etc/bashrc 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/etc/bashrc 2015-03-17 11:10:58.638236425 +0100 +@@ -63,7 +63,7 @@ + + #- Compiler: + # WM_COMPILER = Gcc | Gcc45 | Gcc46 | Gcc47 | Clang | Icc (Intel icc) +-export WM_COMPILER=Gcc ++: ${WM_COMPILER:=Gcc}; export WM_COMPILER + unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH + + #- Architecture: +@@ -81,7 +81,7 @@ + #- MPI implementation: + # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI + # | GAMMA | MPI | QSMPI | SGIMPI +-export WM_MPLIB=SYSTEMOPENMPI ++: ${WM_MPLIB:=SYSTEMOPENMPI}; export WM_MPLIB + + #- Operating System: + # WM_OSTYPE = POSIX | ??? +@@ -115,7 +115,7 @@ + + # Location of third-party software + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION ++: ${WM_THIRD_PARTY_DIR:=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION}; export WM_THIRD_PARTY_DIR + + # Location of site-specific templates etc + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +diff -ru OpenFOAM-2.3.1.orig/etc/config/scotch.sh OpenFOAM-2.3.1/etc/config/scotch.sh +--- OpenFOAM-2.3.1.orig/etc/config/scotch.sh 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/etc/config/scotch.sh 2015-03-17 11:10:09.815948216 +0100 +@@ -33,7 +33,11 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.0 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++if [ -n "${SCOTCH_ROOT}" ] ; then ++ export SCOTCH_ARCH_PATH="${SCOTCH_ROOT}" ++else ++ export SCOTCH_VERSION=scotch_6.0.0 ++ export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++fi + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-2.3.1.orig/etc/config/settings.csh OpenFOAM-2.3.1/etc/config/settings.csh +--- OpenFOAM-2.3.1.orig/etc/config/settings.csh 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/etc/config/settings.csh 2015-03-17 11:10:09.815948216 +0100 +@@ -336,7 +336,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + switch ("$WM_MPLIB") + case SYSTEMOPENMPI: +diff -ru OpenFOAM-2.3.1.orig/etc/config/settings.sh OpenFOAM-2.3.1/etc/config/settings.sh +--- OpenFOAM-2.3.1.orig/etc/config/settings.sh 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/etc/config/settings.sh 2015-03-17 11:10:09.815948216 +0100 +@@ -356,7 +356,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + case "$WM_MPLIB" in + SYSTEMOPENMPI) +@@ -524,6 +524,11 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++ ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C +--- OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-03-17 11:10:09.815948216 +0100 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/Make/options 2015-03-17 11:10:09.815948216 +0100 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-03-17 11:10:09.815948216 +0100 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-2.3.1/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-2.3.1.orig/src/parallel/decompose/scotchDecomp/Make/options 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/parallel/decompose/scotchDecomp/Make/options 2015-03-17 11:10:09.815948216 +0100 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c 2015-03-17 11:10:09.815948216 +0100 +@@ -2,7 +2,7 @@ + + cWARN = -Wall + +-cc = gcc -m64 ++cc = $(MPICC) + + include $(RULES)/c$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c++ OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c++ +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c++ 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c++ 2015-03-17 11:10:09.815948216 +0100 +@@ -2,7 +2,7 @@ + + c++WARN = -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor + +-CC = g++ -m64 ++CC = $(MPICXX) + + include $(RULES)/c++$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/cOpt OpenFOAM-2.3.1/wmake/rules/linux64Gcc/cOpt +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/cOpt 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Gcc/cOpt 2015-03-17 11:10:09.815948216 +0100 +@@ -1,3 +1,3 @@ + cDBUG = +-cOPT = -O3 ++cOPT = $(CFLAGS) + # -fprefetch-loop-arrays +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c++Opt OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c++Opt +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Gcc/c++Opt 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Gcc/c++Opt 2015-03-17 11:10:09.815948216 +0100 +@@ -1,3 +1,3 @@ + c++DBUG = +-c++OPT = -O3 ++c++OPT = $(CXXFLAGS) + # -fprefetch-loop-arrays +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c OpenFOAM-2.3.1/wmake/rules/linux64Icc/c +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Icc/c 2015-03-17 11:10:09.815948216 +0100 +@@ -2,7 +2,7 @@ + + cWARN = + +-cc = icc ++cc = $(MPICC) + + include $(RULES)/c$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c++ OpenFOAM-2.3.1/wmake/rules/linux64Icc/c++ +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c++ 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Icc/c++ 2015-03-17 11:10:09.815948216 +0100 +@@ -2,7 +2,7 @@ + + c++WARN = -wd327,525,654,819,1125,1476,1505,1572 + +-CC = icpc -std=c++0x ++CC = $(MPICXX) + + include $(RULES)/c++$(WM_COMPILE_OPTION) + +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/cOpt OpenFOAM-2.3.1/wmake/rules/linux64Icc/cOpt +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/cOpt 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Icc/cOpt 2015-03-17 11:10:09.815948216 +0100 +@@ -1,2 +1,2 @@ + cDBUG = +-cOPT = -O3 -no-prec-div ++cOPT = $(CFLAGS) +diff -ru OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c++Opt OpenFOAM-2.3.1/wmake/rules/linux64Icc/c++Opt +--- OpenFOAM-2.3.1.orig/wmake/rules/linux64Icc/c++Opt 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/wmake/rules/linux64Icc/c++Opt 2015-03-17 11:10:09.815948216 +0100 +@@ -1,2 +1,2 @@ + c++DBUG = +-c++OPT = -xHost -O2 -no-prec-div ++c++OPT = $(CXXFLAGS) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch new file mode 100644 index 0000000000..6dfeb947a3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch @@ -0,0 +1,55 @@ +diff -ru ThirdParty-2.3.1.ORIG/Allwmake ThirdParty-2.3.1/Allwmake +--- ThirdParty-2.3.1.ORIG/Allwmake 2014-02-06 16:31:37.000000000 +0100 ++++ ThirdParty-2.3.1/Allwmake 2014-07-08 00:32:02.955084962 +0200 +@@ -110,12 +110,12 @@ + ;; + + MPICH) +- if [ -r $MPI_ARCH_PATH/lib/libmpich.so ] ++ if [ -r $MPI_ARCH_PATH/lib64/libmpich.so ] + then + echo " have $WM_MPLIB shared library ($FOAM_MPI)" + echo + echo +- elif [ -r $MPI_ARCH_PATH/lib/libmpich.a ] ++ elif [ -r $MPI_ARCH_PATH/lib64/libmpich.a ] + then + echo " have $WM_MPLIB static library ($FOAM_MPI)" + echo +@@ -195,6 +195,13 @@ + echo " scotch header in $SCOTCH_ARCH_PATH/include" + echo " scotch libs in $FOAM_EXT_LIBBIN" + echo ++elif [ -f $SCOTCH_ARCH_PATH/include/scotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.a \) ] ++then ++ echo " scotch header in $SCOTCH_ARCH_PATH/include" ++ echo " scotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -256,6 +263,13 @@ + echo " ptscotch header in $SCOTCH_ARCH_PATH/include/$FOAM_MPI" + echo " ptscotch libs in $FOAM_EXT_LIBBIN/$FOAM_MPI" + echo ++ elif [ -f $SCOTCH_ARCH_PATH/include/ptscotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.a \) ] ++ then ++ echo " ptscotch header in $SCOTCH_ARCH_PATH/include" ++ echo " ptscotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -296,7 +310,7 @@ + fi + + # verify existence of scotch include +- [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h ] || { ++ [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h -o -f $SCOTCH_ARCH_PATH/include/ptscotch.h ] || { + echo + echo " WARNING: required include file 'ptscotch.h' not found!" + echo diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb new file mode 100644 index 0000000000..a98a4841f7 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' -- GitLab From d35f2df5b0b67ca5ed2b0f7cb2af85a32816bd15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Mar 2015 13:47:09 +0100 Subject: [PATCH 443/911] add comments in OpenFOAM patch files --- easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch | 2 ++ easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch index 9b7f790198..7ad239b41d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch @@ -1,3 +1,5 @@ +fix hardcoded settings, add support for picking up dependencies provided via EasyBuild +author: Kenneth Hoste (kenneth.hoste@ugent.be) diff -ru OpenFOAM-2.3.1.orig/etc/bashrc OpenFOAM-2.3.1/etc/bashrc --- OpenFOAM-2.3.1.orig/etc/bashrc 2014-12-04 18:52:43.000000000 +0100 +++ OpenFOAM-2.3.1/etc/bashrc 2015-03-17 11:10:58.638236425 +0100 diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch index 6dfeb947a3..a2d96019b9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.3.1.patch @@ -1,3 +1,5 @@ +fix lib dir, using an external SCOTCH +author: Kenneth Hoste (kenneth.hoste@ugent.be) diff -ru ThirdParty-2.3.1.ORIG/Allwmake ThirdParty-2.3.1/Allwmake --- ThirdParty-2.3.1.ORIG/Allwmake 2014-02-06 16:31:37.000000000 +0100 +++ ThirdParty-2.3.1/Allwmake 2014-07-08 00:32:02.955084962 +0200 -- GitLab From 9f4ca3f26fb8e2b0023b5547afffdd8fde37c7b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Mar 2015 15:53:22 +0100 Subject: [PATCH 444/911] clean up OpenFOAM patch, don't patch symlink lnInclude/ptscotchDecomp.C --- .../o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch | 22 ------------------- 1 file changed, 22 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch index 7ad239b41d..98f6555f72 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.3.1.patch @@ -83,28 +83,6 @@ diff -ru OpenFOAM-2.3.1.orig/etc/config/settings.sh OpenFOAM-2.3.1/etc/config/se *) export FOAM_MPI=dummy ;; -diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C ---- OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2014-12-04 18:52:43.000000000 +0100 -+++ OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-03-17 11:10:09.815948216 +0100 -@@ -112,6 +112,8 @@ - - \*---------------------------------------------------------------------------*/ - -+#include "mpi.h" -+ - #include "ptscotchDecomp.H" - #include "addToRunTimeSelectionTable.H" - #include "Time.H" -@@ -121,8 +123,8 @@ - - extern "C" - { --#include - #include "mpi.h" -+#include - #include "ptscotch.h" - } - diff -ru OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/Make/options --- OpenFOAM-2.3.1.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2014-12-04 18:52:43.000000000 +0100 +++ OpenFOAM-2.3.1/src/parallel/decompose/ptscotchDecomp/Make/options 2015-03-17 11:10:09.815948216 +0100 -- GitLab From 486a1243c79c4276252cf0acb6e038f6b32d65b4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Mar 2015 15:56:35 +0100 Subject: [PATCH 445/911] added initial Xmipp easyconfig --- .../m/Xmipp/Xmipp-3.1-intel-2015a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb new file mode 100644 index 0000000000..a9deea6d7f --- /dev/null +++ b/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Xmipp' +version = '3.1' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +patches = ['sqlite_imports.patch', 'library_imports.patch'] + +dependencies = [ + ('Python', '2.7.9'), + ('Java', '1.8.0_25', '', True), # TODO: set this to yes in configure + ('freetype', '2.5.3'), + ('gtest', '1.6.0'), # TODO: set this to yes in configure, after patching out all the includes for external/gtest + ('LibTIFF', '4.0.3'), + ('HDF5', '1.8.14', '-gpfs'), + ('libjpeg-turbo', '1.3.1'), + ('FFTW', '3.3.4'), +] + +buildininstalldir = True +unpack_options = '--strip-components=1' + +sanity_check_paths = { + 'files': ['bin/xmipp_mpi_run'], + 'dirs': [], +} + +preconfigopts = """export CXXFLAGS="$CXXFFLAGS -DMPICH_IGNORE_CXX_SEEK -I$EBROOTPYTHON/include/python2.7" && ln -s `which python` xmipp_python && mkdir lib && ln -s $EBROOTPYTHON/lib/python2.7 lib/python2.7 && cd external && tar xf scons.tgz && tar xf bilib.tgz && tar xf condor.tgz && tar xf alglib-3.8.0.cpp.tgz && cd - && mkdir bin && PATH=$PWD:$PATH xmipp_python external/scons/scons.py mode=configure -j 4 --config=force profile=no fast=yes warn=no release=yes gtest=no cuda=no debug=no matlab=no java=no LINKERFORPROGRAMS="$CXX" MPI_BINDIR="$EBROOTIMPI" JAVA_HOME="$JAVA_HOME" JAVAC=javac CC="$CC" CXXFLAGS="$CXXFLAGS" CXX="$CXX" MPI_CC="$MPICC" MPI_CXX="$MPICXX" MPI_INCLUDE="$MPI_INC_DIR" MPI_LIBDIR="$MPI_LIB_DIR" MPI_LINKERFORPROGRAMS="$MPICC" LIBPATH="$LD_LIBRARY_PATH" || """ + +prebuildopts = """export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib && PATH=$PWD:$PATH xmipp_python external/scons/scons.py mode=compile -j 16 || """ + +preinstallopts = "XMIPP_HOME=%(installdir)s PATH=$PWD:$PWD/bin:$PATH PYTHONPATH=$PYTHONPATH:$PWD/protocols:$PWD/libraries/bindings/python/:$EBROOTPYTHON/lib/python2.7/lib-dynload/ python setup.py install || " + +moduleclass = 'vis' -- GitLab From f84701cba915dc2ebaabe06dae0f77bd20a304b3 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 17 Mar 2015 16:01:51 +0100 Subject: [PATCH 446/911] Add Hadoop-2.5.0-cdh5.3.1 and patch them. The patch it to make TeraSort work with native file systems (MAPREDUCE-5528). --- .../Hadoop-2.4.0-seagate-722af1-native.eb | 2 ++ .../h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 27 ++++++++++++++++ .../Hadoop-TeraSort-on-local-filesystem.patch | 31 +++++++++++++++++++ 3 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 1a2bc6a274..1bcf4021ce 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -21,6 +21,8 @@ builddependencies = [ ] dependencies = [(java, javaver)] +patches = [('Hadoop-TeraSort-on-local-filesystem.patch', 0)] + build_native_libs = True moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb new file mode 100644 index 0000000000..fc4e7e2de2 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -0,0 +1,27 @@ +name = 'Hadoop' +version = '2.5.0-cdh5.3.1' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] + +java = 'Java' +javaver = '1.7.0_76' + +builddependencies = [ + ('Maven', '3.2.3'), + ('protobuf', '2.5.0'), + ('CMake', '3.1.3'), +] + +dependencies = [(java, javaver)] + +patches = [('Hadoop-TeraSort-on-local-filesystem.patch', 0)] + +build_native_libs = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch b/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch new file mode 100644 index 0000000000..afe953b518 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch @@ -0,0 +1,31 @@ +diff --git a/hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java b/hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java +index 6022f6c..b913769 100644 +--- hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java ++++ hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java +@@ -28,6 +28,7 @@ + import org.apache.hadoop.conf.Configurable; + import org.apache.hadoop.conf.Configuration; + import org.apache.hadoop.conf.Configured; ++import org.apache.hadoop.filecache.DistributedCache;; + import org.apache.hadoop.fs.FileSystem; + import org.apache.hadoop.fs.Path; + import org.apache.hadoop.io.Text; +@@ -209,8 +210,8 @@ public void setConf(Configuration conf) { + try { + FileSystem fs = FileSystem.getLocal(conf); + this.conf = conf; +- Path partFile = new Path(TeraInputFormat.PARTITION_FILENAME); +- splitPoints = readPartitions(fs, partFile, conf); ++ Path[] localPaths = DistributedCache.getLocalCacheFiles(conf); ++ splitPoints = readPartitions(fs, localPaths[0], conf); + trie = buildTrie(splitPoints, 0, splitPoints.length, new Text(), 2); + } catch (IOException ie) { + throw new IllegalArgumentException("can't read partitions file", ie); +@@ -279,6 +280,7 @@ public static void setOutputReplication(Job job, int value) { + + public int run(String[] args) throws Exception { + LOG.info("starting"); ++ LOG.info("starting with terasort on native filesystem patch"); + Job job = Job.getInstance(getConf()); + Path inputDir = new Path(args[0]); + Path outputDir = new Path(args[1]); -- GitLab From 32d311e8c002f2f7530581228279f8616acc152a Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 17 Mar 2015 16:52:10 +0100 Subject: [PATCH 447/911] Add version suffix of '-native'. --- easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index fc4e7e2de2..76cfd18862 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -1,5 +1,6 @@ name = 'Hadoop' version = '2.5.0-cdh5.3.1' +versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -- GitLab From eaefa10a6bec8bd6d52cf208200675d877bc2a59 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Mar 2015 17:40:43 +0100 Subject: [PATCH 448/911] cleaned up xmipp easyconfig, added patches --- .../m/Xmipp/Xmipp-3.1-intel-2015a.eb | 41 ------- .../x/Xmipp/Xmipp-3.1-intel-2015a.eb | 25 +++++ .../easyconfigs/x/Xmipp/library_imports.patch | 100 ++++++++++++++++++ .../easyconfigs/x/Xmipp/sqlite_imports.patch | 15 +++ 4 files changed, 140 insertions(+), 41 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/library_imports.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch diff --git a/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb deleted file mode 100644 index a9deea6d7f..0000000000 --- a/easybuild/easyconfigs/m/Xmipp/Xmipp-3.1-intel-2015a.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Xmipp' -version = '3.1' - -homepage = 'http://xmipp.cnb.csic.es/' -description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." - -source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] -sources = ['Xmipp-%(version)s-src.tar.gz'] - -toolchain = {'name': 'intel', 'version': '2015a'} - -patches = ['sqlite_imports.patch', 'library_imports.patch'] - -dependencies = [ - ('Python', '2.7.9'), - ('Java', '1.8.0_25', '', True), # TODO: set this to yes in configure - ('freetype', '2.5.3'), - ('gtest', '1.6.0'), # TODO: set this to yes in configure, after patching out all the includes for external/gtest - ('LibTIFF', '4.0.3'), - ('HDF5', '1.8.14', '-gpfs'), - ('libjpeg-turbo', '1.3.1'), - ('FFTW', '3.3.4'), -] - -buildininstalldir = True -unpack_options = '--strip-components=1' - -sanity_check_paths = { - 'files': ['bin/xmipp_mpi_run'], - 'dirs': [], -} - -preconfigopts = """export CXXFLAGS="$CXXFFLAGS -DMPICH_IGNORE_CXX_SEEK -I$EBROOTPYTHON/include/python2.7" && ln -s `which python` xmipp_python && mkdir lib && ln -s $EBROOTPYTHON/lib/python2.7 lib/python2.7 && cd external && tar xf scons.tgz && tar xf bilib.tgz && tar xf condor.tgz && tar xf alglib-3.8.0.cpp.tgz && cd - && mkdir bin && PATH=$PWD:$PATH xmipp_python external/scons/scons.py mode=configure -j 4 --config=force profile=no fast=yes warn=no release=yes gtest=no cuda=no debug=no matlab=no java=no LINKERFORPROGRAMS="$CXX" MPI_BINDIR="$EBROOTIMPI" JAVA_HOME="$JAVA_HOME" JAVAC=javac CC="$CC" CXXFLAGS="$CXXFLAGS" CXX="$CXX" MPI_CC="$MPICC" MPI_CXX="$MPICXX" MPI_INCLUDE="$MPI_INC_DIR" MPI_LIBDIR="$MPI_LIB_DIR" MPI_LINKERFORPROGRAMS="$MPICC" LIBPATH="$LD_LIBRARY_PATH" || """ - -prebuildopts = """export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/lib && PATH=$PWD:$PATH xmipp_python external/scons/scons.py mode=compile -j 16 || """ - -preinstallopts = "XMIPP_HOME=%(installdir)s PATH=$PWD:$PWD/bin:$PATH PYTHONPATH=$PYTHONPATH:$PWD/protocols:$PWD/libraries/bindings/python/:$EBROOTPYTHON/lib/python2.7/lib-dynload/ python setup.py install || " - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb new file mode 100644 index 0000000000..e40410e503 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -0,0 +1,25 @@ +name = 'Xmipp' +version = '3.1' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +patches = ['sqlite_imports.patch', 'library_imports.patch'] + +dependencies = [ + ('Python', '2.7.9'), + ('Java', '1.8.0_25', '', True), # TODO: set this to yes in configure + ('freetype', '2.5.3'), + ('gtest', '1.6.0'), # TODO: set this to yes in configure, after patching out all the includes for external/gtest + ('LibTIFF', '4.0.3'), + ('HDF5', '1.8.14', '-gpfs'), + ('libjpeg-turbo', '1.3.1'), + ('FFTW', '3.3.4'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/library_imports.patch b/easybuild/easyconfigs/x/Xmipp/library_imports.patch new file mode 100644 index 0000000000..401f1eb286 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/library_imports.patch @@ -0,0 +1,100 @@ +diff -ru xmipp/libraries/data/metadata_sql.h xmipp_working/libraries/data/metadata_sql.h +--- xmipp/libraries/data/metadata_sql.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/metadata_sql.h 2015-03-12 17:31:49.701372176 +0100 +@@ -29,7 +29,7 @@ + #include + #include + #include "xmipp_strings.h" +-#include ++#include + #include "metadata_label.h" + #include + class MDSqlStaticInit; +diff -ru xmipp/libraries/data/rwHDF5.h xmipp_working/libraries/data/rwHDF5.h +--- xmipp/libraries/data/rwHDF5.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/rwHDF5.h 2015-03-12 17:32:16.060809000 +0100 +@@ -26,7 +26,7 @@ + #ifndef RWHDF5_H_ + #define RWHDF5_H_ + +-#include "../../external/hdf5-1.8.10/src/hdf5.h" ++#include "hdf5.h" + + + +diff -ru xmipp/libraries/data/rwIMAGIC.cpp xmipp_working/libraries/data/rwIMAGIC.cpp +--- xmipp/libraries/data/rwIMAGIC.cpp 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/rwIMAGIC.cpp 2015-03-12 17:35:53.292172326 +0100 +@@ -40,6 +40,8 @@ + */ + + #define IMAGICSIZE 1024 // Size of the IMAGIC header for each image ++#define SIZEOF_INT sizeof(int) ++ + + ///@defgroup Imagic Imagic File format + ///@ingroup ImageFormats +diff -ru xmipp/libraries/data/rwJPEG.cpp xmipp_working/libraries/data/rwJPEG.cpp +--- xmipp/libraries/data/rwJPEG.cpp 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/rwJPEG.cpp 2015-03-12 17:35:06.781738000 +0100 +@@ -24,7 +24,7 @@ + ***************************************************************************/ + + #include "xmipp_image_base.h" +-#include "../../external/jpeg-8c/jpeglib.h" ++#include "jpeglib.h" + + + //#include +diff -ru xmipp/libraries/data/xmipp_fftw.h xmipp_working/libraries/data/xmipp_fftw.h +--- xmipp/libraries/data/xmipp_fftw.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/xmipp_fftw.h 2015-03-12 17:32:35.751658248 +0100 +@@ -28,7 +28,7 @@ + #define __XmippFFTW_H + + #include +-#include "../../external/fftw-3.3.3/api/fftw3.h" ++#include "fftw3.h" + #include "multidim_array.h" + #include "multidim_array_generic.h" + #include "xmipp_fft.h" +diff -ru xmipp/libraries/data/xmipp_hdf5.h xmipp_working/libraries/data/xmipp_hdf5.h +--- xmipp/libraries/data/xmipp_hdf5.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/xmipp_hdf5.h 2015-03-12 17:32:50.922130000 +0100 +@@ -28,8 +28,8 @@ + + #include + #include +-#include "../../external/hdf5-1.8.10/src/hdf5.h" +-#include "../../external/hdf5-1.8.10/c++/src/H5Cpp.h" ++#include "hdf5.h" ++#include "H5Cpp.h" + #include "matrix1d.h" + + +diff -ru xmipp/libraries/data/xmipp_image_base.h xmipp_working/libraries/data/xmipp_image_base.h +--- xmipp/libraries/data/xmipp_image_base.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/xmipp_image_base.h 2015-03-12 17:34:39.112206978 +0100 +@@ -33,8 +33,8 @@ + #include "xmipp_datatype.h" + // + //// Includes for rwTIFF which cannot be inside it +-#include "../../external/tiff-3.9.4/libtiff/tiffio.h" +-#include "../../external/hdf5-1.8.10/src/hdf5.h" ++#include "tiffio.h" ++#include "hdf5.h" + + + /* Minimum size of a TIFF file to be mapped to a tempfile in case of mapping from +diff -ru xmipp/libraries/data/xmipp_program_sql.h xmipp_working/libraries/data/xmipp_program_sql.h +--- xmipp/libraries/data/xmipp_program_sql.h 2014-04-03 09:46:48.000000000 +0200 ++++ xmipp_working/libraries/data/xmipp_program_sql.h 2015-03-12 17:32:25.300863000 +0100 +@@ -28,7 +28,7 @@ + + #include + #include "xmipp_program.h" +-#include "external/sqlite-3.6.23/sqlite3.h" ++#include "sqlite3.h" + + typedef std::map DictDB; + diff --git a/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch b/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch new file mode 100644 index 0000000000..a24c6b5d9c --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch @@ -0,0 +1,15 @@ +--- xmipp/external/sqliteExt/extension-functions.c 2014-04-03 09:46:46.000000000 +0200 ++++ xmipp_working/external/sqliteExt/extension-functions.c 2015-03-12 17:31:38.192960473 +0100 +@@ -121,10 +121,10 @@ + #define HAVE_TRIM 1 /* LMH 2007-03-25 if sqlite has trim functions */ + + #ifdef COMPILE_SQLITE_EXTENSIONS_AS_LOADABLE_MODULE +-#include "../sqlite-3.6.23/sqlite3ext.h" ++#include "sqlite3ext.h" + SQLITE_EXTENSION_INIT1 + #else +-#include "../sqlite-3.6.23/sqlite3.h" ++#include "sqlite3.h" + #endif + + #include -- GitLab From 438b9988976493fe4ece67ec50eb6a84207c9f95 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Mar 2015 17:43:05 +0100 Subject: [PATCH 449/911] removed todo's --- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index e40410e503..04c3383b73 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -13,9 +13,7 @@ patches = ['sqlite_imports.patch', 'library_imports.patch'] dependencies = [ ('Python', '2.7.9'), - ('Java', '1.8.0_25', '', True), # TODO: set this to yes in configure ('freetype', '2.5.3'), - ('gtest', '1.6.0'), # TODO: set this to yes in configure, after patching out all the includes for external/gtest ('LibTIFF', '4.0.3'), ('HDF5', '1.8.14', '-gpfs'), ('libjpeg-turbo', '1.3.1'), -- GitLab From 7aeb38448263621964e6c40a2be53e466f0f183e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Mar 2015 17:45:53 +0100 Subject: [PATCH 450/911] added clarification about really needing sqlite in python --- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index 04c3383b73..1e915813e0 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} patches = ['sqlite_imports.patch', 'library_imports.patch'] dependencies = [ - ('Python', '2.7.9'), + ('Python', '2.7.9'), # Make sure Python has a working SQlite in it, the install step creates a sqlite db. ('freetype', '2.5.3'), ('LibTIFF', '4.0.3'), ('HDF5', '1.8.14', '-gpfs'), -- GitLab From 38690c3318ac45d4db72037c5680223a3e202d63 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 17 Mar 2015 17:10:43 +0100 Subject: [PATCH 451/911] Minor changes based on boegel's feedback. --- .../h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb | 3 ++- .../easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 4 ++-- .../h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch | 1 + 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 1bcf4021ce..36e84805d1 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%s.tar.gz' % commit] source_urls = ['https://github.com/Seagate/hadoop-on-lustre2/archive'] +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + java = 'Java' javaver = '1.7.0_76' @@ -21,7 +23,6 @@ builddependencies = [ ] dependencies = [(java, javaver)] -patches = [('Hadoop-TeraSort-on-local-filesystem.patch', 0)] build_native_libs = True diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 76cfd18862..67c1c26052 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -10,6 +10,8 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + java = 'Java' javaver = '1.7.0_76' @@ -21,8 +23,6 @@ builddependencies = [ dependencies = [(java, javaver)] -patches = [('Hadoop-TeraSort-on-local-filesystem.patch', 0)] - build_native_libs = True moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch b/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch index afe953b518..6abba099f1 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-TeraSort-on-local-filesystem.patch @@ -1,4 +1,5 @@ diff --git a/hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java b/hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java +Sourced from https://issues.apache.org/jira/browse/MAPREDUCE-5528 index 6022f6c..b913769 100644 --- hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java +++ hadoop-mapreduce-project/hadoop-mapreduce-examples/src/main/java/org/apache/hadoop/examples/terasort/TeraSort.java -- GitLab From 6b7985a62baf1d8a4deb7727f0e339b524546489 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 18 Mar 2015 14:08:10 +0100 Subject: [PATCH 452/911] Hadoop has a buggy parallel build so only use 1 thread. We'll keep the easyblock in case hadoop gets fixed. --- .../easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb | 2 ++ easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 36e84805d1..13c43df595 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -26,4 +26,6 @@ dependencies = [(java, javaver)] build_native_libs = True +parallel = 1 + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 67c1c26052..fea9291ff7 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -25,4 +25,6 @@ dependencies = [(java, javaver)] build_native_libs = True +parallel = 1 + moduleclass = 'tools' -- GitLab From 4abd1c883926fdf80547007aa003012380e74380 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 19 Mar 2015 09:19:32 +0100 Subject: [PATCH 453/911] dummy --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From c07de667b97f0930f0da71dbacb308374218b6ec Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 19 Mar 2015 09:55:10 +0100 Subject: [PATCH 454/911] HTSLib intel,foss 2015a --- .../h/HTSlib/HTSlib-1.2.1-foss-2015a.eb | 27 ++++++++++++++++++ .../h/HTSlib/HTSlib-1.2.1-intel-2015a.eb | 28 ++++++++++++++++++- 2 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb new file mode 100644 index 0000000000..000a05482b --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-foss-2015a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb index 421376db9e..3963d9e539 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015a.eb @@ -1 +1,27 @@ -dummy +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.so"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7f9c5cf2bcbd0f403f9cafb656d66310daca59b5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 19 Mar 2015 09:58:57 +0100 Subject: [PATCH 455/911] dummy --- .../s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From 3107751c06f9e89988e55c569724b2b6e2da5a5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2015 10:12:04 +0100 Subject: [PATCH 456/911] add easyconfigs for GATE v6.2 with intel/2015a + deps --- .../c/CLHEP/CLHEP-2.1.1.0-intel-2015a.eb | 20 +++++ .../c/CMake/CMake-2.8.4-intel-2015a.eb | 22 +++++ .../e/expat/expat-2.1.0-intel-2015a.eb | 15 ++++ .../g/GATE/GATE-6.2-intel-2015a.eb | 23 +++++ .../easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb | 18 ++++ .../g/Geant4/Geant4-9.5.p01-intel-2015a.eb | 24 ++++++ .../libreadline-6.2-intel-2015a.eb | 27 ++++++ .../libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 27 ++++++ .../p/Python/Python-2.7.3-intel-2015a.eb | 85 +++++++++++++++++++ .../r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 39 +++++++++ .../z/zlib/zlib-1.2.7-intel-2015a.eb | 22 +++++ 11 files changed, 322 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2015a.eb new file mode 100644 index 0000000000..fb3888c0b0 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'CLHEP' +version = '2.1.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +# CLHEP compiles with icc instead of icpc +configopts = 'CXX="$CC" CXXFLAGS="$CXXFLAGS -gcc"' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2015a.eb new file mode 100644 index 0000000000..c08d8d2cfd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '2.8.4' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb new file mode 100644 index 0000000000..0eb1188648 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb new file mode 100644 index 0000000000..153cbd2179 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -0,0 +1,23 @@ +name = 'GATE' +version = '6.2' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] +source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] + +patches = ['GATE-%(version)s_Makefile-prefix.patch'] + +dependencies = [ + ('Geant4', '9.5.p01'), + ('CLHEP', '2.1.1.0'), + ('ROOT', 'v5.34.01'), + ('CMake', '2.8.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb new file mode 100644 index 0000000000..9cfba7ecd1 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '1.15' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb new file mode 100644 index 0000000000..bfe0be4aaf --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '9.5.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.1.1.0'), +] + +builddependencies = [('CMake', '2.8.4')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb new file mode 100644 index 0000000000..95bd6329fb --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.2' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb new file mode 100644 index 0000000000..1e588c6831 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.8.0' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.7'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb new file mode 100644 index 0000000000..14b4ce86fc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -0,0 +1,85 @@ +name = 'Python' +version = '2.7.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.6.1' +scipyversion = '0.10.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +patches = ['python_libffi_int128_icc.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +exts_list = [ + ('setuptools', '0.6c11', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.1.2', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.17.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('dateutil', '2.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '0.9.1', { + 'source_urls': ['https://deap.googlecode.com/files/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('paramiko', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb new file mode 100644 index 0000000000..bdb5568e8a --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -0,0 +1,39 @@ +name = 'ROOT' +version = 'v5.34.01' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'icc_ifort_v12.patch' + ] + +python = 'Python' +pyver = '2.7.3' + +dependencies = [ + ('GSL', '1.15'), + ('libxml2', '2.8.0', '-%s-%s' % (python, pyver)), + (python, pyver), + ] + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-intel-2015a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-intel-2015a.eb new file mode 100644 index 0000000000..d4d69bb5d6 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From f1c1df10bc840937641f9369bb3bd32409c91ea4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 19 Mar 2015 10:48:59 +0100 Subject: [PATCH 457/911] dummy2 --- .../SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb | 35 +++++- .../SAMtools-1.2_extHTSlib_Makefile.patch | 108 ++++++++++++++++++ 2 files changed, 142 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb index 421376db9e..d20cd89e7b 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb @@ -1 +1,34 @@ -dummy +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +#patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.2.1'), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch new file mode 100644 index 0000000000..01033c7a28 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch @@ -0,0 +1,108 @@ +--- samtools-1.2/Makefile.orig 2015-02-03 17:27:34.000000000 +0100 ++++ samtools-1.2/Makefile 2015-03-19 10:27:14.487237690 +0100 +@@ -36,9 +36,9 @@ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o +-INCLUDES= -I. -I$(HTSDIR) +-LIBCURSES= -lcurses # -lXCurses +- ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. -I$(EBROOTHTSLIB)/include ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses # -lXCurses ++ZLIB= -L$(EBROOTZLIB)/lib -lz + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin +@@ -82,10 +82,10 @@ + + + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.2.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip ++HTSDIR = $(EBROOTHTSLIB)/include ++#include $(EBROOTHTSLIB)/htslib.mk ++HTSLIB = $(EBROOTHTSLIB)/lib/libhts.a ++BGZIP = $(EBROOTHTSLIB)/bin/bgzip + + + PACKAGE_VERSION = 1.2 +@@ -122,7 +122,7 @@ + $(AR) -csru $@ $(LOBJS) + + samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm $(ZLIB) + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h +@@ -192,31 +192,31 @@ + + + test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz ++ $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) $(ZLIB) + + test_test_h = test/test.h $(htslib_sam_h) + +@@ -235,22 +235,22 @@ + # misc programs + + misc/ace2sam: misc/ace2sam.o +- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(LDLIBS) -lz ++ $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(LDLIBS) $(ZLIB) + + misc/maq2sam-short: misc/maq2sam-short.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(LDLIBS) -lz ++ $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(LDLIBS) $(ZLIB) + + misc/maq2sam-long: misc/maq2sam-long.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(LDLIBS) -lz ++ $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(LDLIBS) $(ZLIB) + + misc/md5fa: misc/md5fa.o misc/md5.o +- $(CC) $(LDFLAGS) -o $@ misc/md5fa.o misc/md5.o $(LDLIBS) -lz ++ $(CC) $(LDFLAGS) -o $@ misc/md5fa.o misc/md5.o $(LDLIBS) $(ZLIB) + + misc/md5sum-lite: misc/md5sum-lite.o + $(CC) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(LDLIBS) + + misc/wgsim: misc/wgsim.o +- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz ++ $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm $(ZLIB) + + misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h + misc/md5.o: misc/md5.c misc/md5.h -- GitLab From c04ba25ac1e8f4522b7c3492786d257862268ab1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2015 11:56:38 +0100 Subject: [PATCH 458/911] remove unrequired patch from Python 2.7.3 intel/2015a easyconfig --- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 14b4ce86fc..c07420a815 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -13,8 +13,6 @@ scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['python_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), -- GitLab From 181669e94ca052aea42ebdcf3647e536f21caddb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2015 12:04:19 +0100 Subject: [PATCH 459/911] bump zlib dep to 1.2.8 in deps of Python/libxml intel/2015a easyconfigs --- .../l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 1e588c6831..833381d4b2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -20,7 +20,7 @@ pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % ('Python', pythonver) dependencies = [ - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ('Python', pythonver), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index c07420a815..58d509004d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -16,7 +16,7 @@ sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), # ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons -- GitLab From c3492ddf23789c15bef5511e4b7b58f7e85e5921 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2015 12:21:21 +0100 Subject: [PATCH 460/911] CMake is a build dep --- easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb index 1b62309c54..f6983e6ed6 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.1-ictce-4.0.6.eb @@ -15,8 +15,8 @@ dependencies = [ ('Geant4', '9.4.p02'), ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), - ('CMake', '2.8.4'), ] +builddependencies = [('CMake', '2.8.4')] parallel = 1 diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb index b3ec8c73df..8cd12c59aa 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('Geant4', '9.5.p01'), ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), - ('CMake', '2.8.4'), ] +builddependencies = [('CMake', '2.8.4')] moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb index f0862bba48..3bac12bc2c 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ ('Geant4', '9.5.p01'), ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), - ('CMake', '2.8.4'), ] +builddependencies = [('CMake', '2.8.4')] moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb index 3fe22c082c..cf9f93f198 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-ictce-4.0.6.eb @@ -17,7 +17,7 @@ dependencies = [ ('Geant4', '9.5.p01'), ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), - ('CMake', '2.8.4'), ] +builddependencies = [('CMake', '2.8.4')] moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb index 153cbd2179..dd8ac9566b 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -17,7 +17,7 @@ dependencies = [ ('Geant4', '9.5.p01'), ('CLHEP', '2.1.1.0'), ('ROOT', 'v5.34.01'), - ('CMake', '2.8.4'), ] +builddependencies = [('CMake', '2.8.4')] moduleclass = 'cae' -- GitLab From fbb18c453468b923d421838b321b9121bd4c5b0a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 19 Mar 2015 14:17:23 +0100 Subject: [PATCH 461/911] SAM and BCFtools with intel and foss 2015a --- .../BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb | 36 ++++++++++ .../BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb | 36 ++++++++++ .../BCFtools-1.2_extHTSlib_Makefile.patch | 65 +++++++++++++++++++ .../SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb | 7 +- .../SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb | 33 ++++++++++ .../SAMtools-1.2_extHTSlib_Makefile.patch | 23 +++++-- 6 files changed, 189 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.2_extHTSlib_Makefile.patch create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb new file mode 100644 index 0000000000..71c37a2d63 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [('HTSlib', '1.2.1')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb new file mode 100644 index 0000000000..197f2b1a9b --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [('HTSlib', '1.2.1')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2_extHTSlib_Makefile.patch b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2_extHTSlib_Makefile.patch new file mode 100644 index 0000000000..a6df8a51d3 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2_extHTSlib_Makefile.patch @@ -0,0 +1,65 @@ +# patch needed to use external HTSlib and ZLIB +# B. Hajgato March 19 2015 +--- bcftools-1.2/Makefile.orig 2015-02-03 17:27:19.000000000 +0100 ++++ bcftools-1.2/Makefile 2015-03-19 13:24:18.595228622 +0100 +@@ -29,14 +29,11 @@ + all: $(PROG) $(TEST_PROG) + + # Adjust $(HTSDIR) to point to your top-level htslib directory +-HTSDIR = htslib-1.2.1 +-include $(HTSDIR)/htslib.mk +-HTSLIB = $(HTSDIR)/libhts.a +-BGZIP = $(HTSDIR)/bgzip +-TABIX = $(HTSDIR)/tabix ++HTSDIR = $(EBROOTHTSLIB)/include ++HTSLIB = $(EBROOTHTSLIB)/lib/libhts.a ++BGZIP = $(EBROOTHTSLIB)/bin/bgzip ++TABIX = $(EBROOTHTSLIB)/bin/tabix + +-CC = gcc +-CFLAGS = -g -Wall -Wc++-compat -O2 + DFLAGS = + OBJS = main.o vcfindex.o tabix.o \ + vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \ +@@ -45,6 +42,7 @@ + vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \ + ccall.o em.o prob1.o kmin.o # the original samtools calling + INCLUDES = -I. -I$(HTSDIR) ++ZLIB= -L$(EBROOTZLIB)/lib -lz + + # The polysomy command is not compiled by default because it brings dependency + # on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL +@@ -102,8 +100,8 @@ + PLUGINS = $(PLUGINC:.c=.so) + PLUGINM = $(PLUGINC:.c=.mk) + +-%.so: %.c version.h version.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts ++%.so: %.c version.h version.c $(EBROOTHTSLIB)/lib/libhts.so ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(EBROOTHTSLIB)/lib -lhts + + -include $(PLUGINM) + +@@ -159,7 +157,7 @@ + $(CC) $(CFLAGS) -o $@ -lm -ldl $< + + bcftools: $(HTSLIB) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS) ++ $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(ZLIB) -lm -ldl $(LDLIBS) + + doc/bcftools.1: doc/bcftools.txt + cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt +--- bcftools-1.2/plugins/fixploidy.mk.orig 2014-10-09 11:01:22.000000000 +0200 ++++ bcftools-1.2/plugins/fixploidy.mk 2015-03-19 13:30:48.125228201 +0100 +@@ -1,2 +1,2 @@ +-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(EBROOTHTSLIB)/lib/libhts.so ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(EBROOTHTSLIB)/lib -lhts +--- bcftools-1.2/plugins/vcf2sex.mk.orig 2014-10-09 11:01:22.000000000 +0200 ++++ bcftools-1.2/plugins/vcf2sex.mk 2015-03-19 13:31:11.227228307 +0100 +@@ -1,2 +1,2 @@ +-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so +- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts ++plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(EBROOTHTSLIB)/lib/libhts.so ++ $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(EBROOTHTSLIB)/lib -lhts diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb index d20cd89e7b..7236af59bb 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb @@ -12,8 +12,8 @@ name = 'SAMtools' version = '1.2' homepage = 'http://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} @@ -21,12 +21,11 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -#patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] dependencies = [ ('HTSlib', '1.2.1'), ('ncurses', '5.9'), - ('zlib', '1.2.8'), ] parallel = 1 diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb new file mode 100644 index 0000000000..556ed34148 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('HTSlib', '1.2.1'), + ('ncurses', '5.9'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch index 01033c7a28..47bf7ec973 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2_extHTSlib_Makefile.patch @@ -1,6 +1,16 @@ --- samtools-1.2/Makefile.orig 2015-02-03 17:27:34.000000000 +0100 -+++ samtools-1.2/Makefile 2015-03-19 10:27:14.487237690 +0100 -@@ -36,9 +36,9 @@ ++++ samtools-1.2/Makefile 2015-03-19 11:19:38.289234982 +0100 +@@ -21,9 +21,7 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc + CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 + LDFLAGS = + LDLIBS = + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 +@@ -36,9 +34,9 @@ cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o @@ -13,7 +23,7 @@ prefix = /usr/local exec_prefix = $(prefix) bindir = $(exec_prefix)/bin -@@ -82,10 +82,10 @@ +@@ -82,10 +80,9 @@ # Adjust $(HTSDIR) to point to your top-level htslib directory @@ -22,13 +32,12 @@ -HTSLIB = $(HTSDIR)/libhts.a -BGZIP = $(HTSDIR)/bgzip +HTSDIR = $(EBROOTHTSLIB)/include -+#include $(EBROOTHTSLIB)/htslib.mk +HTSLIB = $(EBROOTHTSLIB)/lib/libhts.a +BGZIP = $(EBROOTHTSLIB)/bin/bgzip PACKAGE_VERSION = 1.2 -@@ -122,7 +122,7 @@ +@@ -122,7 +119,7 @@ $(AR) -csru $@ $(LOBJS) samtools: $(AOBJS) libbam.a $(HTSLIB) @@ -37,7 +46,7 @@ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h -@@ -192,31 +192,31 @@ +@@ -192,31 +189,31 @@ test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) @@ -78,7 +87,7 @@ test_test_h = test/test.h $(htslib_sam_h) -@@ -235,22 +235,22 @@ +@@ -235,22 +232,22 @@ # misc programs misc/ace2sam: misc/ace2sam.o -- GitLab From 2b2e7cb954793dea43c0023f43bb005048700fa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2015 14:19:33 +0100 Subject: [PATCH 462/911] add easyconfig for Ray v2.3.1 --- .../r/Ray/Ray-2.3.1-intel-2015a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray/Ray-2.3.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/Ray/Ray-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/r/Ray/Ray-2.3.1-intel-2015a.eb new file mode 100644 index 0000000000..8b7237fffb --- /dev/null +++ b/easybuild/easyconfigs/r/Ray/Ray-2.3.1-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Ray' +version = '2.3.1' + +homepage = 'http://sourceforge.net/projects/denovoassembler/' +description = """Ray -- Parallel genome assemblies for parallel DNA sequencing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://download.sourceforge.net/denovoassembler/'] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), +] + +skipsteps = ['configure'] +buildopts = 'PREFIX=%(installdir)s MPI_IO=y CXXFLAGS="$CXXFLAGS" HAVE_LIBZ=y HAVE_LIBBZ2=y' + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['Ray'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7767b36d9825c926fc4e3a5192dc083135073a9f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 20 Mar 2015 12:19:08 +0100 Subject: [PATCH 463/911] zlib added, filenames corrected --- ...ib-1.2.1-intel-2015a.eb => BCFtools-1.2-intel-2015a.eb} | 5 ++++- ...2-HTSlib-1.2.1-foss-2015a.eb => BCFtools-foss-2015a.eb} | 5 ++++- .../s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb | 7 ++++++- .../s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb | 7 ++++++- 4 files changed, 20 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/b/BCFtools/{BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb => BCFtools-1.2-intel-2015a.eb} (93%) rename easybuild/easyconfigs/b/BCFtools/{BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb => BCFtools-foss-2015a.eb} (93%) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb similarity index 93% rename from easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index 197f2b1a9b..156cebe11f 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -15,7 +15,10 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] -dependencies = [('HTSlib', '1.2.1')] +dependencies = [ + ('HTSlib', '1.2.1'), + ('zlib','1.2.8', +] parallel = 1 diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-foss-2015a.eb similarity index 93% rename from easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-foss-2015a.eb index 71c37a2d63..7aa9dcdd5b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-foss-2015a.eb @@ -15,7 +15,10 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] -dependencies = [('HTSlib', '1.2.1')] +dependencies = [ + ('HTSlib', '1.2.1'), + ('zlib', '1.2.8'), +] parallel = 1 diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb index 7236af59bb..c7743a27f3 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb @@ -23,9 +23,14 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] +htslib = 'HTSlib' +htsver = '1.2.1' +versionsuffix = '-%s-%s' % (htslib, htsver) + dependencies = [ - ('HTSlib', '1.2.1'), + (htslib, htsver), ('ncurses', '5.9'), + ('zlib', '1.2.8'), ] parallel = 1 diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb index 556ed34148..ccd0092201 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb @@ -23,9 +23,14 @@ source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(ve patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] +htslib = 'HTSlib' +htsver = '1.2.1' +versionsuffix = '-%s-%s' % (htslib, htsver) + dependencies = [ - ('HTSlib', '1.2.1'), + (htslib, htsver), ('ncurses', '5.9'), + ('zlib', '1.2.8'), ] parallel = 1 -- GitLab From 00d81f1a63eefb7f458cb6b4b3ce33ccc5e9ab3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 20 Mar 2015 12:47:34 +0100 Subject: [PATCH 464/911] Typos corrected --- .../{BCFtools-foss-2015a.eb => BCFtools-1.2-foss-2015a.eb} | 0 easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/BCFtools/{BCFtools-foss-2015a.eb => BCFtools-1.2-foss-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-foss-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb similarity index 100% rename from easybuild/easyconfigs/b/BCFtools/BCFtools-foss-2015a.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb index 156cebe11f..c997c54557 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.2-intel-2015a.eb @@ -17,7 +17,7 @@ patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch'] dependencies = [ ('HTSlib', '1.2.1'), - ('zlib','1.2.8', + ('zlib', '1.2.8'), ] parallel = 1 -- GitLab From 55d5d7ddc20b0838e11310490fa287701bcc0b2c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 20 Mar 2015 13:07:27 +0100 Subject: [PATCH 465/911] Filename corrected --- ....2.1-foss-2015a.eb => SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb} | 0 ....1-intel-2015a.eb => SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SAMtools/{SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb => SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb} (100%) rename easybuild/easyconfigs/s/SAMtools/{SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb => SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb} (100%) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb similarity index 100% rename from easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-foss-2015a.eb rename to easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-foss-2015a-HTSlib-1.2.1.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb similarity index 100% rename from easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-HTSlib-1.2.1-intel-2015a.eb rename to easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015a-HTSlib-1.2.1.eb -- GitLab From 4c1dc0307c9dd925474c536e5a0f07ba0437cde0 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 21 Mar 2015 15:06:41 +0100 Subject: [PATCH 466/911] added checksum. switch to buildopts. fixed error --- .../easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb index 6d59aab26d..ab6ce7f05d 100644 --- a/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb @@ -23,14 +23,14 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # in their website if the version number and date is correct source_urls = ['http://www.sph.umich.edu/csg/cfuchsb/'] sources = ['%(namelower)s.src.tgz'] +checksums = [('md5', 'a8011a4cf8a9be8add07815e9e42246d')] # firt move to folder libStatGen to run make -# then move to foler minimac to run make -premakeopts = ["cd libStatGen && ", "cd minimac && "] +prebuildopts = ["cd libStatGen && "] # in libStatGen folder run just "make" # in minimac folder run "make opt && make openmp" -makeopts = ["", " opt && make openmp"] +buildopts = [" && cd ../minimac && make opt && make openmp"] # parallel build fails parallel = 1 -- GitLab From 018a175df2bc5515627e30dd13175aec103a757b Mon Sep 17 00:00:00 2001 From: "tmwsiy2012@gmail.com" Date: Sat, 21 Mar 2015 22:49:34 -0400 Subject: [PATCH 467/911] first draft for R-3.1.3-foss-2015a.eb --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 375 ++++++++++++++++++ 1 file changed, 375 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb new file mode 100644 index 0000000000..d69a4416b4 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -0,0 +1,375 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-0', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.6', ext_options), + ('bootstrap', '2014.4', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.13', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-19', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-5', ext_options), + ('mclust', '4.4', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.0', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3011.99', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.6-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.10', ext_options), + ('checkmate', '1.5.1', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.5.5', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', ext_options), + ('plotrix', '3.5-10', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-29', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.1-4', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.3', ext_options), + ('RcppArmadillo', '0.4.600.0', ext_options), + ('plyr', '1.8.1', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.8', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-35', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-11', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-8', ext_options), + ('car', '2.0-22', ext_options), + ('colorspace', '1.2-4', ext_options), + ('robustbase', '0.92-2', ext_options), + ('sp', '1.0-17', ext_options), + ('vcd', '1.3-2', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-8', ext_options), + ('mice', '2.22', ext_options), + ('nlme', '3.1-118', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('mgcv', '1.8-4', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-13', ext_options), + ('mixtools', '1.0.2', ext_options), + ('cluster', '1.15.3', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.16-1', ext_options), + ('codetools', '0.2-9', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-62', ext_options), + ('survival', '2.37-7', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-1', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-13', ext_options), + ('zoo', '1.7-11', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-3', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-1', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.3', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.6', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.5', ext_options), + ('sandwich', '2.3-2', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-8', ext_options), + ('VGAM', '0.9-6', ext_options), + ('waveslim', '1.7.3', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-32', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.6.1', ext_options), + ('R.oo', '1.18.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '1.34.0', ext_options), + ('R.matlab', '3.1.1', ext_options), + ('BiocGenerics', '0.12.1', bioconductor_options), + ('Biobase', '2.26.0', bioconductor_options), + ('S4Vectors', '0.4.0', bioconductor_options), + ('IRanges', '2.0.1', bioconductor_options), + ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('AnnotationDbi', '1.28.1', bioconductor_options), + ('XVector', '0.6.0', bioconductor_options), + ('zlibbioc', '1.12.0', bioconductor_options), + ('Biostrings', '2.34.1', bioconductor_options), + ('GenomicRanges', '1.18.4', bioconductor_options), + ('Rsamtools', '1.18.3', bioconductor_options), + ('BiocParallel', '1.0.3', bioconductor_options), + ('GenomicAlignments', '1.2.2', bioconductor_options), + ('ShortRead', '1.24.0', bioconductor_options), + ('graph', '1.44.1', bioconductor_options), + ('gbm', '2.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.1-2', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('Hmisc', '3.14-6', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.4', ext_options), + ('fastcluster', '1.1.15', ext_options), + ('reshape2', '1.4.1', ext_options), + ('chron', '2.3-45', ext_options), + ('data.table', '1.9.4', ext_options), + ('gtable', '0.1.2', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.0', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.11', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-5', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.10.2.2', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.1', ext_options), + ('raster', '2.3-12', ext_options), + ('dismo', '1.0-5', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.2', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '7.1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '1.9-8', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.3-1.1', ext_options), + ('stabs', '0.5-0', ext_options), + ('mboost', '2.4-1', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.05', ext_options), + ('RcppEigen', '0.3.2.3.0', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.3-8', ext_options), + ('rms', '4.2-1', ext_options), + ('RWekajars', '3.7.11-1', ext_options), + ('RWeka', '0.4-23', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-8', ext_options), + ('chemometrics', '1.3.8', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-3', ext_options), + ('knitr', '1.8', ext_options), + ('statmod', '1.4.20', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.34.0', bioconductor_options), + ('BiocInstaller', '1.16.2', bioconductor_options), + ('preprocessCore', '1.28.0', bioconductor_options), + ('affy', '1.44.0', bioconductor_options), + ('GO.db', '3.0.0', bioconductor_options), + ('limma', '3.22.7', bioconductor_options), + ('RBGL', '1.42.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.12.2', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('FactoMineR', '1.28', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-12', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.14', ext_options), + ('kohonen', '2.0.15', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.5', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '0.7.7', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.2.1', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), +] + +moduleclass = 'lang' + -- GitLab From c298ff51fd4edf381e3274205afbb8b0338852d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Mar 2015 09:30:20 +0100 Subject: [PATCH 468/911] bump all extensions to latest version in R 3.1.3 foss/2015a easyconfig --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 158 +++++++++--------- 1 file changed, 80 insertions(+), 78 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index d69a4416b4..fcf0a79b7f 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -58,17 +58,17 @@ exts_list = [ 'utils', # non-standard libraries, should be specified with fixed versions! ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-0', ext_options), + ('abind', '1.4-3', ext_options), ('magic', '1.5-6', ext_options), - ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), ('bit', '1.1-12', ext_options), ('filehash', '2.2-2', ext_options), ('ff', '2.2-13', ext_options), - ('bnlearn', '3.6', ext_options), - ('bootstrap', '2014.4', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), ('combinat', '0.0-8', ext_options), ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.13', ext_options), + ('fdrtool', '1.2.14', ext_options), ('formatR', '1.0', ext_options), ('gtools', '3.4.1', ext_options), ('gdata', '2.13.3', ext_options), @@ -77,21 +77,21 @@ exts_list = [ ('infotheo', '1.2.0', ext_options), ('lars', '1.2', ext_options), ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-19', ext_options), + ('kernlab', '0.9-20', ext_options), ('mime', '0.2', ext_options), ('markdown', '0.7.4', ext_options), ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-5', ext_options), + ('NLP', '0.1-6', ext_options), ('mclust', '4.4', ext_options), ('RANN', '2.4.1', ext_options), ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.0', ext_options), + ('segmented', '0.5-1.1', ext_options), ('som', '0.3-5', ext_options), ('SuppDists', '1.1-9.1', ext_options), ('stabledist', '0.6-6', ext_options), ('survivalROC', '1.0.3', ext_options), ('pspline', '1.0-16', ext_options), - ('timeDate', '3011.99', ext_options), + ('timeDate', '3012.100', ext_options), ('longmemo', '1.0-0', ext_options), ('ADGofTest', '0.3', ext_options), ('ade4', '1.6-2', ext_options), @@ -101,8 +101,8 @@ exts_list = [ ('brew', '1.0-6', ext_options), ('Brobdingnag', '1.2-4', ext_options), ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.10', ext_options), - ('checkmate', '1.5.1', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), ('cubature', '1.1-2', ext_options), ('DEoptimR', '1.0-2', ext_options), ('digest', '0.6.8', ext_options), @@ -119,96 +119,96 @@ exts_list = [ ('logspline', '2.1.5', ext_options), ('ncbit', '2013.03.29', ext_options), ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-10', ext_options), + ('plotrix', '3.5-11', ext_options), ('randomForest', '4.6-10', ext_options), ('scatterplot3d', '0.3-35', ext_options), ('SparseM', '1.6', ext_options), ('tripack', '1.3-6', ext_options), ('irace', '1.06', ext_options), ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-29', ext_options), + ('lattice', '0.20-30', ext_options), ('RColorBrewer', '1.1-2', ext_options), ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-4', ext_options), + ('Matrix', '1.1-5', ext_options), ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.3', ext_options), - ('RcppArmadillo', '0.4.600.0', ext_options), + ('Rcpp', '0.11.5', ext_options), + ('RcppArmadillo', '0.4.650.1.1', ext_options), ('plyr', '1.8.1', ext_options), ('pROC', '1.7.3', ext_options), ('quadprog', '1.5-5', ext_options), ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.8', ext_options), + ('BBmisc', '1.9', ext_options), ('fail', '1.2', ext_options), ('rlecuyer', '0.3-3', ext_options), ('snow', '0.3-13', ext_options), - ('MASS', '7.3-35', ext_options), + ('MASS', '7.3-40', ext_options), ('tree', '1.0-35', ext_options), ('pls', '2.4-3', ext_options), - ('class', '7.3-11', ext_options), + ('class', '7.3-12', ext_options), ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-8', ext_options), - ('car', '2.0-22', ext_options), - ('colorspace', '1.2-4', ext_options), - ('robustbase', '0.92-2', ext_options), + ('nnet', '7.3-9', ext_options), + ('car', '2.0-25', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), ('sp', '1.0-17', ext_options), ('vcd', '1.3-2', ext_options), ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-8', ext_options), + ('rpart', '4.1-9', ext_options), ('mice', '2.22', ext_options), - ('nlme', '3.1-118', ext_options), + ('nlme', '3.1-120', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('mgcv', '1.8-4', ext_options), + ('mgcv', '1.8-5', ext_options), ('logistf', '1.21', ext_options), ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), - ('boot', '1.3-13', ext_options), + ('boot', '1.3-15', ext_options), ('mixtools', '1.0.2', ext_options), - ('cluster', '1.15.3', ext_options), + ('cluster', '2.0.1', ext_options), ('gclus', '1.3.1', ext_options), - ('coda', '0.16-1', ext_options), - ('codetools', '0.2-9', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), ('foreach', '1.4.2', ext_options), ('doMC', '1.3.3', ext_options), ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-62', ext_options), - ('survival', '2.37-7', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), ('gam', '1.09.1', ext_options), ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-1', ext_options), + ('gamlss.dist', '4.3-4', ext_options), ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-13', ext_options), - ('zoo', '1.7-11', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), ('xts', '0.9-7', ext_options), ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-3', ext_options), + ('quantmod', '0.4-4', ext_options), ('lmtest', '0.9-33', ext_options), ('mnormt', '1.5-1', ext_options), ('mvtnorm', '1.0-2', ext_options), ('pcaPP', '1.9-60', ext_options), ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.3', ext_options), + ('lava', '1.4.0', ext_options), ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.6', ext_options), + ('pscl', '1.4.8', ext_options), ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.5', ext_options), + ('BatchJobs', '1.6', ext_options), ('sandwich', '2.3-2', ext_options), ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-8', ext_options), - ('VGAM', '0.9-6', ext_options), - ('waveslim', '1.7.3', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), ('xtable', '1.7-4', ext_options), ('profileModel', '0.5-9', ext_options), ('brglm', '0.5-9', ext_options), ('deSolve', '1.11', ext_options), ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-32', ext_options), + ('tseries', '0.10-34', ext_options), ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.6.1', ext_options), - ('R.oo', '1.18.0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), ('cgdsr', '1.1.33', ext_options), - ('R.utils', '1.34.0', ext_options), - ('R.matlab', '3.1.1', ext_options), + ('R.utils', '2.0.0', ext_options), + ('R.matlab', '3.2.0', ext_options), ('BiocGenerics', '0.12.1', bioconductor_options), ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), @@ -224,23 +224,23 @@ exts_list = [ ('GenomicAlignments', '1.2.2', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), - ('gbm', '2.1', ext_options), + ('gbm', '2.1.1', ext_options), ('dichromat', '2.0-0', ext_options), - ('Formula', '1.1-2', ext_options), + ('Formula', '1.2-0', ext_options), ('acepack', '1.3-3.3', ext_options), - ('Hmisc', '3.14-6', ext_options), + ('Hmisc', '3.15-0', ext_options), ('munsell', '0.4.2', ext_options), ('labeling', '0.3', ext_options), ('scales', '0.2.4', ext_options), - ('fastcluster', '1.1.15', ext_options), + ('fastcluster', '1.1.16', ext_options), ('reshape2', '1.4.1', ext_options), ('chron', '2.3-45', ext_options), ('data.table', '1.9.4', ext_options), ('gtable', '0.1.2', ext_options), ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.0', ext_options), + ('ggplot2', '1.0.1', ext_options), ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.11', ext_options), + ('GeneNet', '1.2.12', ext_options), ('ape', '3.2', ext_options), ('htmltools', '0.2.6', ext_options), ('RJSONIO', '1.3-0', ext_options), @@ -249,7 +249,7 @@ exts_list = [ ('ROCR', '1.0-5', ext_options), ('httpuv', '1.3.2', ext_options), ('R6', '2.0.1', ext_options), - ('shiny', '0.10.2.2', ext_options), + ('shiny', '0.11.1', ext_options), ('adegenet', '1.4-2', ext_options), ('phylobase', '0.6.8', ext_options), ('adephylo', '1.1-6', ext_options), @@ -257,41 +257,41 @@ exts_list = [ ('bigmemory.sri', '0.1.3', ext_options), ('bigmemory', '4.4.6', ext_options), ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.1', ext_options), - ('raster', '2.3-12', ext_options), - ('dismo', '1.0-5', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-33', ext_options), + ('dismo', '1.0-12', ext_options), ('expm', '0.99-1.1', ext_options), ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.2', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), ('extrafont', '0.17', ext_options), - ('fields', '7.1', ext_options), + ('fields', '8.2-1', ext_options), ('shapefiles', '0.7', ext_options), ('fossil', '0.3.7', ext_options), ('geiger', '2.0.3', ext_options), ('glmnet', '1.9-8', ext_options), ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.3-1.1', ext_options), - ('stabs', '0.5-0', ext_options), - ('mboost', '2.4-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), ('msm', '1.5', ext_options), ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('quantreg', '5.05', ext_options), - ('RcppEigen', '0.3.2.3.0', ext_options), + ('quantreg', '5.11', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), ('polspline', '1.1.9', ext_options), ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.3-8', ext_options), - ('rms', '4.2-1', ext_options), - ('RWekajars', '3.7.11-1', ext_options), - ('RWeka', '0.4-23', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), ('slam', '0.1-32', ext_options), ('tm', '0.6', ext_options), - ('TraMineR', '1.8-8', ext_options), - ('chemometrics', '1.3.8', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), ('FNN', '1.1', ext_options), - ('ipred', '0.9-3', ext_options), - ('knitr', '1.8', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.9', ext_options), ('statmod', '1.4.20', ext_options), ('miscTools', '0.6-16', ext_options), ('maxLik', '1.2-4', ext_options), @@ -325,16 +325,16 @@ exts_list = [ ('clValid', '0.6-6', ext_options), ('qvalue', '1.43.0', bioconductor_options), ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.12.2', ext_options), + ('matrixStats', '0.14.0', ext_options), ('samr', '2.0', ext_options), ('DEGseq', '1.20.0', bioconductor_options), ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), - ('FactoMineR', '1.28', ext_options), + ('FactoMineR', '1.29', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-12', ext_options), + ('flexmix', '2.3-13', ext_options), ('prabclus', '2.2-6', ext_options), ('diptest', '0.75-6', ext_options), ('trimcluster', '0.1-2', ext_options), @@ -353,14 +353,14 @@ exts_list = [ ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.5', ext_options), + ('nleqslv', '2.6', ext_options), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), ('RGCCA', '2.0', ext_options), - ('pheatmap', '0.7.7', ext_options), + ('pheatmap', '1.0.2', ext_options), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.2.1', ext_options), + ('openxlsx', '2.4.0', ext_options), ('Rgraphviz', '2.10.0', bioconductor_options), ('pvclust', '1.3-2', ext_options), ('RCircos', '1.1.2', ext_options), @@ -369,6 +369,8 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('Rsubread', '1.16.1', bioconductor_options), ] moduleclass = 'lang' -- GitLab From 2c0dc0f94710a45f78ed899f9c54d7284da13c68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Mar 2015 20:04:21 +0100 Subject: [PATCH 469/911] fix inter-pkg deps for R v3.1.3 --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 26 +++++++++++-------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index fcf0a79b7f..9970cb1722 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -147,6 +147,14 @@ exts_list = [ ('class', '7.3-12', ext_options), ('e1071', '1.6-4', ext_options), ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('mgcv', '1.8-5', ext_options), + ('minqa', '1.2.4', ext_options), + ('nloptr', '1.0.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('lme4', '1.1-7', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('quantreg', '5.11', ext_options), ('car', '2.0-25', ext_options), ('colorspace', '1.2-6', ext_options), ('robustbase', '0.92-3', ext_options), @@ -155,10 +163,8 @@ exts_list = [ ('snowfall', '1.84-6', ext_options), ('rpart', '4.1-9', ext_options), ('mice', '2.22', ext_options), - ('nlme', '3.1-120', ext_options), ('urca', '1.2-8', ext_options), ('fracdiff', '1.4-2', ext_options), - ('mgcv', '1.8-5', ext_options), ('logistf', '1.21', ext_options), ('akima', '0.5-11', ext_options), ('bitops', '1.0-6', ext_options), @@ -228,17 +234,17 @@ exts_list = [ ('dichromat', '2.0-0', ext_options), ('Formula', '1.2-0', ext_options), ('acepack', '1.3-3.3', ext_options), - ('Hmisc', '3.15-0', ext_options), + ('gtable', '0.1.2', ext_options), + ('reshape2', '1.4.1', ext_options), + ('proto', '0.3-10', ext_options), ('munsell', '0.4.2', ext_options), ('labeling', '0.3', ext_options), ('scales', '0.2.4', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.15-0', ext_options), ('fastcluster', '1.1.16', ext_options), - ('reshape2', '1.4.1', ext_options), ('chron', '2.3-45', ext_options), ('data.table', '1.9.4', ext_options), - ('gtable', '0.1.2', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.1', ext_options), ('igraph', '0.7.1', ext_options), ('GeneNet', '1.2.12', ext_options), ('ape', '3.2', ext_options), @@ -277,11 +283,10 @@ exts_list = [ ('nor1mix', '1.2-0', ext_options), ('np', '0.60-2', ext_options), ('polynom', '1.3-8', ext_options), - ('quantreg', '5.11', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), ('polspline', '1.1.9', ext_options), ('TH.data', '1.0-6', ext_options), ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), ('rms', '4.3-0', ext_options), ('RWekajars', '3.7.12-1', ext_options), ('RWeka', '0.4-24', ext_options), @@ -318,7 +323,6 @@ exts_list = [ ('edgeR', '3.8.6', bioconductor_options), ('PFAM.db', '3.0.0', bioconductor_options), ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), ('GGally', '0.5.0', ext_options), ('baySeq', '2.0.50', bioconductor_options), ('beanplot', '1.2', ext_options), @@ -331,6 +335,7 @@ exts_list = [ ('DiscriMiner', '0.1-29', ext_options), ('ellipse', '0.3-8', ext_options), ('leaps', '2.9', ext_options), + ('flashClust', '1.01-2', ext_options), ('FactoMineR', '1.29', ext_options), ('modeltools', '0.2-21', ext_options), ('flexclust', '1.3-4', ext_options), @@ -369,7 +374,6 @@ exts_list = [ ('VennDiagram', '1.6.9', ext_options), ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), - ('GEOquery', '2.32.0', bioconductor_options), ('Rsubread', '1.16.1', bioconductor_options), ] -- GitLab From 7f53b3f9c666e092aacdb40267cbc32b7d74263c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Mar 2015 21:15:21 +0100 Subject: [PATCH 470/911] add easyconfig for R v3.1.3 with intel/2015a --- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 381 ++++++++++++++++++ 1 file changed, 381 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb new file mode 100644 index 0000000000..9ff1e63f74 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -0,0 +1,381 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '4.4', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.6-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.5.5', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', ext_options), + ('plotrix', '3.5-11', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-30', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.1-5', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.5', ext_options), + ('RcppArmadillo', '0.4.650.1.1', ext_options), + ('plyr', '1.8.1', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-40', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-12', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('mgcv', '1.8-5', ext_options), + ('minqa', '1.2.4', ext_options), + ('nloptr', '1.0.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('lme4', '1.1-7', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('quantreg', '5.11', ext_options), + ('car', '2.0-25', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), + ('sp', '1.0-17', ext_options), + ('vcd', '1.3-2', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-9', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-15', ext_options), + ('mixtools', '1.0.2', ext_options), + ('cluster', '2.0.1', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-1', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.4.0', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.8', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-2', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.0.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('BiocGenerics', '0.12.1', bioconductor_options), + ('Biobase', '2.26.0', bioconductor_options), + ('S4Vectors', '0.4.0', bioconductor_options), + ('IRanges', '2.0.1', bioconductor_options), + ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('AnnotationDbi', '1.28.1', bioconductor_options), + ('XVector', '0.6.0', bioconductor_options), + ('zlibbioc', '1.12.0', bioconductor_options), + ('Biostrings', '2.34.1', bioconductor_options), + ('GenomicRanges', '1.18.4', bioconductor_options), + ('Rsamtools', '1.18.3', bioconductor_options), + ('BiocParallel', '1.0.3', bioconductor_options), + ('GenomicAlignments', '1.2.2', bioconductor_options), + ('ShortRead', '1.24.0', bioconductor_options), + ('graph', '1.44.1', bioconductor_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-0', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('gtable', '0.1.2', ext_options), + ('reshape2', '1.4.1', ext_options), + ('proto', '0.3-10', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.4', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.15-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-45', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-5', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-33', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', 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('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.14', ext_options), + ('kohonen', '2.0.15', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.6', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('Rsubread', '1.16.1', bioconductor_options), +] + +moduleclass = 'lang' + -- GitLab From 1b1d525125a974ab20a9bca02a4117cb20d5fb7e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 09:30:47 +0100 Subject: [PATCH 471/911] Dummy --- easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) create mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..421376db9e --- /dev/null +++ b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb @@ -0,0 +1 @@ +dummy -- GitLab From df014f2d05061bc70c5d3875eb183d31ba6cfd9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 10:41:14 +0100 Subject: [PATCH 472/911] fix tiny remark --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 9ff1e63f74..2e15247124 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -378,4 +378,3 @@ exts_list = [ ] moduleclass = 'lang' - -- GitLab From 680423817c7562b0883fc2809b7cf47ad453aab0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Mar 2015 11:24:07 +0100 Subject: [PATCH 473/911] GLPK 4.55 intel-foss 2015a --- .../g/GLPK/GLPK-4.55-foss-2015a.eb | 28 +++++++++++++++++++ .../g/GLPK/GLPK-4.55-intel-2015a.eb | 28 +++++++++++++++++++ .../g/gplk/GPLK-4.55-intel-2015a.eb | 1 - 3 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb new file mode 100644 index 0000000000..00491cc9ba --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb new file mode 100644 index 0000000000..77009b52a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.55' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] + +dependencies = [('GMP', '6.0.0a')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb deleted file mode 100644 index 421376db9e..0000000000 --- a/easybuild/easyconfigs/g/gplk/GPLK-4.55-intel-2015a.eb +++ /dev/null @@ -1 +0,0 @@ -dummy -- GitLab From 953b574b3c30ddd17c44a2248503989dd01dd972 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 14:19:39 +0100 Subject: [PATCH 474/911] bump libXp to v1.0.3 + update deps --- .../inputproto/inputproto-2.3-intel-2015a.eb | 19 ---------- .../l/libX11/libX11-1.6.1-intel-2015a.eb | 37 ------------------- ...2015a.eb => libXdmcp-1.1.2-intel-2015a.eb} | 4 +- ...-2015a.eb => libXext-1.3.3-intel-2015a.eb} | 10 ++--- ...el-2015a.eb => libXp-1.0.3-intel-2015a.eb} | 8 ++-- .../libxcb-1.8-intel-2015a-Python-2.7.8.eb | 35 ------------------ .../xcb-proto-1.7-intel-2015a-Python-2.7.8.eb | 27 -------------- .../xextproto/xextproto-7.2.1-intel-2015a.eb | 25 ------------- .../x/xproto/xproto-7.0.26-intel-2015a.eb | 24 ------------ 9 files changed, 11 insertions(+), 178 deletions(-) delete mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb rename easybuild/easyconfigs/l/libXdmcp/{libXdmcp-1.1.1-intel-2015a.eb => libXdmcp-1.1.2-intel-2015a.eb} (93%) rename easybuild/easyconfigs/l/libXext/{libXext-1.3.2-intel-2015a.eb => libXext-1.3.3-intel-2015a.eb} (83%) rename easybuild/easyconfigs/l/libXp/{libXp-1.0.2-intel-2015a.eb => libXp-1.0.3-intel-2015a.eb} (81%) delete mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb delete mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb deleted file mode 100644 index 0437a042db..0000000000 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'inputproto' -version = '2.3' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X.org InputProto protocol headers.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb deleted file mode 100644 index 70b695c73d..0000000000 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-intel-2015a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libX11' -version = '1.6.1' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X11 client-side library""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] - -pythonversion = '-Python-2.7.8' -builddependencies = [ - ('xextproto', '7.2.1'), - ('xcb-proto', '1.7', pythonversion), - ('kbproto', '1.0.6'), - ('inputproto', '2.3'), - ('xproto', '7.0.26'), -] - -dependencies = [ - ('libxcb', '1.8', pythonversion), - ('xtrans', '1.3.4'), -] - -sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in [ - 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', - 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', - ] - ], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb similarity index 93% rename from easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb rename to easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb index f1b75921a7..0bcd783d04 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXdmcp' -version = '1.1.1' +version = '1.1.2' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ - ('xproto', '7.0.26'), + ('xproto', '7.0.27'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb similarity index 83% rename from easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb rename to easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index b57d363d51..7eaad7c80b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXext' -version = '1.3.2' +version = '1.3.3' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """Common X Extensions library""" @@ -13,13 +13,13 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] dependencies = [ - ('libX11', '1.6.1'), - ('libXdmcp', '1.1.1'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ - ('xproto','7.0.26'), - ('xextproto', '7.2.1'), + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb similarity index 81% rename from easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb rename to easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb index 469ffffd9b..b1de22d8c7 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXp' -version = '1.0.2' +version = '1.0.3' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """libXp provides the X print library.""" @@ -13,13 +13,13 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.2.1'), + ('xextproto', '7.3.0'), ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.1'), - ('libXext', '1.3.2'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3'), ('libXau', '1.0.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb deleted file mode 100644 index 3343368288..0000000000 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-intel-2015a-Python-2.7.8.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxcb' -version = '1.8' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, - latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -patches = ['libxcb-no-pthread-stubs.patch'] - -python = 'Python' -pyver = '2.7.8' -versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [ - (python, pyver), - ('xcb-proto', '1.7', versionsuffix), -] - -preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " - -sanity_check_paths = { - 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", - "-randr", "-record", "-render", "-res", "-screensaver", - "-shape", "-shm", "-sync", "-xevie", "-xf86dri", "-xfixes", - "-xinerama", "-xprint", "-xtest", "-xv", "-xvmc"]], - 'dirs': ['include/xcb', 'lib/pkgconfig'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb deleted file mode 100644 index 1a9784f1e8..0000000000 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-intel-2015a-Python-2.7.8.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xcb-proto' -version = '1.7' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, - latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -toolchain = {'name': 'intel', 'version': '2015a'} - -python = 'Python' -pyver = '2.7.8' -versionsuffix = '-%s-%s' % (python, pyver) -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[0:2]) - -sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb deleted file mode 100644 index e1651c87e5..0000000000 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-intel-2015a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xextproto' -version = '7.2.1' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """XExtProto protocol headers.""" - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files': ['include/X11/extensions/%s' % x for x in [ - 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', - 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', - 'xtestconst.h', 'xtestext1proto.h' - ] - ], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb deleted file mode 100644 index 5c1117654b..0000000000 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2015a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xproto' -version = '7.0.26' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = "X protocol and ancillary headers" - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'optarch': True} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] - -sanity_check_paths = { - 'files' : ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], - 'dirs' : [] -} - -moduleclass = 'devel' -- GitLab From c0b7ca3a828a7923499659d55bec55737a6538b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 14:24:01 +0100 Subject: [PATCH 475/911] add missing libX11 easyconfig --- .../libX11-1.6.3-intel-2015a-Python-2.7.9.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..aec9e4570d --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' +versionsuffix = '-Python-2.7.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +dependencies = [ + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in [ + 'cursorfont.h', 'ImUtil.h', 'Xcms.h', 'XKBlib.h', 'XlibConf.h', 'Xlib.h', 'Xlibint.h', 'Xlib-xcb.h', + 'Xlocale.h', 'Xregion.h', 'Xresource.h', 'Xutil.h', + ] + ], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From aeba82b3d35e94874e52a98e68e70c41e5afbe7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 16:22:36 +0100 Subject: [PATCH 476/911] bump version of AnnotationDbi --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 2e15247124..6cdafd6edc 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -220,7 +220,7 @@ exts_list = [ ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), ('GenomeInfoDb', '1.2.4', bioconductor_options), - ('AnnotationDbi', '1.28.1', bioconductor_options), + ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), ('Biostrings', '2.34.1', bioconductor_options), -- GitLab From 774c95f2bafee2da8478c530d0813ab7ee6ca831 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 17:16:37 +0100 Subject: [PATCH 477/911] fix remarks --- .../easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb | 10 +++++----- .../easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb | 1 + 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb index 7eaad7c80b..7499144fec 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a.eb @@ -12,16 +12,16 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] -dependencies = [ - ('libX11', '1.6.3', '-Python-2.7.9'), - ('libXdmcp', '1.1.2'), -] - builddependencies = [ ('xproto', '7.0.27'), ('xextproto', '7.3.0'), ] +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXdmcp', '1.1.2'), +] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb index b1de22d8c7..fe0d5183a5 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-intel-2015a.eb @@ -22,6 +22,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libXau', '1.0.8'), ] + sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXp.a', 'libXp.so']], 'dirs': [], -- GitLab From 5a072e826932fff76160f8bba7574514ee3df954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 17:33:14 +0100 Subject: [PATCH 478/911] bump libXp to v1.0.3 + update deps --- .../a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb | 25 ----- .../a/Automake/Automake-1.14-goolf-1.5.14.eb | 33 ------- ...14.eb => inputproto-2.3.1-goolf-1.5.14.eb} | 2 +- ...libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb} | 16 ++-- .../l/libXau/libXau-1.0.8-goolf-1.5.14.eb | 2 +- ...5.14.eb => libXdmcp-1.1.2-goolf-1.5.14.eb} | 4 +- ....5.14.eb => libXext-1.3.3-goolf-1.5.14.eb} | 10 +- ...-1.5.14.eb => libXp-1.0.3-goolf-1.5.14.eb} | 8 +- .../l/libtool/libtool-2.4.5-goolf-1.5.14.eb | 17 ---- ... libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb} | 15 +-- .../m/M4/M4-1.4.17-goolf-1.5.14.eb | 23 ----- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 95 ------------------- ...b-proto-1.11-goolf-1.5.14-Python-2.7.9.eb} | 4 +- ....14.eb => xextproto-7.3.0-goolf-1.5.14.eb} | 2 +- ....5.14.eb => xproto-7.0.27-goolf-1.5.14.eb} | 2 +- ...1.5.14.eb => xtrans-1.3.5-goolf-1.5.14.eb} | 2 +- 16 files changed, 29 insertions(+), 231 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb rename easybuild/easyconfigs/i/inputproto/{inputproto-2.3-goolf-1.5.14.eb => inputproto-2.3.1-goolf-1.5.14.eb} (96%) rename easybuild/easyconfigs/l/libX11/{libX11-1.6.1-goolf-1.5.14.eb => libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb} (72%) rename easybuild/easyconfigs/l/libXdmcp/{libXdmcp-1.1.1-goolf-1.5.14.eb => libXdmcp-1.1.2-goolf-1.5.14.eb} (93%) rename easybuild/easyconfigs/l/libXext/{libXext-1.3.2-goolf-1.5.14.eb => libXext-1.3.3-goolf-1.5.14.eb} (83%) rename easybuild/easyconfigs/l/libXp/{libXp-1.0.2-goolf-1.5.14.eb => libXp-1.0.3-goolf-1.5.14.eb} (81%) delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb rename easybuild/easyconfigs/l/libxcb/{libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb => libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb} (79%) delete mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb rename easybuild/easyconfigs/x/xcb-proto/{xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb => xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb} (95%) rename easybuild/easyconfigs/x/xextproto/{xextproto-7.2.1-goolf-1.5.14.eb => xextproto-7.3.0-goolf-1.5.14.eb} (97%) rename easybuild/easyconfigs/x/xproto/{xproto-7.0.26-goolf-1.5.14.eb => xproto-7.0.27-goolf-1.5.14.eb} (97%) rename easybuild/easyconfigs/x/xtrans/{xtrans-1.3.4-goolf-1.5.14.eb => xtrans-1.3.5-goolf-1.5.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb deleted file mode 100644 index 3ca1111122..0000000000 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.5.14.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Autoconf' -version = '2.69' - -homepage = 'http://www.gnu.org/software/autoconf/' -description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure - software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual - user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating - system features that the package can use, in the form of M4 macro calls.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('M4', '1.4.16')] - -sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", - "autoscan", "autoupdate", "ifnames"]], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb deleted file mode 100644 index 64606d8726..0000000000 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-goolf-1.5.14.eb +++ /dev/null @@ -1,33 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'Automake' -version = "1.14" - -homepage = 'http://www.gnu.org/software/automake/automake.html' -description = "Automake: GNU Standards-compliant Makefile generator" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('Autoconf', '2.69')] - -sanity_check_paths = { - 'files': ['bin/automake', 'bin/aclocal'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb similarity index 96% rename from easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb rename to easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb index 56a7e864e0..66fc05b6d4 100644 --- a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.1-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'inputproto' -version = '2.3' +version = '2.3.1' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X.org InputProto protocol headers.""" diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb similarity index 72% rename from easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb rename to easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb index 09434cd3d2..7e6d887343 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-goolf-1.5.14-Python-2.7.9.eb @@ -1,7 +1,8 @@ easyblock = 'ConfigureMake' name = 'libX11' -version = '1.6.1' +version = '1.6.3' +versionsuffix = '-Python-2.7.9' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """X11 client-side library""" @@ -11,18 +12,17 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] -pythonversion = '-Python-2.7.8' builddependencies = [ - ('xextproto', '7.2.1'), - ('xcb-proto', '1.7', pythonversion), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), ('kbproto', '1.0.6'), - ('inputproto', '2.3'), - ('xproto', '7.0.26'), ] dependencies = [ - ('libxcb', '1.8', pythonversion), - ('xtrans', '1.3.4'), + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb index e1924b4781..2de39a52c7 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.5.14.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] dependencies = [ - ('xproto', '7.0.26'), + ('xproto', '7.0.27'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb similarity index 93% rename from easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb rename to easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb index c63e8fb713..dfac851674 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXdmcp' -version = '1.1.1' +version = '1.1.2' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] builddependencies = [ - ('xproto', '7.0.26'), + ('xproto', '7.0.27'), ] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb similarity index 83% rename from easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb rename to easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index 730c692843..7e3f435c5b 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXext' -version = '1.3.2' +version = '1.3.3' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """Common X Extensions library""" @@ -13,13 +13,13 @@ sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] dependencies = [ - ('libX11', '1.6.1'), - ('libXdmcp', '1.1.1'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXdmcp', '1.1.2'), ] builddependencies = [ - ('xproto','7.0.26'), - ('xextproto', '7.2.1'), + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb similarity index 81% rename from easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb rename to easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb index 2b397002a4..9da42c6bbb 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.3-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libXp' -version = '1.0.2' +version = '1.0.3' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """libXp provides the X print library.""" @@ -13,13 +13,13 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ - ('xextproto', '7.2.1'), + ('xextproto', '7.3.0'), ('printproto', '1.0.5'), ] dependencies = [ - ('libX11', '1.6.1'), - ('libXext', '1.3.2'), + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3'), ('libXau', '1.0.8'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb deleted file mode 100644 index c98f951ee7..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.5-goolf-1.5.14.eb +++ /dev/null @@ -1,17 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.5' - -homepage = 'http://www.gnu.org/software/libtool' -description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries - behind a consistent, portable interface.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] - -builddependencies = [('M4', '1.4.17')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb similarity index 79% rename from easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb rename to easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb index 497d6bc032..4b1ba8a05b 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxcb' -version = '1.8' +version = '1.11' homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, @@ -14,23 +14,14 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['libxcb-no-pthread-stubs.patch'] -builddependencies = [ - ('M4', '1.4.17'), - ('Automake', '1.14'), - ('Autoconf', '2.69'), - ('libtool', '2.4.5'), -] - python = 'Python' -pyver = '2.7.8' +pyver = '2.7.9' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), - ('xcb-proto', '1.7', versionsuffix), + ('xcb-proto', '1.11', versionsuffix), ] -preconfigopts = "rm -r aclocal.m4 configure Makefile.in ltmain.sh && ./autogen.sh && " - sanity_check_paths = { 'files' : ['lib/libxcb%s.a' % x for x in ["", "-composite", "-damage", "-dpms", "-dri2", "-glx", "-randr", "-record", "-render", "-res", "-screensaver", diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb deleted file mode 100644 index 39d957f556..0000000000 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-goolf-1.5.14.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'M4' -version = '1.4.17' - -homepage = 'http://www.gnu.org/software/m4/m4.html' -description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible - although it has some extensions (for example, handling more than 9 positional parameters to macros). - GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -configopts = "--enable-cxx" - -sanity_check_paths = { - 'files': ["bin/m4"], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb deleted file mode 100644 index df184b1c3e..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ /dev/null @@ -1,95 +0,0 @@ -name = 'Python' -version = '2.7.8' - -homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - -toolchain = {'name': 'goolf', 'version': '1.5.14'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -numpyversion = '1.8.1' -scipyversion = '0.14.0' - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] - -# libffi build in python is still broken, see http://bugs.python.org/issue4130 -patches = ['python-2.7_libffi-include-xmmintrin.patch'] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.8'), - ('libreadline', '6.3'), - ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons -] - -osdependencies = [('openssl-devel', 'libssl-dev')] - -# order is important! -# Version updated 08/JULY/2014 -exts_list = [ - ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), - ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], - }), - ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], - }), - ('numpy', numpyversion, { - 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s-mkl.patch' % numpyversion, - ], - }), - ('scipy', scipyversion, { - 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], - }), - ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], - }), - ('mpi4py', '1.3.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], - }), - ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], - }), - ('lockfile', '0.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], - }), - ('Cython', '0.20.2', { - 'source_urls': ['http://www.cython.org/release/'], - }), - ('dateutil', '2.2', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], - }), - ('deap', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - }), - ('decorator', '3.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - }), - ('arff', '2.0.1', { - 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], - }), - ('paramiko', '1.14.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - }), - ('pyparsing', '2.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb similarity index 95% rename from easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb rename to easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb index 2c38355a2b..5321244281 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.7-goolf-1.5.14-Python-2.7.8.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'xcb-proto' -version = '1.7' +version = '1.11' homepage = 'http://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -pyver = '2.7.8' +pyver = '2.7.9' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb similarity index 97% rename from easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb rename to easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb index 6b4cef16fe..19c9e6fc6f 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'xextproto' -version = '7.2.1' +version = '7.3.0' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """XExtProto protocol headers.""" diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb similarity index 97% rename from easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb rename to easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index a5635671e9..818673c9f9 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'xproto' -version = '7.0.26' +version = '7.0.27' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = "X protocol and ancillary headers" diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb similarity index 97% rename from easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb rename to easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb index f6435d5d2b..2286309947 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.4-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'xtrans' -version = '1.3.4' +version = '1.3.5' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """xtrans includes a number of routines to make X implementations transport-independent; -- GitLab From bd9a19cadab4d345c16d6c14cece430b868786e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 18:18:46 +0100 Subject: [PATCH 479/911] fix remarks --- .../l/libXext/libXext-1.3.3-goolf-1.5.14.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb index 7e3f435c5b..63124eca9a 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-goolf-1.5.14.eb @@ -12,16 +12,16 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] -dependencies = [ - ('libX11', '1.6.3', '-Python-2.7.9'), - ('libXdmcp', '1.1.2'), -] - builddependencies = [ ('xproto', '7.0.27'), ('xextproto', '7.3.0'), ] +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXdmcp', '1.1.2'), +] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ 'dpms.h', 'extutil.h', 'MITMisc.h', 'multibuf.h', 'security.h', 'shape.h', 'sync.h', 'Xag.h', 'Xcup.h', -- GitLab From 61966bab2cefc75e0ea738a8959439450a9bb84e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Mar 2015 21:13:28 +0100 Subject: [PATCH 480/911] drop unrequired patch file for libxcb --- .../l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb index 4b1ba8a05b..bd5e7ed56d 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-goolf-1.5.14-Python-2.7.9.eb @@ -12,8 +12,6 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['libxcb-no-pthread-stubs.patch'] - python = 'Python' pyver = '2.7.9' versionsuffix = '-%s-%s' % (python, pyver) -- GitLab From 2542456c9b5b8ecc6764519276aa7a90f2e5e2c2 Mon Sep 17 00:00:00 2001 From: "tmwsiy2012@gmail.com" Date: Mon, 23 Mar 2015 19:27:51 -0400 Subject: [PATCH 481/911] first draft for R-3.1.3-foss-2015a.eb --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 9970cb1722..6af8bc63b2 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -220,7 +220,7 @@ exts_list = [ ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), ('GenomeInfoDb', '1.2.4', bioconductor_options), - ('AnnotationDbi', '1.28.1', bioconductor_options), + ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), ('Biostrings', '2.34.1', bioconductor_options), -- GitLab From b87d628c908caaf967f4d9eb9c4e81fffb15b115 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 10:58:34 +0100 Subject: [PATCH 482/911] bump libXp version --- .../a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb index 83a0bf5863..c680dc7f26 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-goolf-1.5.14-20141023.eb @@ -20,7 +20,7 @@ dependencies = [ ('R', '3.1.2'), ('PyQt', '4.11.3', '-Python-2.7.9'), ('tcsh', '6.18.01'), - ('libXp', '1.0.2'), + ('libXp', '1.0.3'), ] modextrapaths = {'PATH': ['']} -- GitLab From 07c8e3063bc44cf2cdcbe51ef7cf1c7f70f3f139 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 11:34:03 +0100 Subject: [PATCH 483/911] bump Xmipp deps to latest version --- .../LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb | 31 +++++++++++++++++++ .../libjpeg-turbo-1.4.0-intel-2015a.eb | 2 +- .../x/Xmipp/Xmipp-3.1-intel-2015a.eb | 8 ++--- 3 files changed, 36 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb new file mode 100644 index 0000000000..8e0c167845 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +# misleading name, this is a 'stable' release +version = '4.0.4beta' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb index 639a4e904b..765e1c4ea1 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-intel-2015a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libjpeg-turbo' version = '1.4.0' -homepage = 'http://sourceforge.net/libjpeg-turbo/' +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. """ diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index 1e915813e0..c8872fd3a8 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -12,11 +12,11 @@ toolchain = {'name': 'intel', 'version': '2015a'} patches = ['sqlite_imports.patch', 'library_imports.patch'] dependencies = [ - ('Python', '2.7.9'), # Make sure Python has a working SQlite in it, the install step creates a sqlite db. - ('freetype', '2.5.3'), - ('LibTIFF', '4.0.3'), + ('Python', '2.7.9'), # should have a working sqlite, and provide numpy + ('freetype', '2.5.5'), + ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14', '-gpfs'), - ('libjpeg-turbo', '1.3.1'), + ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ] -- GitLab From 014c825f23453408344926d5e791f0a958dea335 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 11:56:41 +0100 Subject: [PATCH 484/911] add http download URL for LibTIFF --- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb | 5 ++++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb | 5 ++++- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb | 5 ++++- 5 files changed, 20 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb index 64a60f0f66..9875af8f63 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.4.10.eb @@ -18,7 +18,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb index ea5c5f104f..3fa3aba61e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb @@ -18,7 +18,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb index 8607639444..87e3b72f57 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-5.3.0.eb @@ -18,7 +18,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb index a1c8f2c16c..a06a26e3be 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014b.eb @@ -17,7 +17,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'intel', 'version': '2014b'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb index 8e0c167845..a1149ab376 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-intel-2015a.eb @@ -18,7 +18,10 @@ version = '4.0.4beta' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'intel', 'version': '2015a'} -- GitLab From 83ffaa134d4ff3f85046775dd3a4c37493fef7d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 12:19:04 +0100 Subject: [PATCH 485/911] add missing Java dep for Xmipp --- easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb | 15 +++++++++++++++ .../easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 1 + 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb new file mode 100644 index 0000000000..f3234cbd87 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_40' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index c8872fd3a8..441a24c254 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} patches = ['sqlite_imports.patch', 'library_imports.patch'] dependencies = [ + ('Java', '1.8.0_40'), ('Python', '2.7.9'), # should have a working sqlite, and provide numpy ('freetype', '2.5.5'), ('LibTIFF', '4.0.4beta'), -- GitLab From 1f15959bff12c2b5e2b3af00b35c303bd2590fd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 12:30:55 +0100 Subject: [PATCH 486/911] Java is a dummy dep --- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index 441a24c254..f1d74006ee 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} patches = ['sqlite_imports.patch', 'library_imports.patch'] dependencies = [ - ('Java', '1.8.0_40'), + ('Java', '1.8.0_40', '', True), ('Python', '2.7.9'), # should have a working sqlite, and provide numpy ('freetype', '2.5.5'), ('LibTIFF', '4.0.4beta'), -- GitLab From c3c3e93f66bfe09ec99c09fd5e22e687725f7ec1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 12:40:33 +0100 Subject: [PATCH 487/911] fix Minimac 'version' --- ...f-1.4.10.eb => Minimac-20140110-goolf-1.4.10.eb} | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/m/Minimac/{Minimac-2013.7.17-goolf-1.4.10.eb => Minimac-20140110-goolf-1.4.10.eb} (78%) diff --git a/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb similarity index 78% rename from easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb rename to easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb index ab6ce7f05d..c110a85228 100644 --- a/easybuild/easyconfigs/m/Minimac/Minimac-2013.7.17-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/Minimac/Minimac-20140110-goolf-1.4.10.eb @@ -3,11 +3,10 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = 'Minimac' -version = '2013.7.17' -versionsuffix = '-beta' +version = '20140110' homepage = 'http://genome.sph.umich.edu/wiki/Minimac' description = """ Minimac is a low memory, computationally efficient implementation @@ -19,13 +18,11 @@ description = """ Minimac is a low memory, computationally efficient implementat toolchain = {'name': 'goolf', 'version': '1.4.10'} -# the source file doesn't include version in the name so probably you should check -# in their website if the version number and date is correct -source_urls = ['http://www.sph.umich.edu/csg/cfuchsb/'] -sources = ['%(namelower)s.src.tgz'] +# # download minimac.src.tgz from http://www.sph.umich.edu/csg/cfuchsb and rename to include version/datestamp +sources = ['%(namelower)s-%(version)s.src.tgz'] checksums = [('md5', 'a8011a4cf8a9be8add07815e9e42246d')] -# firt move to folder libStatGen to run make +# first move to folder libStatGen to run make prebuildopts = ["cd libStatGen && "] # in libStatGen folder run just "make" -- GitLab From 1dcc0fbff05b380da5a494cac9eaa1871b6efe3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 13:08:34 +0100 Subject: [PATCH 488/911] add missing SQLite dependency --- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index f1d74006ee..bd7faf3909 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -19,6 +19,7 @@ dependencies = [ ('HDF5', '1.8.14', '-gpfs'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), + ('SQLite', '3.8.8.1'), # must match SQLite used by Python ] moduleclass = 'vis' -- GitLab From 31ec437a5d39d01d11b1544b1797110d80ccacea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 13:30:59 +0100 Subject: [PATCH 489/911] add easyconfigs for Minimac3 --- .../m/Minimac3/Minimac3-1.0.10-foss-2015a.eb | 28 +++++++++++++++++++ .../m/Minimac3/Minimac3-1.0.10-intel-2015a.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb new file mode 100644 index 0000000000..3f8c039cdb --- /dev/null +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Minimac3' +version = '1.0.10' + +homepage = 'http://genome.sph.umich.edu/wiki/Minimac3' +description = """Minimac3 is a lower memory and more computationally efficient implementation of the genotype + imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more + computationally efficient way with no loss of accuracy.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['ftp://share.sph.umich.edu/minimac3/'] +sources = ['%(name)s.v%(version)s.tar.gz'] + +dependencies = [('zlib', '1.2.8')] + +prebuildopts = 'CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' + +files_to_copy = [(['bin/Minimac3'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Minimac3'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb new file mode 100644 index 0000000000..e493e1ad48 --- /dev/null +++ b/easybuild/easyconfigs/m/Minimac3/Minimac3-1.0.10-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Minimac3' +version = '1.0.10' + +homepage = 'http://genome.sph.umich.edu/wiki/Minimac3' +description = """Minimac3 is a lower memory and more computationally efficient implementation of the genotype + imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more + computationally efficient way with no loss of accuracy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['ftp://share.sph.umich.edu/minimac3/'] +sources = ['%(name)s.v%(version)s.tar.gz'] + +dependencies = [('zlib', '1.2.8')] + +prebuildopts = 'CFLAGS="$CFLAGS -wd751 -L$EBROOTZLIB/lib"' +buildopts = 'CC="$CC" CXX="$CXX" F77="$F77" OPTFLAG_OPT="$CFLAGS"' + +files_to_copy = [(['bin/Minimac3'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Minimac3'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 7410b00087afc19efbe0e9db554f01059b3dfdde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 15:46:56 +0100 Subject: [PATCH 490/911] use enhanced patch file for ROOT v5.34.01 with intel/2015a --- .../r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 4 +-- .../r/ROOT/ROOT-v5.34.01_recent-ifort.patch | 33 +++++++++++++++++++ 2 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index bdb5568e8a..6fd56a833c 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -12,8 +12,8 @@ sources = ['%s_%s.source.tar.gz' % (name.lower(), version)] source_urls = ['ftp://root.cern.ch/root/'] patches = [ 'configure_FftwFromMkl_28.patch', - 'icc_ifort_v12.patch' - ] + 'ROOT-%(version)s_recent-ifort.patch', +] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch new file mode 100644 index 0000000000..d942f876ee --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch @@ -0,0 +1,33 @@ +--- root/config/Makefile.linuxx8664icc.orig 2012-07-13 15:31:26.000000000 +0200 ++++ root/config/Makefile.linuxx8664icc 2015-03-24 15:38:53.604641000 +0100 +@@ -85,6 +85,16 @@ + ICC_GE_101 = 120 + endif + ++ifeq ($(ICC_MAJOR),15) ++CXXFLAGS += -m64 -wd1572 -wd279 ++CFLAGS += -m64 -wd1572 -wd279 ++CINTCXXFLAGS += -m64 -wd1572 -wd279 ++CINTCFLAGS += -m64 -wd1572 -wd279 ++LDFLAGS += -m64 ++ICC_GE_9 = 15 ++ICC_GE_101 = 150 ++endif ++ + # System libraries: + SYSLIBS = -limf -lm -ldl $(OSTHREADLIBDIR) $(OSTHREADLIB) \ + $(ALLOCLIBDIR) $(ALLOCLIB) -rdynamic +@@ -96,8 +106,12 @@ + ifeq ($(F77),ifort) + F77 = ifort + F77FLAGS = -fPIC ++ifeq ($(ICC_MAJOR),15) ++F77LIBS := -L$(shell which ifort | sed -e 's|bin/ifort|lib/intel64|') \ ++ -lifcore ++F77FLAGS += -m64 + ifeq ($(ICC_MAJOR),12) +-F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib|') \ ++F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib/intel64|') \ + -lifcore + F77FLAGS += -m64 + else -- GitLab From d35bee622827998e65b987faa260c6d93c4a31d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 15:55:11 +0100 Subject: [PATCH 491/911] fix PyQt source_urls, configopts, Py module name --- .../p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 3a7c99d3b4..7dd0220668 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -12,10 +12,11 @@ description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt appli toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] -source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-x11-gpl-%(version)s'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] python = 'Python' pyver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -24,6 +25,12 @@ dependencies = [ ('Qt', '4.8.6'), ] -configopts = " configure-ng.py --confirm-license" +configopts = "configure-ng.py --confirm-license" +configopts += "--destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += "--no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} moduleclass = 'vis' -- GitLab From 6e3e81780ed7c3a99a07fa877a1c059a0ffdc0db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 15:57:06 +0100 Subject: [PATCH 492/911] fix ROOT patch file --- .../r/ROOT/ROOT-v5.34.01_recent-ifort.patch | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch index d942f876ee..bf96aaac1d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01_recent-ifort.patch @@ -1,5 +1,5 @@ --- root/config/Makefile.linuxx8664icc.orig 2012-07-13 15:31:26.000000000 +0200 -+++ root/config/Makefile.linuxx8664icc 2015-03-24 15:38:53.604641000 +0100 ++++ root/config/Makefile.linuxx8664icc 2015-03-24 15:56:30.697799907 +0100 @@ -85,6 +85,16 @@ ICC_GE_101 = 120 endif @@ -17,7 +17,7 @@ # System libraries: SYSLIBS = -limf -lm -ldl $(OSTHREADLIBDIR) $(OSTHREADLIB) \ $(ALLOCLIBDIR) $(ALLOCLIB) -rdynamic -@@ -96,8 +106,12 @@ +@@ -96,8 +106,13 @@ ifeq ($(F77),ifort) F77 = ifort F77FLAGS = -fPIC @@ -25,9 +25,17 @@ +F77LIBS := -L$(shell which ifort | sed -e 's|bin/ifort|lib/intel64|') \ + -lifcore +F77FLAGS += -m64 ++else ifeq ($(ICC_MAJOR),12) -F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib|') \ +F77LIBS := -L$(shell which ifort | sed -e 's|bin/intel64/ifort|compiler/lib/intel64|') \ -lifcore F77FLAGS += -m64 else +@@ -111,5 +126,6 @@ + endif + endif + endif ++endif + + # Extras -- GitLab From 1ebe2b10f4f47e11923e5d41d38d489588359fe5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 15:57:51 +0100 Subject: [PATCH 493/911] fix typo in PyQt easyconfig --- .../easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 7dd0220668..5f54e02167 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[:2]) +pythonshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ -- GitLab From 5baa9ad29157d4729ed0fc094274def9904f3825 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 16:01:10 +0100 Subject: [PATCH 494/911] fix spacing in PyQt easyconfig --- .../p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 5f54e02167..35c97630e9 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -26,8 +26,8 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += "--destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver -configopts += "--no-sip-files" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" options = {'modulename': 'PyQt4'} -- GitLab From 1f4ab43a8f2aa1a605e5ac9c21ab87f1c42dbb10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 16:15:56 +0100 Subject: [PATCH 495/911] makeopts -> buildopts --- easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb | 3 +-- easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb index 7caa293ce4..2c50b49d22 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-goolf-1.4.10.eb @@ -22,7 +22,7 @@ sources = [SOURCE_TAR_GZ] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] -makeopts = ' CC=$CC' +buildopts = ' CC=$CC' parallel = 1 @@ -34,4 +34,3 @@ sanity_check_paths = { } moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb index 1f7d3bd2f0..ec92fe5f04 100644 --- a/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/pigz/pigz-2.3.1-ictce-6.2.5.eb @@ -22,7 +22,7 @@ sources = [SOURCE_TAR_GZ] # README recommends zlib 1.2.6 or higher dependencies = [('zlib', '1.2.8')] -makeopts = ' CC=$CC' +buildopts = ' CC=$CC' parallel = 1 @@ -34,4 +34,3 @@ sanity_check_paths = { } moduleclass = 'tools' - -- GitLab From ad019134667f85695cf4e08259f5be36942c5e6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 16:28:16 +0100 Subject: [PATCH 496/911] include required patch for GATE v6.2 with intel/2015a --- easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb index dd8ac9566b..b6ef9ed9c1 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-6.2-intel-2015a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [('%%(namelower)s_v%s_tar_gz_15843.gz' % '_'.join(version.split('.')), "tar xfvz %s")] source_urls = ['http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/'] -patches = ['GATE-%(version)s_Makefile-prefix.patch'] +patches = [ + 'GATE-%(version)s_Makefile-prefix.patch', + 'GATE-%(version)s_GCC-4.7.patch', +] dependencies = [ ('Geant4', '9.5.p01'), -- GitLab From cc68b6b9d17bdd0a87a114f84ee7cc5f77f61ed7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:44:46 +0100 Subject: [PATCH 497/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.3 intel/2015a easyconfig --- easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 58d509004d..91d0cee83b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From 9e27023a4a17b5e725a7191bc48910427f814ef8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:45:57 +0100 Subject: [PATCH 498/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.8 and 3.4.1 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb | 6 ++++++ 4 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 8fc41a9000..8ef1b28d6b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index e1f4863c86..478804a887 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -69,6 +69,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -87,6 +90,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 37561dbbd7..65ec137785 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -66,6 +66,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -84,6 +87,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 648a65cc92..b64218f00f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -68,6 +68,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -86,6 +89,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From 39635a4726ed15b769b6a929d8fadd958b39f50b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:46:41 +0100 Subject: [PATCH 499/911] add six/ecdsa as dep for dateutil/paramiko in Python easyconfigs using iqacml toolchain --- easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 3b99a9a692..3dd0016674 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -63,6 +63,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -81,6 +84,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index d5bc39c85f..1496901c99 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -64,6 +64,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -82,6 +85,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From afc77b309efe490d54570fed5a6032b0a902b52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:47:52 +0100 Subject: [PATCH 500/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.5 easyconfigs --- .../p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index b1cf4f2c33..47b8de7acf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index 61bbf93bff..a9868e2f66 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index 4702e95c66..b3e31e4ea3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -62,6 +62,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -80,6 +83,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 6b7e21c3ad..ec5e6c7a3a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -60,6 +60,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -78,6 +81,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 50bb8eaa10..4625232be8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -60,6 +60,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -78,6 +81,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From c0a2565162b9b4b51b50b88944cc17c15789c299 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:48:10 +0100 Subject: [PATCH 501/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.6 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb | 6 ++++++ 3 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index ab16192e19..ba61389fd5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.19.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 8450ef1ade..575fabb0e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -62,6 +62,9 @@ exts_list = [ ('Cython', '0.19.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -80,6 +83,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 84e3eb01be..8b621ebdee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -62,6 +62,9 @@ exts_list = [ ('Cython', '0.19.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -80,6 +83,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From 289c2bc527aaf4b09f2208cde6fa25138f40220c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:49:38 +0100 Subject: [PATCH 502/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.3 cg*olf easyconfigs --- .../easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 6 ++++++ .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 6 ++++++ .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 6 ++++++ 4 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 1634c92386..5625804833 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 9da359d558..eea5ccfa5e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index 1f7939f4ae..a6794c06c9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index ad3be578b7..dc891b7530 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From d6ba5acd34b0e002e75ad0edd47239635184c1a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:50:17 +0100 Subject: [PATCH 503/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.3 g*olf easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 6 ++++++ .../easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 6 ++++++ .../easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 6 ++++++ .../p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 87842fb428..51cfbe4606 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 2831a2cc23..311b197edf 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index b776fb0b02..80c8900b94 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 78603dc07b..f847189fab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index ed4e0133ca..b2a76a28d3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 05b7c9748b..077f9d9e7e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From 32a8a4776e24094d85bb8a9f61170600723765ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 19:51:04 +0100 Subject: [PATCH 504/911] add six/ecdsa as dep for dateutil/paramiko in Python 2.7.3 easyconfigs with Intel-based toolchain --- easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 6 ++++++ easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index aa705e3789..930a85f683 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 5ff8d51fe5..f86e562788 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index b5fe2d5275..401dc6dd76 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index 811713df94..e19d9c8443 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -57,6 +57,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -75,6 +78,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 130b9064da..31732a9f47 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -59,6 +59,9 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -77,6 +80,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.12.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), -- GitLab From 4144a3024e1cb29214c1f0fd63ab065734890769 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 20:33:27 +0100 Subject: [PATCH 505/911] use --with-verbs rather than the deprecated --with-openib for OpenMPI --- .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 10 +++------- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 10 +++------- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 10 +++------- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 10 +++------- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 10 +++------- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 10 +++------- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 4 ++-- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 4 ++-- 10 files changed, 25 insertions(+), 49 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index a9ae46a639..1f4d38649b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -15,17 +15,13 @@ patches = ['OpenMPI-%(version)s-vt_cupti_events.patch'] dependencies = [('hwloc', '1.7.2')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 5f84390df9..094489afc4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -15,17 +15,13 @@ patches = ['OpenMPI-%(version)s-vt_cupti_events.patch'] dependencies = [('hwloc', '1.8')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index 7431826b3c..d9eca98720 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -13,17 +13,13 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.9')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index f9db89a192..fb7afbbd41 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -13,17 +13,13 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.10.0')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index 9beccee040..e1057430c2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index 23f7fbec5a..f73d19d32c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -12,19 +12,15 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading dependencies = [('hwloc', '1.9')] -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 4450b68758..3841ad29d2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -13,12 +13,12 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.10.1')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-openib +# needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index 6b3ec45d87..e90682df3b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -13,17 +13,13 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d dependencies = [('hwloc', '1.10.0')] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading -# needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index 43c4c3d031..a3c918320f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -12,14 +12,14 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading dependencies = [('hwloc', '1.10.0')] -# needed for --with-openib +# needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index 23433689d8..d7df86c8d6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += ' CC=icc FC=ifort CXX=icpc ' @@ -20,7 +20,7 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.10.0')] -# needed for --with-openib +# needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { -- GitLab From 02c77208e4a3d3b4df1ac1dfbeedcb804f1a31d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2015 20:37:21 +0100 Subject: [PATCH 506/911] fix osdeps spec in OpenMPI easyconfigs, stop relying on OS_NAME --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 6 +----- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 6 +----- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 6 +----- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 1 + .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 6 +----- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 6 +----- 11 files changed, 11 insertions(+), 50 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index 7a690ab154..fe72e01efd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -15,11 +15,7 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --with-o configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 65a5c05009..3f5d4cafd7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -18,11 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.6')] # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index e8dab7a8ac..68114cf721 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -19,11 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index bd0832e690..109447fa55 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -19,11 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 1505eba3ad..7d3922cea0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -19,11 +19,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index cbe729175a..21bd882ac7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -22,11 +22,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index a0f0714984..394c231617 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -18,11 +18,7 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 4cad97973f..908f092bfa 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -21,11 +21,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index fe19ab4c9f..c9d45613df 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -20,6 +20,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] +# needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 905ab46028..85b6644c9f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -18,11 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.8.1')] # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 5164388442..79c31e1c3d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -18,11 +18,7 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] # needed for --with-openib -if OS_NAME in ['debian', 'ubuntu']: - osdependencies = ['libibverbs-dev'] -else: - # OK for OS_NAME == redhat, fedora, RHEL, SL, centos - osdependencies = ['libibverbs-devel'] +osdependencies = [('libibverbs-dev','libibverbs-devel')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + -- GitLab From 643b4b9d03f52480c70e67b7289bff407fca9eb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Mar 2015 09:46:49 +0100 Subject: [PATCH 507/911] add easyconfig for lxml v3.4.2 with intel/2015a --- .../lxml-3.4.2-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..db1b7a5deb --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'lxml' +version = '3.4.2' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28'), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'lib' + -- GitLab From caf3a4cc0969188e9b5a863c42b1148bd04ba6cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Mar 2015 10:04:04 +0100 Subject: [PATCH 508/911] style fix --- .../easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb | 1 - .../easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb | 1 - .../easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb index 7ab203990e..6899577527 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb index 7c17d46955..1e39e76f87 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb index db1b7a5deb..0b5c2b72a8 100644 --- a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2015a-Python-2.7.9.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - -- GitLab From 2961c78c4e6b19233e59d3dfc1ca7403f3a9ffb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Mar 2015 14:41:18 +0100 Subject: [PATCH 509/911] get rid of LDSHARED line in zlib easyconfig --- easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb index 9a7769b77c..32533e0df9 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.5-ictce-5.5.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' +patches = ['zlib-%(version)s-detected-icc.patch'] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], -- GitLab From 7259dec519cf6996dd1f00a9514f7ceef8be87dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Mar 2015 14:48:06 +0100 Subject: [PATCH 510/911] add zlib dep to Tcl 8.6.3 easyconfigs --- easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb | 4 ++++ easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb | 4 ++++ easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb | 4 ++++ easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb | 4 ++++ 5 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb index 7affc5dcb2..b3a8beb767 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-GCC-4.9.2.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb index 391e0178fc..45613c8d4e 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb index b13013fafe..5aa437f573 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-gompi-1.5.16.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'gompi', 'version': '1.5.16'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb index dbe7dcaaa1..f169881758 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.5.14.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb index fab2dfdb6c..945189208b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-intel-2015a.eb @@ -12,6 +12,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +dependencies = [ + ('zlib', '1.2.8'), +] + configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' runtest = 'test' -- GitLab From 86c640dece9e1929fed1ac3fce878be59be5d026 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 08:53:05 +0100 Subject: [PATCH 511/911] {bio}[intel/2015a] BEDTools 2.23.0 --- .../b/BEDTools/BEDTools-2.23.0-intel-2015a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb new file mode 100644 index 0000000000..1ebb68b4ac --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb @@ -0,0 +1,29 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/'] +sources = ['v%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From 0944a456af1b195104c92efbc2a14f41b0f7fef7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:02:28 +0100 Subject: [PATCH 512/911] enhance files_to_copy in BEDTools easyconfigs --- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index acb234afd4..36c561073e 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -15,11 +15,11 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index 8b2873ae74..1339526329 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -15,11 +15,11 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb index 22c311e675..e784118a14 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -19,11 +19,11 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb index 1631b47200..d8000f9159 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb @@ -17,11 +17,11 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/arq5x/bedtools2/archive/'] sources = ['v%(version)s.tar.gz'] -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb index eff9f8d9ca..0f5a579f6e 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb @@ -19,11 +19,11 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb index 1ebb68b4ac..0ddc9b27d8 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb @@ -19,11 +19,11 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': files_to_copy, + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], } moduleclass = 'bio' -- GitLab From a01b731a699d555c68cfe493a88721c6236fdd7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:04:25 +0100 Subject: [PATCH 513/911] README -> README.md --- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb | 2 +- easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index 36c561073e..b12a1735c0 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index 1339526329..cf86fb61cf 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb index e784118a14..82e5478df3 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb index d8000f9159..88d7ab07dc 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/arq5x/bedtools2/archive/'] sources = ['v%(version)s.tar.gz'] -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb index 0f5a579f6e..44bbeb346c 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb index 0ddc9b27d8..d6d66e8578 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], -- GitLab From 2e566d1576409d4a1d1f81cbad8be150904e8073 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:19:04 +0100 Subject: [PATCH 514/911] {numlib}[intel/2015a] PETSc/SLEPc 3.5.3 --- .../c/CMake/CMake-3.2.1-intel-2015a.eb | 22 ++++++++++++++ .../h/Hypre/Hypre-2.10.0b-intel-2015a.eb | 22 ++++++++++++++ .../m/METIS/METIS-5.1.0-intel-2015a.eb | 22 ++++++++++++++ .../PETSc-3.5.3-intel-2015a-Python-2.7.9.eb | 30 +++++++++++++++++++ .../SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 19 ++++++++++++ 5 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000..4982739fa2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb new file mode 100644 index 0000000000..160c06dcb8 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.10.0b' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +# download via https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b_reg.php +sources = [SOURCELOWER_TAR_GZ] + +start_dir = "src" + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb new file mode 100644 index 0000000000..ef2bf9ff97 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb @@ -0,0 +1,22 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' +description = """METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, +and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the +multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] + +patches = ['METIS_IDXTYPEWIDTH.patch'] + +builddependencies = [('CMake', '3.0.0')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..6f526fc72b --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +name = 'PETSc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['PETSc_ranlib-fix.patch'] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +dependencies = [ + ('Boost', '1.57.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.4.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.10.0b'), +] + +builddependencies = [('CMake', '3.2.1')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2253b31148 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'SLEPc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of + large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either + standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial + SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.grycap.upv.es/slepc/download/download.php?filename='] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('PETSc', '3.5.3', versionsuffix)] + +moduleclass = 'numlib' -- GitLab From e91b085d363eeb0522ce5178e6687b207b49ec80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:25:35 +0100 Subject: [PATCH 515/911] only include 'tutorial' for latest BEDTools version, drop RELEASE_HISTORY (not updated) --- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb | 4 ++-- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index b12a1735c0..3ef9441cda 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -15,11 +15,11 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index cf86fb61cf..238a596ad4 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -15,11 +15,11 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb index 82e5478df3..fd405d9247 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -19,11 +19,11 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb index 88d7ab07dc..91498fff43 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.19.1-goolf-1.4.10.eb @@ -17,11 +17,11 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://github.com/arq5x/bedtools2/archive/'] sources = ['v%(version)s.tar.gz'] -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb index 44bbeb346c..92af179960 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.22.0-intel-2014b.eb @@ -19,11 +19,11 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], - 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test', 'tutorial'], + 'dirs': ['docs', 'data', 'genomes', 'scripts', 'test'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb index d6d66e8578..6160ea7421 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-intel-2015a.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md', 'RELEASE_HISTORY'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'tutorial', 'README.md'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], -- GitLab From 93eb34019c4dceb6bc9747caddd89d792be7d0e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Mar 2015 10:36:53 +0100 Subject: [PATCH 516/911] README.md -> README.rst for old BEDTools versions --- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index 3ef9441cda..ba457aaa3a 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index 238a596ad4..e21399a897 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -15,7 +15,7 @@ sources = ['%(name)s.v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb index fd405d9247..3d93f1ffe1 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.md'] +files_to_copy = ['bin', 'docs', 'data', 'genomes', 'scripts', 'test', 'README.rst'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], -- GitLab From 8031b31db717fbb23eb489eb1859a807808057f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 11:39:40 +0100 Subject: [PATCH 517/911] add easyconfig for ABAQUS v6.13.5 --- .../a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb new file mode 100644 index 0000000000..3f6f20e906 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -0,0 +1,15 @@ +name = 'ABAQUS' +version = '6.13.5-linux-x86_64' + +homepage = 'http://www.simulia.com/products/abaqus_fea.html' +description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%s-%s.tgz' % (name, version.split('-')[0])] + +builddependencies = [('Java', '1.7.0_60')] + +preinstallopts = "export CHECK_DISK_SPACE=OFF && " + +moduleclass = 'cae' -- GitLab From 08fe8cca49fe15022486cf6d6a1fbacbaaebcab6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 12:32:51 +0100 Subject: [PATCH 518/911] fix remark w.r.t. versionsuffix for ABAQUS, sync ABAQUS easyconfigs w.r.t. Java builddep and preinstallopts --- .../easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 9 +++++++-- .../easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 5 +++-- .../easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 5 +++-- 3 files changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index f3d5536662..b75c3fcda9 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -1,11 +1,16 @@ name = 'ABAQUS' -version = '6.12.1-linux-x86_64' +version = '6.12.1' +versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s-%s.tgz' % (name, version.split('-')[0])] +sources = [SOURCE_TGZ] + +builddependencies = [('Java', '1.7.0_60')] + +preinstallopts = "export CHECK_DISK_SPACE=OFF && " moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index 3f6f20e906..5f10d53c00 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -1,12 +1,13 @@ name = 'ABAQUS' -version = '6.13.5-linux-x86_64' +version = '6.13.5' +versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s-%s.tgz' % (name, version.split('-')[0])] +sources = [SOURCE_TGZ] builddependencies = [('Java', '1.7.0_60')] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index 47622c51e0..db92841b05 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -1,12 +1,13 @@ name = 'ABAQUS' -version = '6.14.1-linux-x86_64' +version = '6.14.1' +versionsuffix = '-linux-x86_64' homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA." toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s-%s.tgz' % (name, version.split('-')[0])] +sources = [SOURCE_TGZ] builddependencies = [('Java', '1.7.0_60')] -- GitLab From e67c6f672ebcdbccbc1c869bfb4ef7c1a0095d6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:25:27 +0100 Subject: [PATCH 519/911] reinclude FIAT and ScientificPython (that depends on an older numpy) as PETSc deps --- .../FIAT-1.5.0-intel-2015a-Python-2.7.9.eb | 35 ++++++++++++++++++ .../PETSc-3.5.3-intel-2015a-Python-2.7.9.eb | 2 ++ ...icPython-2.9.4-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..03fe5cf7a1 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.5.0' + +homepage = 'ttps://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order +instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating +arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ScientificPython', '2.9.4', versionsuffix), + ('sympy', '0.7.6', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/FIAT' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb index 6f526fc72b..4842cf5227 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -18,8 +18,10 @@ parmetis = 'ParMETIS' parmetis_ver = '4.0.3' dependencies = [ ('Boost', '1.57.0', versionsuffix), + ('FIAT', '1.5.0', versionsuffix), ('METIS', '5.1.0'), (parmetis, parmetis_ver), + ('ScientificPython', '2.9.4', versionsuffix), ('SCOTCH', '6.0.4'), ('SuiteSparse', '4.4.3', '-%s-%s' % (parmetis, parmetis_ver)), ('Hypre', '2.10.0b'), diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..0170615e9c --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'ScientificPython' +version = '2.9.4' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/Scientific' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From bb78d65b3db5a14742bed3f7de4e8352598b0981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:26:20 +0100 Subject: [PATCH 520/911] add missing sympy/numpy easyconfigs --- .../easyconfigs/n/numpy/numpy-1.8.1-mkl.patch | 213 ++++++++++++++++++ .../numpy-1.8.2-intel-2015a-Python-2.7.9.eb | 26 +++ .../sympy-0.7.6-intel-2015a-Python-2.7.9.eb | 32 +++ 3 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch new file mode 100644 index 0000000000..363f95c19f --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch @@ -0,0 +1,213 @@ +diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py +--- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ur numpy-1.8.1.orig/numpy/distutils/system_info.py numpy-1.8.1-2/numpy/distutils/system_info.py +--- numpy-1.8.1.orig/numpy/distutils/system_info.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/system_info.py 2014-07-08 15:32:34.480063940 +0200 +@@ -600,7 +600,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + return self.get_libs(key, '') +@@ -642,6 +642,23 @@ + lib_dirs) + return info + ++ def check_libs_all(self,lib_dir,libs,opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks for all libraries as shared libraries first, then ++ static (or vice versa if self.search_static_first is True). ++ """ ++ exts = self.library_extensions() ++ info = None ++ for ext in exts: ++ info = self._check_libs_all(lib_dir,libs,opt_libs,[ext]) ++ if info is not None: ++ break ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), lib_dir) ++ return info ++ + def check_libs2(self, lib_dirs, libs, opt_libs=[]): + """If static or shared libraries are available then return + their info dictionary. +@@ -655,6 +672,18 @@ + lib_dirs) + return info + ++ def check_libs2_all(self, lib_dirs, libs, opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks each library for shared or static. ++ """ ++ exts = self.library_extensions() ++ info = self._check_libs_all(lib_dirs,libs,opt_libs,exts) ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), os.pathsep.join(lib_dirs)) ++ return info ++ + def _lib_list(self, lib_dir, libs, exts): + assert is_string(lib_dir) + liblist = [] +@@ -665,6 +694,9 @@ + lib_prefixes = ['lib'] + # for each library name, see if we can find a file for it. + for l in libs: ++ if l[0]=='-': ++ liblist.append(l) ++ continue + for ext in exts: + for prefix in lib_prefixes: + p = self.combine_paths(lib_dir, prefix + l + ext) +@@ -680,6 +712,19 @@ + break + return liblist + ++ def _lib_list_all(self, lib_dirs, libs, exts): ++ assert (type(lib_dirs)==list) ++ if lib_dirs: ++ assert is_string(lib_dirs[0]) ++ liblist=[] ++ for lib_dir in lib_dirs: ++ ls=self._lib_list(lib_dir,libs,exts) ++ for l in ls: ++ log.info("(_lib_list_all) Found %s in %s"%(l,lib_dir)) ++ if l not in liblist: ++ liblist.append(l) ++ return liblist ++ + def _check_libs(self, lib_dirs, libs, opt_libs, exts): + """Find mandatory and optional libs in expected paths. + +@@ -721,6 +766,22 @@ + else: + return None + ++ def _check_libs_all(self, lib_dirs, libs, opt_libs, exts): ++ found_libs_unordered = self._lib_list_all(lib_dirs, libs, exts) ++ # ensure same order as in lib_dirs ++ found_libs = [] ++ for lib_dir in libs: ++ if lib_dir in found_libs_unordered: ++ found_libs.append(lib_dir) ++ if len(found_libs) == len(libs): ++ info = {'libraries' : found_libs, 'library_dirs' : lib_dirs} ++ opt_found_libs = self._lib_list_all(lib_dirs, opt_libs, exts) ++ if len(opt_found_libs) == len(opt_libs): ++ info['libraries'].extend(opt_found_libs) ++ return info ++ else: ++ return ++ + def combine_paths(self, *args): + """Return a list of existing paths composed by all combinations + of items from the arguments. +@@ -953,9 +1014,11 @@ + lib_dirs = self.get_lib_dirs() + incl_dirs = self.get_include_dirs() + mkl_libs = self.get_libs('mkl_libs', self._lib_mkl) +- info = self.check_libs2(lib_dirs, mkl_libs) +- if info is None: ++ mkl = None ++ mkl = self.check_libs2_all(lib_dirs,mkl_libs) ++ if mkl is None: + return ++ info = mkl + dict_append(info, + define_macros=[('SCIPY_MKL_H', None)], + include_dirs=incl_dirs) +@@ -1017,16 +1080,13 @@ + atlas = None + lapack = None + atlas_1 = None +- for d in lib_dirs: +- atlas = self.check_libs2(d, atlas_libs, []) +- lapack_atlas = self.check_libs2(d, ['lapack_atlas'], []) +- if atlas is not None: +- lib_dirs2 = [d] + self.combine_paths(d, ['atlas*', 'ATLAS*']) +- lapack = self.check_libs2(lib_dirs2, lapack_libs, []) +- if lapack is not None: +- break +- if atlas: +- atlas_1 = atlas ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) ++ lapack_atlas = self.check_libs2_all(lib_dirs, ['lapack_atlas']) ++ if atlas is not None: ++ lib_dirs2 = lib_dirs + self.combine_paths(lib_dirs,['atlas*','ATLAS*']) ++ lapack = self.check_libs2_all(lib_dirs2, lapack_libs) ++ if atlas: ++ atlas_1 = atlas + log.info(self.__class__) + if atlas is None: + atlas = atlas_1 +@@ -1105,7 +1165,8 @@ + info = {} + atlas_libs = self.get_libs('atlas_libs', + self._lib_names + self._lib_atlas) +- atlas = self.check_libs2(lib_dirs, atlas_libs, []) ++ atlas = None ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) + if atlas is None: + return + include_dirs = self.get_include_dirs() +@@ -1153,8 +1214,10 @@ + lib_dirs = self.get_lib_dirs() + + lapack_libs = self.get_libs('lapack_libs', self._lib_names) +- info = self.check_libs(lib_dirs, lapack_libs, []) +- if info is None: ++ lapack = self.check_libs_all(lib_dirs, lapack_libs, []) ++ if lapack is not None: ++ info = lapack ++ else: + return + info['language'] = 'f77' + self.set_info(**info) +@@ -1548,8 +1611,10 @@ + lib_dirs = self.get_lib_dirs() + + blas_libs = self.get_libs('blas_libs', self._lib_names) +- info = self.check_libs(lib_dirs, blas_libs, []) +- if info is None: ++ blas = self.check_libs_all(lib_dirs, blas_libs, []) ++ if blas is not None: ++ info = blas ++ else: + return + info['language'] = 'f77' # XXX: is it generally true? + self.set_info(**info) +diff -ur numpy-1.8.1.orig/numpy/distutils/unixccompiler.py numpy-1.8.1-2/numpy/distutils/unixccompiler.py +--- numpy-1.8.1.orig/numpy/distutils/unixccompiler.py 2014-03-25 20:43:23.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/unixccompiler.py 2014-07-08 15:34:01.924063926 +0200 +@@ -111,3 +111,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..db3bc90ff5 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.8.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4722866acf --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'sympy' +version = '0.7.6' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sympy' % pythonshortversion], +} + +moduleclass = 'math' -- GitLab From 94b31baab93d43b55ee13dab50729911dcc0e85a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Mar 2015 15:27:23 +0100 Subject: [PATCH 521/911] add easyconfigs for gmsh and getdp --- .../g/getdp/getdp-2.5.0-intel-2015a.eb | 24 +++++++++++++++++++ .../g/gmsh/gmsh-2.9.1-intel-2015a.eb | 23 ++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb new file mode 100644 index 0000000000..1a8738bd04 --- /dev/null +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'getdp' +version = '2.5.0' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://geuz.org/getdp' +description = """GetDP is an open source finite element solver using mixed elements to discretize de Rham-type + complexes in one, two and three dimensions.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/getdp/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +dependencies = [ + ('GSL', '1.16'), + ('PETSc', '3.5.3', versionsuffix), + ('SLEPc', '3.5.3', versionsuffix), +] + +separate_build_dir = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb new file mode 100644 index 0000000000..00701f2eb2 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '2.9.1' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/gmsh/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0' + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From c53159e9b1f6e748446c586a61d452b1256708d0 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Fri, 27 Mar 2015 21:33:13 -0400 Subject: [PATCH 522/911] adding a couple of dummy versions --- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb | 38 +++++++++++++++++++ easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 33 ++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb new file mode 100644 index 0000000000..065470ac86 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Bundle' + +name = 'Ruby-FPM' +rubyver = '2.1.5' +version = '%s-1.0.0' % rubyver + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# these are extensions for Ruby +exts_defaultclass = 'RubyGem' +exts_filter = ("gem list %(ext_name)s -i", "") + +dependencies = [ + ('Ruby', rubyver), +] + +name_tmpl = '%(name)s-%(version)s.gem' +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} +exts_list = [ + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('fpm', '1.3.3', ext_options), +] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb new file mode 100644 index 0000000000..cce8d3ff7e --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + -- GitLab From 8275b0d35d1500a2ed85288af4d8ef3003e27986 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Mar 2015 16:06:09 +0200 Subject: [PATCH 523/911] include pkg-config as build dep for mc --- .../easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb | 1 + .../p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb | 27 +++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb index 893cc852b8..96e39f3ada 100644 --- a/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mc/mc-4.8.13-GCC-4.9.2.eb @@ -29,6 +29,7 @@ dependencies = [ ] builddependencies = [ + ('pkg-config', '0.28'), ('Automake', '1.15'), ('libtool', '2.4.5'), ] diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb new file mode 100644 index 0000000000..68447b95f4 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.28' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 1359b212eac21b78f957155054558aa2edd0c3fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Mar 2015 17:06:29 +0200 Subject: [PATCH 524/911] fix source_urls for libevent --- .../easyconfigs/l/libevent/libevent-2.0.21-intel-2014b.eb | 5 ++++- .../easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.21-intel-2014b.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.21-intel-2014b.eb index 682b29be82..71829b4c94 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.21-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.21-intel-2014b.eb @@ -10,7 +10,10 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://github.com/downloads/libevent/libevent/'] +source_urls = [ + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/downloads/%(name)s/%(name)s/', +] sources = ['%(name)s-%(version)s-stable.tar.gz'] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index 78c88db863..75b8531ffa 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -10,7 +10,10 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} +source_urls = [ + 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', + 'https://github.com/downloads/%(name)s/%(name)s/', +] sources = ['%(name)s-%(version)s-stable.tar.gz'] -source_urls = ['https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%version_major_minor)s/'] moduleclass = 'lib' -- GitLab From 3ba4692ba8994664497e8b9811389227242d808b Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 30 Mar 2015 20:59:47 -0400 Subject: [PATCH 525/911] adding ncurses dep --- easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index 99ee62947e..cd1b05dd17 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] dependencies = [ + ('ncurses', '5.9'), ('libevent', '2.0.22'), ] -- GitLab From 50f6b4524071ca159ef8c2d65aa48c1866d3a10e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Mar 2015 11:21:44 +0200 Subject: [PATCH 526/911] add easyconfigs for AFNI, PyQt and SIP with intel/2015a --- ...NI-linux_openmp_64-intel-2015a-20141023.eb | 33 +++++++++++++++++ .../PyQt-4.11.3-intel-2015a-Python-2.7.9.eb | 36 +++++++++++++++++++ .../SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb new file mode 100644 index 0000000000..f082a4fbeb --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-linux_openmp_64-intel-2015a-20141023.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'PackedBinary' + +name = 'AFNI' +version = 'linux_openmp_64' +versionsuffix = '-20141023' + +homepage = 'http://afni.nimh.nih.gov' +description = """Free software for analysis and display of FMRI data """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://afni.nimh.nih.gov/pub/dist/tgz/'] +sources = ['%(version)s.tgz'] +checksums = ['8800092268d8bfc05611515b0795dae2'] + +dependencies = [ + ('R', '3.1.2'), + ('PyQt', '4.11.3', '-Python-2.7.9'), + ('tcsh', '6.18.01'), + ('libXp', '1.0.3'), +] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['afni'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..aab3898aa9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.3' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.4', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2de546ee64 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.4' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' -- GitLab From d31e2766fa8c2ddce8d0102126ed46833424ba8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Mar 2015 12:59:48 +0200 Subject: [PATCH 527/911] add easyconfig for extra R extensions that require additional dependencies --- .../c/cURL/cURL-7.41.0-intel-2015a.eb | 30 ++++++ .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 +++++ .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 99 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++ .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 +++++ 5 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb new file mode 100644 index 0000000000..7c9526c34b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.41.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +# dependencies = [('OpenSSL', '1.0.1m')] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..ba650f6541 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-1.0.1f_icc-fixes.patch', + 'OpenSSL-1.0.1i-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000..7ec2e95168 --- /dev/null +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -0,0 +1,99 @@ +easyblock = 'Bundle' + +name = 'R-extra' +version = '20150323' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('Tcl', '8.6.4'), + ('Tk', '8.6.4'), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('RCurl', '1.95-4.5', ext_options), # requires cURL + ('XML', '3.98-1.1', ext_options), # requires libxml2 + # extensions below requires one or more extensions that have an external dependency listed above + ('picante', '1.6-2', ext_options), + ('spacodiR', '0.13.0115', ext_options), + ('picante', '1.6-2', ext_options), + ('httr', '0.6.1', ext_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('rtracklayer', '1.26.2', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('GenomicFeatures', '1.18.4', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGprofile', '1.8.0', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('Gviz', '1.10.10', bioconductor_options), + ('methyAnalysis', '1.8.0', bioconductor_options), + ('pathview', '1.6.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('spliceR', '1.8.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..de684154a7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 7107eab21457aab90348ddca0c6ce07219e29c0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Mar 2015 16:22:22 +0200 Subject: [PATCH 528/911] use bare Python as a build dep for GLib --- easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb index 78ac531e4f..8db2b243a8 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.42.1-GCC-4.9.2.eb @@ -16,6 +16,6 @@ dependencies = [ ('libffi', '3.2.1'), ('gettext', '0.19.4'), ] -builddependencies = [('Python', '2.7.9', '', ('foss', '2015a'))] +builddependencies = [('Python', '2.7.9', '-bare')] moduleclass = 'vis' -- GitLab From eb47e55a0f3cf3e335995609cad4c2dfdb25d3bc Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 1 Apr 2015 15:47:24 +0200 Subject: [PATCH 529/911] added seqtk --- .../s/seqtk/seqtk-sgdp-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb new file mode 100644 index 0000000000..df4c09e56a --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' +name = 'seqtk' +version = 'sgdp' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/lh3/seqtk/archive/'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = ["seqtk", "trimadap"] +sanity_check_paths = { + 'files': files_to_copy, + 'dirs': [], +} +modextrapaths = { + 'PATH': ['$root'], +} + + +moduleclass = 'bio' -- GitLab From 368a89ac56362c72dacf11663a0d3edb1b40edc0 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 1 Apr 2015 16:02:03 +0200 Subject: [PATCH 530/911] Update seqtk-sgdp-intel-2015a.eb --- easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb index df4c09e56a..633a514e9d 100644 --- a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb +++ b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb @@ -1,9 +1,11 @@ easyblock = 'MakeCp' + name = 'seqtk' version = 'sgdp' homepage = 'https://github.com/lh3/seqtk/' -description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" toolchain = {'name': 'intel', 'version': '2015a'} @@ -17,9 +19,9 @@ sanity_check_paths = { 'files': files_to_copy, 'dirs': [], } + modextrapaths = { 'PATH': ['$root'], } - moduleclass = 'bio' -- GitLab From 65c508d1923c2eaed963bad9660e8ccb05cc3544 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 1 Apr 2015 16:02:11 +0200 Subject: [PATCH 531/911] Update seqtk-sgdp-intel-2015a.eb --- easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb index 633a514e9d..4aa619b6d7 100644 --- a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb +++ b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb @@ -15,6 +15,7 @@ source_urls = ['https://github.com/lh3/seqtk/archive/'] buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' files_to_copy = ["seqtk", "trimadap"] + sanity_check_paths = { 'files': files_to_copy, 'dirs': [], -- GitLab From 59862578bf23f7600433696c48b04a67575f2126 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 1 Apr 2015 16:03:53 +0200 Subject: [PATCH 532/911] Update seqtk-sgdp-intel-2015a.eb --- easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb index 4aa619b6d7..e8b719da0f 100644 --- a/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb +++ b/easybuild/easyconfigs/s/seqtk/seqtk-sgdp-intel-2015a.eb @@ -22,7 +22,7 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': ['$root'], + 'PATH': [''], } moduleclass = 'bio' -- GitLab From 8dd30b3d61c7374d592d17afd1139f0ff06d6b6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 11:43:37 +0200 Subject: [PATCH 533/911] add easyconfig for Bison v3.0.4 --- .../b/Bison/Bison-3.0.4-GCC-4.9.2.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..40326aa6c3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From 4bcbacf1aeda60fe715922c20ef77edc3f58f326 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 11:44:23 +0200 Subject: [PATCH 534/911] {tools}[intel/2015a] util-linux 2.26.1 (REVIEW) --- .../util-linux-2.26.1-intel-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb new file mode 100644 index 0000000000..5c77395971 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From dc686d0cce9e68dcce018c6d651a9e91e9253219 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 11:54:57 +0200 Subject: [PATCH 535/911] include --without-python in util-linux easyconfig --- .../easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb index 5c77395971..b640735411 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-intel-2015a.eb @@ -20,6 +20,8 @@ configopts += '--disable-wall --disable-use-tty-group ' configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " dependencies = [('ncurses', '5.9')] -- GitLab From eccd8d37c184e95ffaefd240d0f707d0cbeb4b69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 12:11:50 +0200 Subject: [PATCH 536/911] {vis}[intel/2015a] motif 2.3.4 with libX11 1.6.3 (REVIEW) --- .../l/libICE/libICE-1.0.9-intel-2015a.eb | 27 +++++++++++ .../l/libSM/libSM-1.2.2-intel-2015a.eb | 28 +++++++++++ .../libXt-1.1.4-intel-2015a-libX11-1.6.3.eb | 41 ++++++++++++++++ .../motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 47 +++++++++++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb | 19 ++++++++ 5 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb new file mode 100644 index 0000000000..57f6a9f4e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000..7d8fcfe61a --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..507c378340 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', libx11ver, '-Python-2.7.9'), +] + +builddependencies = [ + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..af0e37ef27 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.4' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libXt', '1.1.4', versionsuffix), + ('libXau', '1.0.8'), + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.16'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.5.5'), + ('libjpeg-turbo', '1.4.0'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('libtool', '2.4.5', '', ('GCC', '4.9.2')), + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), + ('util-linux', '2.26.1'), +] + +preconfigopts = "./autogen.sh && " + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb new file mode 100644 index 0000000000..159e636639 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] + +sanity_check_paths = { + 'files' : ['include/X11/bitmaps/gray'], + 'dirs' : [] +} + +moduleclass = 'devel' -- GitLab From 90f82fc33c672da56907eac2fa780afb122b077e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 12:37:01 +0200 Subject: [PATCH 537/911] include Autotools as build dep, rather than only libtool --- .../easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb index af0e37ef27..e2cf7a0446 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -28,7 +28,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] builddependencies = [ - ('libtool', '2.4.5', '', ('GCC', '4.9.2')), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), ('flex', '2.5.39', '', ('GCC', '4.9.2')), ('Bison', '3.0.4', '', ('GCC', '4.9.2')), ('util-linux', '2.26.1'), -- GitLab From 7bbe28c2ab6f98dd788b27abf735222961966954 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Apr 2015 13:09:32 +0200 Subject: [PATCH 538/911] enable lowopt for motif with intel/2015a to dance around compiler segfault --- .../easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb index e2cf7a0446..3197280c43 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -9,6 +9,8 @@ description = """Motif refers to both a graphical user interface (GUI) specifica It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" toolchain = {'name': 'intel', 'version': '2015a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} sources = ['%(name)s-%(version)s-src.tgz'] source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 243d569d112dda1ce81227797bd8dee8f9a11746 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 27 Mar 2015 16:27:48 +0100 Subject: [PATCH 539/911] Support for hanythingondemand. --- ...ondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++++ ...netaddr-0.7.13-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++ ...tifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 26 ++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..caad6b3b27 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '2.2.0' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +installopts='--single-version-externally-managed --record=record' + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.3.5', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '1.9.1', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.13', versionsuffix), +] + +options = {'modulename': 'hod'} + diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..b1bffb16b3 --- /dev/null +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'netaddr' +version = '0.7.13' + +homepage = 'https://pypi.python.org/pypi/netaddr' +description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network addresses""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netaddr'} + diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..26d54445b2 --- /dev/null +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'netifaces' +version = '0.10.4' + +homepage = 'https://pypi.python.org/pypi/netifaces' +description = """netifaces provides a (hopefully portable-ish) way for Python +programmers to get access to a list of the network interfaces on the local +machine, and to obtain the addresses of those network interfaces.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://pypi.python.org/packages/source/n/%(namelower)s/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netifaces'} + -- GitLab From e5834194ea70de5b46c106e48e8dfdacdc4c0dff Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 30 Mar 2015 16:44:34 +0200 Subject: [PATCH 540/911] Add pbs_python since it wasn't in EB upstream. --- ...s_python-4.3.5-intel-2015a-Python-2.7.9.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c47f57e15e --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,60 @@ +name = 'pbs_python' +version = '4.3.5' +easyblock = 'ConfigureMake' + +homepage = '' +description = """The pbs_python package is a wrapper class for the Torque Batch System C library. With this package, you + now can write utilities and extensions in Python instead of C. This package was developed to replace xpbsmon by an + ASCII version named pbsmon. PBSQuery is also included in this package. This is a Python module built on top of the pbs + Python module to simplify querying the batch server. There are a lot of examples included in the source package. + """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [ + 'http://ftp.sara.nl/pub/outgoing/', + 'https://raw.github.com/adaptivecomputing/torque/4.2-dev/src/include/', + 'https://oss.trac.surfsara.nl/pbs_python/raw-attachment/ticket/36/', + ] + +# torque-devel is missing a log.h file we need, so we ship it. +my_startdir = "%s-%s/" % (name, version) + +place_for_include_file = "include/torque" +copy_cmd = 'mkdir -p %s%%s && cp %%%%s %s%%s ' % (my_startdir, my_startdir) +sources = [ + SOURCE_TAR_GZ, + ('log.h', copy_cmd % (place_for_include_file, place_for_include_file)), + ('pbs_wrap_4.2.c', copy_cmd % ('src', 'src')), +] +patches = [ + 'docdir.patch', + 'setup.py.in_4.2.patch', +] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +osdependencies = ['torque-devel'] +dependencies = [ + (python, pythonver), +] + +# this is needed for setup.py script +preconfigopts = 'export PBS_PYTHON_INCLUDEDIR="$PWD/%s" && ' % place_for_include_file +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = ' %s export CFLAGS="$CFLAGS -I$PWD/%s -I/usr/include/torque/" && ' % (preconfigopts, place_for_include_file) +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages/' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%spbs" % pythonpath] +} + +moduleclass = 'tools' -- GitLab From 3ec8c9adf9bf3ff6729a9f254be9def38e9a99d5 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 30 Mar 2015 16:49:38 +0200 Subject: [PATCH 541/911] Add patches! --- .../easyconfigs/p/pbs_python/docdir.patch | 12 ++++ .../p/pbs_python/setup.py.in_4.2.patch | 55 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbs_python/docdir.patch create mode 100644 easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch diff --git a/easybuild/easyconfigs/p/pbs_python/docdir.patch b/easybuild/easyconfigs/p/pbs_python/docdir.patch new file mode 100644 index 0000000000..7c012d8e84 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/docdir.patch @@ -0,0 +1,12 @@ +--- Makefile.in.orig 2013-11-25 16:19:27.813530658 +0100 ++++ Makefile.in 2013-11-25 16:19:41.980755196 +0100 +@@ -5,7 +5,7 @@ + exec_prefix=$(PREFIX) + BINDIR=$(PREFIX)/bin + +-DOCDIR=/usr/share/doc/pbs-python ++DOCDIR=@docdir@ + EXAMPLES=$(DOCDIR)/examples + + .PHONY: install pythonlib +~ diff --git a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch new file mode 100644 index 0000000000..978ba571fd --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch @@ -0,0 +1,55 @@ +diff -uN pbs_python-4.3.5.orig/setup.py.in pbs_python-4.3.5/setup.py.in +--- pbs_python-4.3.5.orig/setup.py.in 2013-12-05 19:49:17.601962399 +0100 ++++ pbs_python-4.3.5/setup.py.in 2013-12-05 19:49:45.713469496 +0100 +@@ -7,8 +7,10 @@ + + import sys + import os ++import glob + +-from distutils.core import setup, Extension ++from distutils.core import setup, Extension ++from distutils.version import LooseVersion + + # Strip off the -L it is also added by the python setup tools + # +@@ -25,13 +27,6 @@ + ### Make symlinks to right torque version + # + VERSION = "@pbs_version@" +-tmp = VERSION.split('.') +- +-major_version = int(tmp[0]) +-minor_version = int(tmp[1]) +-#build_version = int(tmp[2]) +-build_version = int(tmp[2].split('-')[0]) +- + + os.chdir('src') + +@@ -43,7 +38,23 @@ + except OSError: + pass + +-if major_version >= 2 and minor_version >= 4 and build_version >= 7: ++if LooseVersion(VERSION) >= LooseVersion('4.2'): ++ inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') ++ os.environ['CC']=os.environ['CXX'] ++ os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) ++ ++ if not os.path.exists(os.path.join(inc,'log.h')): ++ print 'Failed to find log.h in inlcude dir %s. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable)'%inc ++ sys.exit(2) ++ ++ for fn in glob.glob('*.h'): ++ os.remove(fn) ++ ++ os.symlink('pbs_wrap_4.2.c', 'pbs_wrap.c') ++ os.symlink('pbs_2.4.py', 'pbs.py') ++ ++ TORQUE_VERSION='TORQUE_4_2' ++elif LooseVersion(VERSION) >= LooseVersion('2.4.7'): + os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c') + os.symlink('pbs_2.4.py', 'pbs.py') + TORQUE_VERSION='TORQUE_2_4' + -- GitLab From 34c9845a27e6d0d1be0bc06158337df19b235e90 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 31 Mar 2015 11:40:11 +0200 Subject: [PATCH 542/911] Add vsc-mympirun and vsc-base files for hanythingondemand. --- .../easyconfigs/v/vsc-base/vsc-base-1.9.1.eb | 19 ++++++++++++++ .../v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 25 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb create mode 100755 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb new file mode 100644 index 0000000000..8fc4fb35d9 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependentPythonPackage' +name = 'vsc-base' +version = "1.9.1" # tweaked by EasyBuild (was: '1.7.3') + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'https://github.com/hpcugent/vsc-base/archive/', +] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb new file mode 100755 index 0000000000..f471f436a3 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -0,0 +1,25 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun' +version = '3.4.2' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +dependencies = [ + ('vsc-base', '1.9.1'), + ('setuptools', '1.4.2'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +moduleclass = 'tools' -- GitLab From 7e44e4a88c86c6680629c91baffef7d471f989da Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 31 Mar 2015 14:15:51 +0200 Subject: [PATCH 543/911] Add moduleclass to the .eb files. --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 1 + .../n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb | 1 + .../n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index caad6b3b27..fbd087f56f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -33,3 +33,4 @@ dependencies = [ options = {'modulename': 'hod'} +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb index b1bffb16b3..7a57c70dfb 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb @@ -22,3 +22,4 @@ dependencies = [ options = {'modulename': 'netaddr'} +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index 26d54445b2..f15deeb6e3 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -24,3 +24,4 @@ dependencies = [ options = {'modulename': 'netifaces'} +moduleclass = 'tools' -- GitLab From ba2fd41945cd0ed98486d1044ec15daec0e0d491 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 11:55:55 +0200 Subject: [PATCH 544/911] bump netaddr to 0.7.14 --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 2 +- ...thon-2.7.9.eb => netaddr-0.7.14-intel-2015a-Python-2.7.9.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/netaddr/{netaddr-0.7.13-intel-2015a-Python-2.7.9.eb => netaddr-0.7.14-intel-2015a-Python-2.7.9.eb} (96%) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index fbd087f56f..c74a578c62 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -28,7 +28,7 @@ dependencies = [ ('vsc-mympirun', '3.4.2', '', True), ('vsc-base', '1.9.1', '', True), ('netifaces', '0.10.4', versionsuffix), - ('netaddr', '0.7.13', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), ] options = {'modulename': 'hod'} diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb similarity index 96% rename from easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb index 7a57c70dfb..e729baad33 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'netaddr' -version = '0.7.13' +version = '0.7.14' homepage = 'https://pypi.python.org/pypi/netaddr' description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network addresses""" -- GitLab From ab061e012414a36e2fe76b4e7d8cc70c8cf5b00c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 11:59:10 +0200 Subject: [PATCH 545/911] fix source URLs for netaddr and netifaces --- .../n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb | 2 +- .../n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb index e729baad33..a12196a3b8 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb @@ -8,7 +8,7 @@ description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index f15deeb6e3..26cfac901b 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -10,7 +10,7 @@ machine, and to obtain the addresses of those network interfaces.""" toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://pypi.python.org/packages/source/n/%(namelower)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From ebbacfbdc8ce8b7ef2d03c7e93123fc05b147774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 12:16:23 +0200 Subject: [PATCH 546/911] bump vsc-base to v2.0.4 --- .../hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 2 +- .../v/vsc-base/{vsc-base-1.9.1.eb => vsc-base-2.0.4.eb} | 8 +++----- .../easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 4 ++-- 3 files changed, 6 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/v/vsc-base/{vsc-base-1.9.1.eb => vsc-base-2.0.4.eb} (76%) diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index c74a578c62..6e8188683e 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -26,7 +26,7 @@ dependencies = [ (python, pythonver), ('pbs_python', '4.3.5', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '1.9.1', '', True), + ('vsc-base', '2.0.4', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb similarity index 76% rename from easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb rename to easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb index 8fc4fb35d9..24862f2519 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.9.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb @@ -1,6 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' + name = 'vsc-base' -version = "1.9.1" # tweaked by EasyBuild (was: '1.7.3') +version = '2.0.4' homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" @@ -8,11 +9,8 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = {'name': 'dummy', 'version': 'dummy'} - sources = [SOURCE_TAR_GZ] -source_urls = [ - 'https://github.com/hpcugent/vsc-base/archive/', -] +source_urls = [PYPI_SOURCE] options = {'modulename': 'vsc.utils'} diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb index f471f436a3..f1a22d74a6 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -3,7 +3,7 @@ easyblock = 'VSCPythonPackage' name = 'vsc-mympirun' version = '3.4.2' -homepage = 'http://hpcugent.github.com/vsc-mympirun/' +homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [ - ('vsc-base', '1.9.1'), + ('vsc-base', '2.0.4'), ('setuptools', '1.4.2'), ] -- GitLab From c5cb70531a08c30bca372a3505b5f125d0645fdf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Apr 2015 14:02:22 +0200 Subject: [PATCH 547/911] use most recent pbs_python, use VersionIndependentPythonPackage for HOD --- ...ondemand-2.2.0-intel-2015a-Python-2.7.9.eb | 8 +-- .../easyconfigs/p/pbs_python/docdir.patch | 12 ---- ...s_python-4.3.5-intel-2015a-Python-2.7.9.eb | 60 ------------------- ...s_python-4.6.0-intel-2015a-Python-2.7.9.eb | 41 +++++++++++++ .../p/pbs_python/pbs_python-4.6.0_CC.patch | 20 +++++++ .../p/pbs_python/setup.py.in_4.2.patch | 55 ----------------- 6 files changed, 64 insertions(+), 132 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pbs_python/docdir.patch delete mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch delete mode 100644 easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb index 6e8188683e..581c70ff5f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'VersionIndependentPythonPackage' name = 'hanythingondemand' version = '2.2.0' @@ -16,15 +16,13 @@ sources = ['%s.tar.gz' % version] python = 'Python' pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pythonshortver = '.'.join(pythonver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonver) -installopts='--single-version-externally-managed --record=record' - # a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime dependencies = [ (python, pythonver), - ('pbs_python', '4.3.5', versionsuffix), + ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), ('vsc-base', '2.0.4', '', True), ('netifaces', '0.10.4', versionsuffix), diff --git a/easybuild/easyconfigs/p/pbs_python/docdir.patch b/easybuild/easyconfigs/p/pbs_python/docdir.patch deleted file mode 100644 index 7c012d8e84..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/docdir.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- Makefile.in.orig 2013-11-25 16:19:27.813530658 +0100 -+++ Makefile.in 2013-11-25 16:19:41.980755196 +0100 -@@ -5,7 +5,7 @@ - exec_prefix=$(PREFIX) - BINDIR=$(PREFIX)/bin - --DOCDIR=/usr/share/doc/pbs-python -+DOCDIR=@docdir@ - EXAMPLES=$(DOCDIR)/examples - - .PHONY: install pythonlib -~ diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb deleted file mode 100644 index c47f57e15e..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.3.5-intel-2015a-Python-2.7.9.eb +++ /dev/null @@ -1,60 +0,0 @@ -name = 'pbs_python' -version = '4.3.5' -easyblock = 'ConfigureMake' - -homepage = '' -description = """The pbs_python package is a wrapper class for the Torque Batch System C library. With this package, you - now can write utilities and extensions in Python instead of C. This package was developed to replace xpbsmon by an - ASCII version named pbsmon. PBSQuery is also included in this package. This is a Python module built on top of the pbs - Python module to simplify querying the batch server. There are a lot of examples included in the source package. - """ - -toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': True} - -source_urls = [ - 'http://ftp.sara.nl/pub/outgoing/', - 'https://raw.github.com/adaptivecomputing/torque/4.2-dev/src/include/', - 'https://oss.trac.surfsara.nl/pbs_python/raw-attachment/ticket/36/', - ] - -# torque-devel is missing a log.h file we need, so we ship it. -my_startdir = "%s-%s/" % (name, version) - -place_for_include_file = "include/torque" -copy_cmd = 'mkdir -p %s%%s && cp %%%%s %s%%s ' % (my_startdir, my_startdir) -sources = [ - SOURCE_TAR_GZ, - ('log.h', copy_cmd % (place_for_include_file, place_for_include_file)), - ('pbs_wrap_4.2.c', copy_cmd % ('src', 'src')), -] -patches = [ - 'docdir.patch', - 'setup.py.in_4.2.patch', -] - -python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) - -osdependencies = ['torque-devel'] -dependencies = [ - (python, pythonver), -] - -# this is needed for setup.py script -preconfigopts = 'export PBS_PYTHON_INCLUDEDIR="$PWD/%s" && ' % place_for_include_file -configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" -prebuildopts = ' %s export CFLAGS="$CFLAGS -I$PWD/%s -I/usr/include/torque/" && ' % (preconfigopts, place_for_include_file) -preinstallopts = prebuildopts - -pythonpath = 'lib/python%s/site-packages/' % pythonshortver -modextrapaths = {"PYTHONPATH": pythonpath} - -sanity_check_paths = { - 'files': [], - 'dirs': ["%spbs" % pythonpath] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..2b1f46d33d --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = ['pbs_python-%(version)s_CC.patch'] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch new file mode 100644 index 0000000000..00d8259263 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch @@ -0,0 +1,20 @@ +--- pbs_python-4.6.0/setup.py.in.orig 2015-04-01 13:51:18.158956461 +0200 ++++ pbs_python-4.6.0/setup.py.in 2015-04-01 13:52:02.249359723 +0200 +@@ -37,7 +37,7 @@ + if LooseVersion(VERSION) >= LooseVersion('5.0'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): +@@ -55,7 +55,7 @@ + elif LooseVersion(VERSION) >= LooseVersion('4.2'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): diff --git a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch b/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch deleted file mode 100644 index 978ba571fd..0000000000 --- a/easybuild/easyconfigs/p/pbs_python/setup.py.in_4.2.patch +++ /dev/null @@ -1,55 +0,0 @@ -diff -uN pbs_python-4.3.5.orig/setup.py.in pbs_python-4.3.5/setup.py.in ---- pbs_python-4.3.5.orig/setup.py.in 2013-12-05 19:49:17.601962399 +0100 -+++ pbs_python-4.3.5/setup.py.in 2013-12-05 19:49:45.713469496 +0100 -@@ -7,8 +7,10 @@ - - import sys - import os -+import glob - --from distutils.core import setup, Extension -+from distutils.core import setup, Extension -+from distutils.version import LooseVersion - - # Strip off the -L it is also added by the python setup tools - # -@@ -25,13 +27,6 @@ - ### Make symlinks to right torque version - # - VERSION = "@pbs_version@" --tmp = VERSION.split('.') -- --major_version = int(tmp[0]) --minor_version = int(tmp[1]) --#build_version = int(tmp[2]) --build_version = int(tmp[2].split('-')[0]) -- - - os.chdir('src') - -@@ -43,7 +38,23 @@ - except OSError: - pass - --if major_version >= 2 and minor_version >= 4 and build_version >= 7: -+if LooseVersion(VERSION) >= LooseVersion('4.2'): -+ inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') -+ os.environ['CC']=os.environ['CXX'] -+ os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) -+ -+ if not os.path.exists(os.path.join(inc,'log.h')): -+ print 'Failed to find log.h in inlcude dir %s. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable)'%inc -+ sys.exit(2) -+ -+ for fn in glob.glob('*.h'): -+ os.remove(fn) -+ -+ os.symlink('pbs_wrap_4.2.c', 'pbs_wrap.c') -+ os.symlink('pbs_2.4.py', 'pbs.py') -+ -+ TORQUE_VERSION='TORQUE_4_2' -+elif LooseVersion(VERSION) >= LooseVersion('2.4.7'): - os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c') - os.symlink('pbs_2.4.py', 'pbs.py') - TORQUE_VERSION='TORQUE_2_4' - -- GitLab From b7aebb937fd98e5e1cbe5b6ba80ee91e3abd1af3 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Apr 2015 13:50:54 +0200 Subject: [PATCH 548/911] Bump hod and vsc-base for bug fixes. --- ...gondemand-2.2.1-intel-2015a-Python-2.7.9.eb} | 4 ++-- .../easyconfigs/v/vsc-base/vsc-base-2.1.2.eb | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/hanythingondemand/{hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb => hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb} (94%) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb similarity index 94% rename from easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index 581c70ff5f..241e630c35 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'VersionIndependentPythonPackage' name = 'hanythingondemand' -version = '2.2.0' +version = '2.2.1' homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. @@ -24,7 +24,7 @@ dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.0.4', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb new file mode 100644 index 0000000000..b0db50051e --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb @@ -0,0 +1,17 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'vsc-base' +version = '2.1.2' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' -- GitLab From f2af4369e6b2f2d212d1ac736d6e943b338b608f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Thu, 2 Apr 2015 14:48:24 +0200 Subject: [PATCH 549/911] Bump vsc-base version. --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb index f1a22d74a6..e24521bcf5 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [ - ('vsc-base', '2.0.4'), + ('vsc-base', '2.1.2'), ('setuptools', '1.4.2'), ] -- GitLab From a297788484eb778faeef5c9f335a58cc3b33c9b4 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Thu, 2 Apr 2015 12:45:56 -0400 Subject: [PATCH 550/911] adding fpm to the dummy Ruby install --- .../Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb | 38 ------------------- .../r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb | 38 ------------------- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 19 ++++++++++ 3 files changed, 19 insertions(+), 76 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb delete mode 100644 easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb deleted file mode 100644 index 1aa58a2ac6..0000000000 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0-foss-2015a.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'Bundle' - -name = 'Ruby-FPM' -rubyver = '2.1.5' -version = '%s-1.0.0' % rubyver - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -# these are extensions for Ruby -exts_defaultclass = 'RubyGem' -exts_filter = ("gem list %(ext_name)s -i", "") - -dependencies = [ - ('Ruby', rubyver), -] - -name_tmpl = '%(name)s-%(version)s.gem' -ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], - 'source_tmpl': name_tmpl, -} -exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), - ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), -] diff --git a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb b/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb deleted file mode 100644 index 065470ac86..0000000000 --- a/easybuild/easyconfigs/r/Ruby-FPM/Ruby-FPM-2.1.5-1.0.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'Bundle' - -name = 'Ruby-FPM' -rubyver = '2.1.5' -version = '%s-1.0.0' % rubyver - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# these are extensions for Ruby -exts_defaultclass = 'RubyGem' -exts_filter = ("gem list %(ext_name)s -i", "") - -dependencies = [ - ('Ruby', rubyver), -] - -name_tmpl = '%(name)s-%(version)s.gem' -ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], - 'source_tmpl': name_tmpl, -} -exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), - ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), -] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index cce8d3ff7e..ec8aac5c94 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -31,3 +31,22 @@ configopts = "--disable-install-doc --enable-shared" moduleclass = 'lang' +name_tmpl = '%(name)s-%(version)s.gem' + +ext_options = { + 'source_urls': [ + 'http://rubygems.org/downloads/', # gem archive + ], + 'source_tmpl': name_tmpl, +} + +exts_list = [ + ('ffi', '1.9.6', ext_options), + ('childprocess', '0.5.5', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.9', ext_options), + ('clamp', '0.6.4', ext_options), + ('fpm', '1.3.3', ext_options), +] -- GitLab From e77b57269e1d454e80a383ec30c5c6d1c2eea0c4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 3 Apr 2015 16:15:04 +0200 Subject: [PATCH 551/911] added some pandas --- .../p/pandas/pandas-0.16.0-intel-2015a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb new file mode 100644 index 0000000000..d8f4627e56 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "pandas" +version = "0.16.0" + +homepage = "http://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 42777cfcc27e91ed8e4803d24b4cdf89bd354dbc Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 3 Apr 2015 16:35:24 +0200 Subject: [PATCH 552/911] fixed filename --- ...0-intel-2015a.eb => pandas-0.16.0-intel-2015a-Python-2.7.9.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/pandas/{pandas-0.16.0-intel-2015a.eb => pandas-0.16.0-intel-2015a-Python-2.7.9.eb} (100%) diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a.eb rename to easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb -- GitLab From 476505091f8f333a882e611d068bebc32b5cb9f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Apr 2015 13:35:02 +0200 Subject: [PATCH 553/911] replace use of $root with %(installdir)s --- easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 355b27d3e6..9dcb92d748 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -53,7 +53,7 @@ sanity_check_paths = { } modextravars = { - 'BIOINFOCONFDIR': '$root/bios/conf', + 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', } moduleclass = 'bio' -- GitLab From 1eb6cd64d29cd9510a131f39baf2c164268ed0a8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 14:01:49 +0200 Subject: [PATCH 554/911] added new PyYAML with intel 2015a --- .../PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..adc1d69d57 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = "PyYAML" +version = "3.11" + +homepage = "http://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libyaml', '0.1.4'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % py_short_ver], +} + +moduleclass = 'lib' -- GitLab From 5a8f25c7dd5bc201dc7fa5e008db23b13439afac Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 14:11:14 +0200 Subject: [PATCH 555/911] added forgotten libyaml --- .../l/libyaml/libyaml-0.1.4-intel-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb new file mode 100644 index 0000000000..6cc4254bea --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.4' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.so"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' -- GitLab From 4cd2ead1b1b4b9c9a19f6400cb7c9f6061835c53 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 3 Apr 2015 12:57:44 +0200 Subject: [PATCH 556/911] Support IPython 3.0. --- .../IPython-3.0.0-intel-2015a-Python-2.7.9.eb | 40 +++++++++++++++++++ .../o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb | 27 +++++++++++++ ...Q-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb | 31 ++++++++++++++ .../util-linux-2.22.2-intel-2015a.eb | 29 ++++++++++++++ 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..941a1d3d1c --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.0.0' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://archive.ipython.org/release/%(version)s/'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '2.7' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('pyzmq', '2.0.1', versionsuffix, '-zmq3'), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', "") + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb new file mode 100644 index 0000000000..9ac5fd9480 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] +sources = ['%s-%s.tar.gz' % ('libpgm', version)] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..022cf3fe3b --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,31 @@ +name = 'PyZMQ' +version = '2.2.0.1' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +zmqversion = '3.2.2' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb new file mode 100644 index 0000000000..7cdce40ba2 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.22.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' -- GitLab From 5a631ddc9892e26f84e2e8cc753e71b1c9cedc1c Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 7 Apr 2015 14:47:53 +0200 Subject: [PATCH 557/911] WIP support for IPython. --- .../IPython-3.0.0-intel-2015a-Python-2.7.9.eb | 3 +- ...MQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb | 34 ++++++++++++++++++ ...requests-2.6.0-intel-2015a-Python-2.7.9.eb | 30 ++++++++++++++++ .../z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb | 36 +++++++++++++++++++ 4 files changed, 102 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb index 941a1d3d1c..bda10584b8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb @@ -24,7 +24,8 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), ('pysqlite', '2.6.3', versionsuffix), - ('pyzmq', '2.0.1', versionsuffix, '-zmq3'), + ('PyZMQ', '14.5.0', '%s-zmq3' % versionsuffix), + ('requests', '2.6.0', versionsuffix) ] # override extensions sanity check, default filter that imports a Python module doesn't work here diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000..b297340fc3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.5.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +zmqversion = '3.2.2' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..4a577a2051 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.6.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pythonshortversion, version, pythonshortversion) ], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..537584a82a --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['ZeroMQ-%(version)s_icc.patch'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 1ef7de76cd6442722940f1c74fd8d37f35d7a9c9 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:54:48 +0200 Subject: [PATCH 558/911] Update libyaml-0.1.4-intel-2015a.eb --- easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb index 6cc4254bea..7b42e2d083 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'libyaml' -version = '0.1.4' +version = '0.1.6' homepage = 'http://pyyaml.org/wiki/LibYAML' description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" -- GitLab From 42afd7c6dd49bc848146fa0d6e60fd659bfb2ae2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:54:57 +0200 Subject: [PATCH 559/911] Rename libyaml-0.1.4-intel-2015a.eb to libyaml-0.1.6-intel-2015a.eb --- ...{libyaml-0.1.4-intel-2015a.eb => libyaml-0.1.6-intel-2015a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/libyaml/{libyaml-0.1.4-intel-2015a.eb => libyaml-0.1.6-intel-2015a.eb} (100%) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-intel-2015a.eb rename to easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb -- GitLab From 1c9bf47a32741683d5c671afd202554f7a7ee7a4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 7 Apr 2015 15:55:07 +0200 Subject: [PATCH 560/911] Update PyYAML-3.11-intel-2015a-Python-2.7.9.eb --- .../p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb index adc1d69d57..bd74a7c6d1 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('libyaml', '0.1.4'), + ('libyaml', '0.1.6'), ] options = {'modulename': 'yaml'} -- GitLab From b6a99c2a39116ce3fc6fd07e3b51415b85e0f0fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Apr 2015 17:31:32 +0200 Subject: [PATCH 561/911] stop relying on $MKLROOT in ROOT easyconfigs --- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb | 2 +- easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb index fb2d479661..55aab9105b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb @@ -32,7 +32,7 @@ configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index 6fd56a833c..c0e1e4e91e 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -32,7 +32,7 @@ configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index 74c34689f1..cc50539ec7 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -36,7 +36,7 @@ configopts = ' --disable-xft --disable-xrootd --disable-mysql' # enable features configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' -configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' -- GitLab From 4f90d7aafa04678d9f6316d3eced8ea82c0fd1ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Apr 2015 17:36:49 +0200 Subject: [PATCH 562/911] fix indent --- easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 9dcb92d748..418cc4118e 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -53,7 +53,7 @@ sanity_check_paths = { } modextravars = { - 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', + 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', } moduleclass = 'bio' -- GitLab From 719a4f865622e804799f81f249797da18ab007e2 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Tue, 7 Apr 2015 22:49:27 +0200 Subject: [PATCH 563/911] Added Cray Toolchain Configs. --- .../easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 18 ++++++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 18 ++++++++++++++++++ .../c/CrayIntel/CrayIntel-5.1.29.eb | 18 ++++++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.25.eb | 18 ++++++++++++++++++ 6 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb new file mode 100644 index 0000000000..940aef1f65 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb new file mode 100644 index 0000000000..286a0ba710 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..2494f6ad7d --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..8f621e3fe9 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb new file mode 100644 index 0000000000..be8eff9d45 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.1.29' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb new file mode 100644 index 0000000000..ed28f41efb --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.25' + +homepage = 'http://hpcugent.github.io/easybuild/' +description = """This is a shim module for having EB pick up the Cray +Programming Environment (PrgEnv-*) modules. This module implements the EB +toolchain module for each of the cray modules.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [] +sources = [] +dependencies = [] + +moduleclass = 'toolchain' + -- GitLab From 6b0e3808d926bb872e1b03863cc163185fa48978 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Tue, 7 Apr 2015 23:29:53 +0200 Subject: [PATCH 564/911] Addressed remarks. --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 11 ++--------- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 11 ++--------- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 11 ++--------- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 11 ++--------- 6 files changed, 12 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index 940aef1f65..f09961bd60 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayCCE' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 286a0ba710..ff0774c751 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayCCE' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index 2494f6ad7d..d2d1520bce 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayGNU' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 8f621e3fe9..afc8c6010c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayGNU' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index be8eff9d45..6cb4679750 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayIntel' version = '5.1.29' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index ed28f41efb..f24f574b3f 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -3,16 +3,9 @@ easyblock = 'Toolchain' name = 'CrayIntel' version = '5.2.25' -homepage = 'http://hpcugent.github.io/easybuild/' -description = """This is a shim module for having EB pick up the Cray -Programming Environment (PrgEnv-*) modules. This module implements the EB -toolchain module for each of the cray modules.""" +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = [] -sources = [] -dependencies = [] - moduleclass = 'toolchain' - -- GitLab From 0f709b5dccc6325285acd9624c88254d8b01ae92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 12:09:21 +0200 Subject: [PATCH 565/911] add easyconfig (and patch) for pyhull + Qhull with intel/2015a, set $CPATH correctly in existing Qhull easyconfigs --- .../c/CMake/CMake-3.2.1-GCC-4.9.2.eb | 22 ++++++++++++ .../pyhull-1.5.4-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ .../pyhull-1.5.4_use-provided-Qhull.patch | 26 ++++++++++++++ .../q/Qhull/Qhull-2012.1-ictce-7.1.2.eb | 4 +++ .../q/Qhull/Qhull-2012.1-intel-2014b.eb | 4 +++ .../q/Qhull/Qhull-2012.1-intel-2015a.eb | 31 +++++++++++++++++ 6 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..f556c35a24 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c71d39213e --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = "pyhull" +version = "1.5.4" +homepage = "http://pythonhosted.org/pyhull/" +description = """Pyhull is a Python wrapper to qhull (http://www.qhull.org/) for the computation of the convex hull, + Delaunay triangulation and Voronoi diagram. It is written as a Python C extension, with both high-level and low-level + interfaces to qhull. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['pyhull-%(version)s_use-provided-Qhull.patch'] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('Qhull', '2012.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pv)s/site-packages/pyhull-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': py_short_ver}], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch new file mode 100644 index 0000000000..718405a70d --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch @@ -0,0 +1,26 @@ +let pyhull use provided Qhull rather than having it (re)build (parts of) Qhull itself +author: Kenneth Hoste (HPC-UGent) +--- pyhull-1.5.4/setup.py.orig 2015-04-07 21:30:35.000000000 +0200 ++++ pyhull-1.5.4/setup.py 2015-04-08 11:24:48.913427316 +0200 +@@ -7,14 +7,18 @@ + from setuptools import setup, Extension, find_packages + + src_dir = "src" +-include_dirs = glob.glob(os.path.join("src", "libqhull")) +-sources = glob.glob(os.path.join("src", "libqhull", "*.c")) ++include_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'include', 'libqhull')] ++library_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'lib')] ++sources = [] + if sys.platform.strip() == "darwin": + include_dirs += glob.glob(os.path.join("src", "fmemopen")) + sources += glob.glob(os.path.join("src", "fmemopen", "*.c")) + extension = Extension('pyhull._pyhull', + include_dirs=include_dirs, +- sources=[os.path.join(src_dir, '_pyhull.c')] + sources) ++ library_dirs=library_dirs, ++ libraries=['qhull'], ++ sources=[os.path.join(src_dir, '_pyhull.c')] + sources, ++ ) + + long_description = """ + Pyhull is a Python wrapper to Qhull (http://www.qhull.org/) for the diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 9aa673f99d..dd5a337d1f 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 35f7fe3a72..188d2a929c 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb new file mode 100644 index 0000000000..d32af2c654 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2012.1' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = ['Qhull-2012.1-intel-fix.patch'] + +builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.so'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +moduleclass = 'math' -- GitLab From 7e51eec446f832f110baadcf32a1d2d1125102d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:14:47 +0200 Subject: [PATCH 566/911] SWIG is build dependency for python-meep, style fixes in Meep easyconfigs --- easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb | 2 +- ...on-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 12 +++++------- .../python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb | 12 +++++------- .../python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb | 12 +++++------- 5 files changed, 17 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb index 99b133b3f5..15da01ed14 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb index 67e5d881fb..475c5f321c 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2643e2c09c..082e6cbbfd 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb index 67aaeea480..8656294b31 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb index dccd4207fd..82f6fac9ed 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb @@ -10,18 +10,16 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' -- GitLab From 624f2876e96c7e4f6f38e78fec5f0d6a25a4f697 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:16:10 +0200 Subject: [PATCH 567/911] add easyconfig for python-meep 1.4.2 on top of Python/2.7.9 and Meep/1.3 --- .../g/GMP/GMP-5.0.5-intel-2015a.eb | 22 ++++++++++++ .../g/guile/guile-1.8.8-intel-2015a.eb | 31 ++++++++++++++++ .../h/Harminv/Harminv-1.4-intel-2015a.eb | 19 ++++++++++ .../l/libctl/libctl-3.2.2-intel-2015a.eb | 20 +++++++++++ .../l/libffi/libffi-3.0.13-intel-2015a.eb | 25 +++++++++++++ .../l/libtool/libtool-2.4.2-intel-2015a.eb | 15 ++++++++ .../libunistring-0.9.3-intel-2015a.eb | 26 ++++++++++++++ .../m/Meep/Meep-1.3-intel-2015a.eb | 35 +++++++++++++++++++ .../pkg-config-0.27.1-intel-2015a.eb | 27 ++++++++++++++ ...1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 27 ++++++++++++++ .../SWIG-3.0.5-intel-2015a-Python-2.7.9.eb | 23 ++++++++++++ 11 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb new file mode 100644 index 0000000000..21b43d921f --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '5.0.5' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, + operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb new file mode 100644 index 0000000000..abc19c54da --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.13'), + ('libreadline', '6.2'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb new file mode 100644 index 0000000000..8b0afc7b1f --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given + a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) + in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['http://ab-initio.mit.edu/harminv/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..0de2f0bd93 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '3.2.2' + +homepage = 'http://ab-initio.mit.edu/libctl' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +source_urls = ['http://ab-initio.mit.edu/libctl/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('guile', '1.8.8')] + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb new file mode 100644 index 0000000000..1a559500ae --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.0.13' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libffi-%(version)s_include-xmmintrin.patch'] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb new file mode 100644 index 0000000000..eddb4ada02 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb new file mode 100644 index 0000000000..93d202fc27 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['libunistring_icc_builtin_nan-inf.patch'] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.so', 'include/unistring'] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb new file mode 100644 index 0000000000..270e349f06 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.3' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Meep' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Meep-1.2_version-string-without-spaces.patch'] + +dependencies = [ + ('Harminv', '1.4'), + ('HDF5', '1.8.14', '-gpfs'), + ('libctl', '3.2.2'), + ('GSL', '1.16'), + ('FFTW', '3.3.4') +] + +configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb new file mode 100644 index 0000000000..ddfabeac31 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.27.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb new file mode 100644 index 0000000000..0da5220c97 --- /dev/null +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -0,0 +1,27 @@ +name = 'python-meep' +version = '1.4.2' + +homepage = 'https://code.launchpad.net/python-meep' +description = """Python wrapper for the Meep FDTD solver.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} + +source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] +sources = [SOURCELOWER_TAR] + +patches = ['MPI_destructor_1.3.patch'] + +python = 'Python' +pythonver = '2.7.9' +meep = 'Meep' +meepver = '1.3' +versionsuffix = '-%s-%s-%s-%s' % (python, pythonver, meep, meepver) + +dependencies = [ + (python, pythonver), + (meep, meepver), +] +builddependencies = [('SWIG', '3.0.5', '-%s-%s' % (python, pythonver))] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..3193585375 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.5' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' -- GitLab From 42a68f8a93daf6e82791432ccb857a55cf7a41bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:25:17 +0200 Subject: [PATCH 568/911] fix patch for Meep v1.3 --- easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb | 2 +- .../Meep/Meep-1.3_version-string-without-spaces.patch | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 270e349f06..822615186c 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-1.2_version-string-without-spaces.patch'] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch new file mode 100644 index 0000000000..90cebc9859 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch @@ -0,0 +1,11 @@ +--- meep-1.3/libctl/Makefile.in.orig 2015-03-31 17:47:53.000000000 +0200 ++++ meep-1.3/libctl/Makefile.in 2015-04-08 13:23:54.206192661 +0200 +@@ -369,7 +369,7 @@ + ############################################################################## + + # what is printed out when invoking your program with --version: +-VERSION_STRING = "Meep @VERSION@, Copyright (C) 2005-2015 Massachusetts Insitute of Technology." ++VERSION_STRING = "Meep_@VERSION@,_Copyright_(C)_2005-2015_Massachusetts_Insitute_of_Technology." + MY_DEFS = -DHAVE_CTL_HOOKS=1 -DHAVE_CTL_EXPORT_HOOK=1 + PROGRAM_NAME = meep + SPECIFICATION_FILE = $(PROGRAM_NAME).scm -- GitLab From 6c00f9fb66c618ea421c6b1e7c68dad7ea2a2543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:48:32 +0200 Subject: [PATCH 569/911] stick to SWIG 2.x for pyhton-meep --- ...1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 2 +- .../SWIG-2.0.12-intel-2015a-Python-2.7.9.eb | 23 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb index 0da5220c97..f9f82b9d18 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -22,6 +22,6 @@ dependencies = [ (python, pythonver), (meep, meepver), ] -builddependencies = [('SWIG', '3.0.5', '-%s-%s' % (python, pythonver))] +builddependencies = [('SWIG', '2.0.12', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f049ac6af0 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '2.0.12' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' -- GitLab From f0c8dcfae8501554cfd63862bfa0b441efae38e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 13:53:07 +0200 Subject: [PATCH 570/911] add pandas extension to Python 2.7.9 easyconfigs --- easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 0f382d98ba..d228f95a16 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -107,6 +107,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 4ec2b0ce97..e667c4f618 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -107,6 +107,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index db9c0d75b8..06dcabeb70 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -110,6 +110,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' -- GitLab From 359a12c02b15b329634fd515b3141e29a5e7fdd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 14:17:17 +0200 Subject: [PATCH 571/911] fix remark, bump libreadline in guile easyconfig to 6.3 --- easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb | 2 +- .../python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 1 + .../python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb | 1 + .../p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb | 1 + .../python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb | 1 + 5 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb index abc19c54da..d66e7cf118 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -18,7 +18,7 @@ dependencies = [ ('libunistring', '0.9.3'), ('pkg-config', '0.27.1'), ('libffi', '3.0.13'), - ('libreadline', '6.2'), + ('libreadline', '6.3'), ] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 082e6cbbfd..ee4f9a4c40 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb index 8656294b31..562323eb53 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb index 82f6fac9ed..afe2d60a9b 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb @@ -20,6 +20,7 @@ dependencies = [ (python, pythonver), ('Meep', '1.2'), ] + builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb index f9f82b9d18..bfb66e3979 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -22,6 +22,7 @@ dependencies = [ (python, pythonver), (meep, meepver), ] + builddependencies = [('SWIG', '2.0.12', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' -- GitLab From 1ec86e9797f2c27805ca03034fd796d2dd6e7709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:06:27 +0200 Subject: [PATCH 572/911] Added LAPACK-3.5.0-gompi-1.5.16.eb --- LAPACK-3.5.0-gompi-1.5.16.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 LAPACK-3.5.0-gompi-1.5.16.eb diff --git a/LAPACK-3.5.0-gompi-1.5.16.eb b/LAPACK-3.5.0-gompi-1.5.16.eb new file mode 100644 index 0000000000..0027dce752 --- /dev/null +++ b/LAPACK-3.5.0-gompi-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'LAPACK' +version = "3.5.0" + +homepage = 'http://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = [homepage] + +moduleclass = 'numlib' -- GitLab From 3b3cab12c5ae47fb540c24c3f9069006db5702a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:06:57 +0200 Subject: [PATCH 573/911] Added OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0 --- OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 52 ++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb diff --git a/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..fe4211f53c --- /dev/null +++ b/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' -- GitLab From 917b1507a2042f4b0cb8dd0b26fbb5ee77668169 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:07:36 +0200 Subject: [PATCH 574/911] Added FFTW-3.3.4-gompi-1.5.16 --- FFTW-3.3.4-gompi-1.5.16.eb | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 FFTW-3.3.4-gompi-1.5.16.eb diff --git a/FFTW-3.3.4-gompi-1.5.16.eb b/FFTW-3.3.4-gompi-1.5.16.eb new file mode 100644 index 0000000000..6ae444ae02 --- /dev/null +++ b/FFTW-3.3.4-gompi-1.5.16.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.4' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 265f11d2a8c4be3d91b7821b2bac123aeb82fa8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:08:19 +0200 Subject: [PATCH 575/911] Added ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0 --- ...mpi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb diff --git a/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..a52473e7ff --- /dev/null +++ b/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff)] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' -- GitLab From 6bcfeee22cce3af60a529eaa801a54c5944e8eb2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:08:52 +0200 Subject: [PATCH 576/911] Added goolf-1.5.16 --- goolf-1.5.16.eb | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 goolf-1.5.16.eb diff --git a/goolf-1.5.16.eb b/goolf-1.5.16.eb new file mode 100644 index 0000000000..e9cea8d51b --- /dev/null +++ b/goolf-1.5.16.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.5.16' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.8.3' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blas_suff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.5.16 + (blaslib, blasver, blas_suff, comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blas_suff), comp_mpi_tc) +] + +moduleclass = 'toolchain' -- GitLab From 589908c611d3899c8e3e9fbaa02105ff50281c8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:21:42 +0200 Subject: [PATCH 577/911] easyconfigs moved to the right directories --- .../easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb | 0 .../easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb | 0 .../o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 0 .../ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename FFTW-3.3.4-gompi-1.5.16.eb => easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb (100%) rename LAPACK-3.5.0-gompi-1.5.16.eb => easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb (100%) rename OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb => easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb (100%) rename ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb => easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb (100%) diff --git a/FFTW-3.3.4-gompi-1.5.16.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb similarity index 100% rename from FFTW-3.3.4-gompi-1.5.16.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb diff --git a/LAPACK-3.5.0-gompi-1.5.16.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb similarity index 100% rename from LAPACK-3.5.0-gompi-1.5.16.eb rename to easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb diff --git a/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb similarity index 100% rename from OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb diff --git a/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb similarity index 100% rename from ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb -- GitLab From 026f640280842616cbb3aa9a2461b9c66444827e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 15:48:35 +0200 Subject: [PATCH 578/911] goolf-1.5.16 moved to the right directory --- goolf-1.5.16.eb => easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename goolf-1.5.16.eb => easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb (100%) diff --git a/goolf-1.5.16.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb similarity index 100% rename from goolf-1.5.16.eb rename to easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb -- GitLab From 597d8d8d4f62739c956f9b8cd431aeb96ff7525c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 8 Apr 2015 16:21:52 +0200 Subject: [PATCH 579/911] Added HPL-2.0-goolf-1.5.16.eb --- .../easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb new file mode 100644 index 0000000000..d327bfbbab --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.0' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic +on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the +High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 68012ca4f308fa11d9bff36163d41ad913384c5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:18:34 +0200 Subject: [PATCH 580/911] {data}[intel/2015a] h5py 2.5.0 (REVIEW) --- ...5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb new file mode 100644 index 0000000000..108b726ecc --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +hdf5suff = '-gpfs' +versionsuffix = '-%s-%s%s' % (python, pythonver, hdf5suff) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.14', hdf5suff), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'dirs': [], +} + +moduleclass = 'data' -- GitLab From 5a881154a9d5bfd525dc3ae6a15f3ecb0ec95fc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:20:51 +0200 Subject: [PATCH 581/911] {math}[intel/2015a] numpy 1.9.2 + scipy 0.15.1 (REVIEW) --- .../numpy-1.9.2-intel-2015a-Python-2.7.9.eb | 26 +++++++++++++++++++ .../scipy-0.15.1-intel-2015a-Python-2.7.9.eb | 19 ++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bc4a69d14c --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f67514e591 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' -- GitLab From ee6196e68bae9e32808d708233440c569ad74500 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Apr 2015 21:48:51 +0200 Subject: [PATCH 582/911] {vis}[intel/2015a] grace 5.1.23 (REVIEW) --- .../g/grace/grace-5.1.23-intel-2015a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb new file mode 100644 index 0000000000..208d216f7b --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.23' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2015a'} + +dependencies = [ + ('motif', '2.3.4', '-libX11-1.6.3'), + ('netCDF', '4.3.2'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From e37e42a351a2dcfc55e6b7a82768600fe1acf6a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 10:19:41 +0200 Subject: [PATCH 583/911] add easyconfigs for WIEN2k 14.1 and 14.2 with intel/2015a --- .../w/WIEN2k/WIEN2k-14.1-intel-2015a.eb | 46 +++++++++++++++++++ .../w/WIEN2k/WIEN2k-14.2-intel-2015a.eb | 40 ++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb new file mode 100644 index 0000000000..a5d641a90f --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb new file mode 100644 index 0000000000..5149928839 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb @@ -0,0 +1,40 @@ +name = 'WIEN2k' +version = '14.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['1179be3b3bcb021af4c65fefea579ca6'] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' -- GitLab From 838b269bf30cdb61ccdc69e7a6ef3deed8995455 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 9 Apr 2015 12:59:00 +0200 Subject: [PATCH 584/911] Added GDAL-1.9.2-goolf-1.5.16 and zlib-1.2.8 dependency --- .../g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb | 24 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-goolf-1.5.16.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb new file mode 100644 index 0000000000..14deb76474 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.5.16.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '1.9.2' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb new file mode 100644 index 0000000000..9b56c2bffb --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From c72cd834e99c897e89f4b93d4f1a9bd1b1155004 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 13:36:29 +0200 Subject: [PATCH 585/911] fix remar --- .../h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb index 108b726ecc..d6f4de7c55 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb @@ -9,24 +9,24 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to amounts of data.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'usempi': False} +toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[0:2]) hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pythonver, hdf5suff) +versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) dependencies = [ - (python, pythonver), + (python, pyver), ('HDF5', '1.8.14', hdf5suff), ] sanity_check_paths = { - 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pythonshortver, pythonshortver)], + 'files': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], 'dirs': [], } -- GitLab From b5a1b36a088fed3e74c8594b5b8cbaae72fcaaff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 13:56:43 +0200 Subject: [PATCH 586/911] add easyconfigs for monty 0.6.4 and latest dev version by @gmatteo --- ...tel-2015a-Python-2.7.9-gmatteo-20150325.eb | 36 +++++++++++++++++++ .../monty-0.6.4-intel-2015a-Python-2.7.9.eb | 35 ++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb create mode 100644 easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb new file mode 100644 index 0000000000..14e4a5ef3b --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'http://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/gmatteo/monty/archive/'] +sources = ['3152d41.tar.gz'] +checksums = ['d8afe0556fd29191e66babb31750b7c4'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-gmatteo-20150325' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', '-%s-%s' % (python, pythonversion)), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..7d2b055f0b --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'http://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', versionsuffix), +] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 81a2023fabbd4db4e95b6da25b663b08501efc0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 14:46:38 +0200 Subject: [PATCH 587/911] fix remark --- ...ty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb index 14e4a5ef3b..1dfd105d74 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -10,14 +10,17 @@ description = """Monty implements supplementary useful functions for Python that toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://github.com/gmatteo/monty/archive/'] -sources = ['3152d41.tar.gz'] +commit = '3152d41' +extrasuff = 'gmatteo-20150325' + +source_urls = ['https://github.com/gmatteo/monty/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] checksums = ['d8afe0556fd29191e66babb31750b7c4'] python = 'Python' pythonversion = '2.7.9' -versionsuffix = '-%s-%s-gmatteo-20150325' % (python, pythonversion) +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) dependencies = [ (python, pythonversion), -- GitLab From 9f2d54c31bf5d52e27f5da2c064c5f0bb503788c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 14:51:44 +0200 Subject: [PATCH 588/911] {chem}[intel/2015a] pymatgen 3.0.13 + spglib 1.7.3 (REVIEW) --- ...tel-2015a-Python-2.7.9-gmatteo-20150407.eb | 39 +++++++++++++++++++ ...ymatgen-3.0.13-intel-2015a-Python-2.7.9.eb | 35 +++++++++++++++++ .../s/spglib/spglib-1.7.3-intel-2015a.eb | 21 ++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb new file mode 100644 index 0000000000..8e35e9a845 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +homepage = 'http://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +commit = 'd9b9a17' +extrasuff = 'gmatteo-20150407' + +source_urls = ['https://github.com/gmatteo/pymatgen/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] +checksums = ['461ad0f8bb8109f547dc3b708240f85f'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..73ac37040a --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +homepage = 'http://pypi.python.org/pypi/pymatgen' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb new file mode 100644 index 0000000000..f6b34ab670 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.so'], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' -- GitLab From ac4f675693433096562844f8cb97cd3a2f9d33b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:23:44 +0200 Subject: [PATCH 589/911] {bio}[intel/2015a] FSL 5.0.8 + deps (REVIEW) --- .../f/FSL/FSL-5.0.8-intel-2015a.eb | 24 +++++++++++++++++ .../fixesproto/fixesproto-5.0-intel-2015a.eb | 19 ++++++++++++++ .../f/freeglut/freeglut-2.8.1-intel-2015a.eb | 21 +++++++++++++++ .../inputproto/inputproto-2.3-intel-2015a.eb | 19 ++++++++++++++ .../libXfixes/libXfixes-5.0.1-intel-2015a.eb | 24 +++++++++++++++++ .../l/libXi/libXi-1.7.4-intel-2015a.eb | 26 +++++++++++++++++++ 6 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb new file mode 100644 index 0000000000..dd4d60386c --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'FSL' +version = '5.0.8' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_ictce-wd803.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '2.8.1'), + ('expat', '2.1.0'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb new file mode 100644 index 0000000000..5d430a5301 --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb new file mode 100644 index 0000000000..f501cd2fef --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'freeglut' +version = '2.8.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +dependencies = [('libXi', '1.7.4')] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb new file mode 100644 index 0000000000..0437a042db --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb new file mode 100644 index 0000000000..3129ec62b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.so'], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb new file mode 100644 index 0000000000..20988d4e6e --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), + ('libXext', '1.3.3'), + ('inputproto', '2.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.so', 'lib/libXi.a'], + 'dirs' : [], +} + +moduleclass = 'vis' -- GitLab From a18dadcaa3b0401c4c7fdf1d826147da8957a989 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:37:44 +0200 Subject: [PATCH 590/911] add missing patch file for FSL --- .../f/FSL/FSL-5.0.8_makefile_fixes.patch | 343 ++++++++++++++++++ 1 file changed, 343 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch new file mode 100644 index 0000000000..908f2f4205 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch @@ -0,0 +1,343 @@ +diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-14 22:43:15.344366000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-14 22:43:15.363590000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-14 22:43:15.385466000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk 2007-12-19 15:40:57.000000000 +0100 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-14 22:43:15.402328000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk 2007-12-19 15:33:53.000000000 +0100 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-14 22:43:15.415331000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-14 22:43:15.438919000 +0200 +@@ -16,8 +16,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-14 22:43:15.455595000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc-2 +-CXX = c++-2 ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-14 22:43:15.473639000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-14 22:43:15.494398000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/config/linux_32-gcc2.96/systemvars.mk 2007-07-25 17:21:07.000000000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-14 22:43:15.507210000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.2/systemvars.mk 2007-07-25 17:21:08.000000000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-14 22:43:15.524309000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.3/systemvars.mk 2007-07-25 17:21:09.000000000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-14 22:43:15.539643000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.4/systemvars.mk 2007-07-25 17:21:10.000000000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-14 22:43:15.559881000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.0/systemvars.mk 2007-07-25 17:21:11.000000000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-14 22:43:15.573696000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.1/systemvars.mk 2012-04-20 11:37:28.000000000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-14 22:43:15.590022000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc3.4/systemvars.mk 2007-07-25 17:21:12.000000000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-14 22:43:15.605655000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.0/systemvars.mk 2007-07-25 17:21:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-14 22:43:15.624046000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.1/systemvars.mk 2007-07-25 11:19:45.000000000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-14 22:43:15.635678000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.2/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-14 22:43:15.648658000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2014-06-14 23:23:58.456480000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-14 22:43:15.658171000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + +diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-14 22:43:15.674176000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + ARCHLDFLAGS = -static +diff -ru fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 ++++ fsl/src/libmeshutils/Makefile 2013-05-14 22:43:15.320209000 +0200 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +diff -ru fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile +--- fsl.orig/src/melodic/Makefile 2013-03-13 21:22:35.000000000 +0100 ++++ fsl/src/melodic/Makefile 2013-05-14 22:44:13.016352000 +0200 +@@ -3,7 +3,7 @@ + include ${FSLCONFDIR}/default.mk + + OPTFLAGS = -O3 -Wno-deprecated -ggdb +-OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui ++#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui + + PROJNAME = melodic + +--- fsl/src/film/Makefile.orig 2014-06-15 00:43:34.908901000 +0200 ++++ fsl/src/film/Makefile 2014-06-15 00:43:52.303973000 +0200 +@@ -26,7 +26,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} -- GitLab From 70f461af0c36d24eeedc3cdb28215d186b26cd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 16:56:32 +0200 Subject: [PATCH 591/911] {chem}[intel/2015a] ABINIT 7.11.6 + libxc 2.2.2 (WIP) --- .../a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 29 +++++++++++++++++ .../l/libxc/libxc-2.2.2-intel-2015a.eb | 32 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb new file mode 100644 index 0000000000..e5ab48448f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.11.6' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' +configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000..25c12f798e --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' -- GitLab From 7855d8bc89e23f990ab0a32703cd16d209067fb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2015 17:11:42 +0200 Subject: [PATCH 592/911] add another missing patch file for FSL --- .../f/FSL/FSL-5.0.8_ictce-wd803.patch | 300 ++++++++++++++++++ 1 file changed, 300 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch new file mode 100644 index 0000000000..c798885107 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch @@ -0,0 +1,300 @@ +diff -ru fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:14:37.710187000 +0200 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:19:46.085324000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2012-03-21 12:30:53.000000000 +0100 ++++ fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2013-05-15 00:19:48.066557000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-04-09 18:00:32.000000000 +0200 ++++ fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-05-15 00:19:49.812861000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:14:37.712623000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:19:51.866756000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:14:37.737794000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:19:53.537845000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:14:37.745810000 +0200 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:19:55.229757000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:14:37.751696000 +0200 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:19:57.417620000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/fsl/config/generic/systemvars.mk 2013-05-15 00:14:37.757155000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-15 00:19:59.724851000 +0200 +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk fsl/config/gnu_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk 2011-04-19 10:47:52.000000000 +0200 ++++ fsl/config/gnu_64-gcc4.4/systemvars.mk 2013-05-15 00:20:03.204842000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:14:37.763457000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:20:05.347565000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:14:37.769108000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:20:06.913095000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:14:37.775138000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:20:08.480567000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:14:37.781755000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:20:10.043882000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:14:37.787130000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:20:11.484066000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:14:37.794387000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:20:12.921148000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:14:37.799247000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:20:14.478184000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:14:37.805358000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:20:16.819361000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:14:37.811876000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:20:18.322853000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:14:37.817395000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:20:20.465845000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:14:37.823453000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:20:22.065237000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:14:37.829561000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:20:23.601865000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:14:37.835868000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:20:25.058756000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2013-05-15 00:20:26.561348000 +0200 +@@ -29,7 +29,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:14:37.841452000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:20:28.072793000 +0200 +@@ -12,7 +12,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:14:37.847832000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:20:29.505593000 +0200 +@@ -12,7 +12,7 @@ + ARCHLDFLAGS = -static + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn -- GitLab From 9fd5c72eb012bb71f7307a2472ab0d7edcfe7206 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 13 Apr 2015 09:36:10 +0200 Subject: [PATCH 593/911] First try at GCC 5.1 --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 47 + .../GCC/mpfr-3.1.2-allpatches-20141204.patch | 1628 +++++++++++++++++ 2 files changed, 1675 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb new file mode 100644 index 0000000000..7a65f31c78 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -0,0 +1,47 @@ +name = "GCC" +version = '5.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '37cdc2eb0adf92e421c0841748ac1471', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +#withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch new file mode 100644 index 0000000000..df1aaea434 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch @@ -0,0 +1,1628 @@ +# All mpfr patches as of 2014-12-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:52:52.000000000 +0000 +@@ -0,0 +1 @@ ++exp_2 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:52:52.000000000 +0000 +@@ -1 +1 @@ +-3.1.2 ++3.1.2-p1 +diff -Naurd mpfr-3.1.2-a/src/exp_2.c mpfr-3.1.2-b/src/exp_2.c +--- mpfr-3.1.2-a/src/exp_2.c 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp_2.c 2013-09-26 10:52:52.000000000 +0000 +@@ -204,7 +204,7 @@ + for (k = 0; k < K; k++) + { + mpz_mul (ss, ss, ss); +- exps <<= 1; ++ exps *= 2; + exps += mpz_normalize (ss, ss, q); + } + mpfr_set_z (s, ss, MPFR_RNDN); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2" ++#define MPFR_VERSION_STRING "3.1.2-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:52:52.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2"; ++ return "3.1.2-p1"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:56:55.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:56:55.000000000 +0000 +@@ -0,0 +1 @@ ++fits-smallneg +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:56:55.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p1 ++3.1.2-p2 +diff -Naurd mpfr-3.1.2-a/src/fits_u.h mpfr-3.1.2-b/src/fits_u.h +--- mpfr-3.1.2-a/src/fits_u.h 2013-03-13 15:37:35.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_u.h 2013-09-26 10:56:55.000000000 +0000 +@@ -32,17 +32,20 @@ + int res; + + if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ return MPFR_IS_ZERO (f) ? 1 : 0; /* Zero always fits */ + + e = MPFR_GET_EXP (f); + ++ if (MPFR_IS_NEG (f)) ++ return e >= 1 ? 0 /* f <= -1 does not fit */ ++ : rnd != MPFR_RNDN ? MPFR_IS_LIKE_RNDU (rnd, -1) /* directed mode */ ++ : e < 0 ? 1 /* f > -1/2 fits in MPFR_RNDN */ ++ : mpfr_powerof2_raw(f); /* -1/2 fits, -1 < f < -1/2 don't */ ++ ++ /* Now it fits if ++ (a) f <= MAXIMUM ++ (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ + /* first compute prec(MAXIMUM); fits in an int */ + for (s = MAXIMUM, prec = 0; s != 0; s /= 2, prec ++); + +diff -Naurd mpfr-3.1.2-a/src/fits_uintmax.c mpfr-3.1.2-b/src/fits_uintmax.c +--- mpfr-3.1.2-a/src/fits_uintmax.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_uintmax.c 2013-09-26 10:56:55.000000000 +0000 +@@ -27,51 +27,19 @@ + #include "mpfr-intmax.h" + #include "mpfr-impl.h" + +-#ifdef _MPFR_H_HAVE_INTMAX_T +- +-/* We can't use fits_u.h <= mpfr_cmp_ui */ +-int +-mpfr_fits_uintmax_p (mpfr_srcptr f, mpfr_rnd_t rnd) +-{ +- mpfr_exp_t e; +- int prec; +- uintmax_t s; +- mpfr_t x; +- int res; +- +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ +- +- e = MPFR_GET_EXP (f); +- +- /* first compute prec(MAXIMUM); fits in an int */ +- for (s = MPFR_UINTMAX_MAX, prec = 0; s != 0; s /= 2, prec ++); +- +- /* MAXIMUM needs prec bits, i.e. MAXIMUM = 2^prec - 1 */ +- +- /* if e <= prec - 1, then f < 2^(prec-1) < MAXIMUM */ +- if (e <= prec - 1) +- return 1; ++/* Note: though mpfr-impl.h is included in fits_u.h, we also include it ++ above so that it gets included even when _MPFR_H_HAVE_INTMAX_T is not ++ defined; this is necessary to avoid an empty translation unit, which ++ is forbidden by ISO C. Without this, a failing test can be reproduced ++ by creating an invalid stdint.h somewhere in the default include path ++ and by compiling MPFR with "gcc -ansi -pedantic-errors". */ + +- /* if e >= prec + 1, then f >= 2^prec > MAXIMUM */ +- if (e >= prec + 1) +- return 0; ++#ifdef _MPFR_H_HAVE_INTMAX_T + +- MPFR_ASSERTD (e == prec); ++#define FUNCTION mpfr_fits_uintmax_p ++#define MAXIMUM MPFR_UINTMAX_MAX ++#define TYPE uintmax_t + +- /* hard case: first round to prec bits, then check */ +- mpfr_init2 (x, prec); +- mpfr_set (x, f, rnd); +- res = MPFR_GET_EXP (x) == e; +- mpfr_clear (x); +- return res; +-} ++#include "fits_u.h" + + #endif +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:56:55.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p1" ++#define MPFR_VERSION_STRING "3.1.2-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:56:55.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p1"; ++ return "3.1.2-p2"; + } +diff -Naurd mpfr-3.1.2-a/tests/tfits.c mpfr-3.1.2-b/tests/tfits.c +--- mpfr-3.1.2-a/tests/tfits.c 2013-03-13 15:37:45.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tfits.c 2013-09-26 10:56:55.000000000 +0000 +@@ -33,155 +33,176 @@ + #include "mpfr-intmax.h" + #include "mpfr-test.h" + +-#define ERROR1 { printf("Initial error for x="); mpfr_dump(x); exit(1); } +-#define ERROR2 { printf("Error for x="); mpfr_dump(x); exit(1); } ++#define ERROR1(N) \ ++ do \ ++ { \ ++ printf("Error %d for rnd = %s and x = ", N, \ ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); \ ++ mpfr_dump(x); \ ++ exit(1); \ ++ } \ ++ while (0) + + static void check_intmax (void); + + int + main (void) + { +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + + tests_start_mpfr (); + + mpfr_init2 (x, 256); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (1); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (2); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (3); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (4); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (5); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (6); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (7); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (8); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (9); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (10); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (11); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (12); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (13); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (14); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (15); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (16); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (17); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (18); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check small positive op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (19); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (20); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (21); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (22); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (23); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (24); + +- /* Check all other values */ +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- mpfr_mul_2exp (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_mul_2exp (x, x, 40, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (25); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (26); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (27); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (28); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (29); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (30); + +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, INT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check all other values */ ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ mpfr_mul_2exp (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (31); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (32); ++ mpfr_mul_2exp (x, x, 40, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (33); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (34); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (35); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (36); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (37); + +- mpfr_set_si (x, 1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (38); ++ mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (39); ++ mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (40); ++ mpfr_set_ui (x, INT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (41); ++ mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (42); ++ mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (43); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; ++ mpfr_set_si (x, 1, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (44); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (45); ++ ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (46); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (47); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (48); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (49); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (50); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (51); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + + check_intmax (); + +@@ -189,85 +210,98 @@ + return 0; + } + +-static void check_intmax (void) ++static void ++check_intmax (void) + { + #ifdef _MPFR_H_HAVE_INTMAX_T +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + +- mpfr_init2 (x, sizeof (uintmax_t)*CHAR_BIT); ++ mpfr_init2 (x, sizeof (uintmax_t) * CHAR_BIT); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (52); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (53); + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (54); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (55); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (56); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (57); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check positive small op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (58); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (59); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (60); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (61); + +- /* Check hugest */ +- mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check hugest */ ++ mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (62); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (63); + +- /* Check all other values */ +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_sub_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check all other values */ ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (64); ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (65); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (66); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (67); ++ mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (68); ++ mpfr_sub_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (69); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (70); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (71); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + #endif + } +- +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-10-09 13:34:21.000000000 +0000 +@@ -0,0 +1 @@ ++clang-divby0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-10-09 13:34:21.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p2 ++3.1.2-p3 +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-03-13 15:37:36.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 +@@ -468,8 +468,16 @@ + #define MPFR_LIMBS_PER_FLT ((IEEE_FLT_MANT_DIG-1)/GMP_NUMB_BITS+1) + + /* Visual C++ doesn't support +1.0/0.0, -1.0/0.0 and 0.0/0.0 +- at compile time. */ +-#if defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200) ++ at compile time. ++ Clang with -fsanitize=undefined is a bit similar due to a bug: ++ http://llvm.org/bugs/show_bug.cgi?id=17381 ++ but even without its sanitizer, it may be better to use the ++ double_zero version until IEEE 754 division by zero is properly ++ supported: ++ http://llvm.org/bugs/show_bug.cgi?id=17000 ++*/ ++#if (defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200)) || \ ++ defined(__clang__) + static double double_zero = 0.0; + # define DBL_NAN (double_zero/double_zero) + # define DBL_POS_INF ((double) 1.0/double_zero) +@@ -501,6 +509,8 @@ + (with Xcode 2.4.1, i.e. the latest one). */ + #define LVALUE(x) (&(x) == &(x) || &(x) != &(x)) + #define DOUBLE_ISINF(x) (LVALUE(x) && ((x) > DBL_MAX || (x) < -DBL_MAX)) ++/* The DOUBLE_ISNAN(x) macro is also valid on long double x ++ (assuming that the compiler isn't too broken). */ + #ifdef MPFR_NANISNAN + /* Avoid MIPSpro / IRIX64 / gcc -ffast-math (incorrect) optimizations. + The + must not be replaced by a ||. With gcc -ffast-math, NaN is +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-10-09 13:34:21.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p2" ++#define MPFR_VERSION_STRING "3.1.2-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-10-09 13:34:21.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p2"; ++ return "3.1.2-p3"; + } +diff -Naurd mpfr-3.1.2-a/tests/tget_flt.c mpfr-3.1.2-b/tests/tget_flt.c +--- mpfr-3.1.2-a/tests/tget_flt.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tget_flt.c 2013-10-09 13:34:21.000000000 +0000 +@@ -28,9 +28,17 @@ + main (void) + { + mpfr_t x, y; +- float f, g, infp; ++ float f, g; + int i; ++#if !defined(MPFR_ERRDIVZERO) ++ float infp; ++#endif ++ ++ tests_start_mpfr (); + ++#if !defined(MPFR_ERRDIVZERO) ++ /* The definition of DBL_POS_INF involves a division by 0. This makes ++ "clang -O2 -fsanitize=undefined -fno-sanitize-recover" fail. */ + infp = (float) DBL_POS_INF; + if (infp * 0.5 != infp) + { +@@ -38,8 +46,7 @@ + fprintf (stderr, "(this is probably a compiler bug, please report)\n"); + exit (1); + } +- +- tests_start_mpfr (); ++#endif + + mpfr_init2 (x, 24); + mpfr_init2 (y, 24); +@@ -353,6 +360,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#if !defined(MPFR_ERRDIVZERO) + f = mpfr_get_flt (x, MPFR_RNDN); /* first round to 2^128 (even rule), + thus we should get +Inf */ + g = infp; +@@ -376,6 +384,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#endif + + mpfr_clear (x); + mpfr_clear (y); +diff -Naurd mpfr-3.1.2-a/tests/tset_ld.c mpfr-3.1.2-b/tests/tset_ld.c +--- mpfr-3.1.2-a/tests/tset_ld.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tset_ld.c 2013-10-09 13:34:21.000000000 +0000 +@@ -47,8 +47,11 @@ + static int + Isnan_ld (long double d) + { +- double e = (double) d; +- if (DOUBLE_ISNAN (e)) ++ /* Do not convert d to double as this can give an overflow, which ++ may confuse compilers without IEEE 754 support (such as clang ++ -fsanitize=undefined), or trigger a trap if enabled. ++ The DOUBLE_ISNAN macro should work fine on long double. */ ++ if (DOUBLE_ISNAN (d)) + return 1; + LONGDOUBLE_NAN_ACTION (d, goto yes); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-11-15 00:51:49.323334999 +0000 +@@ -0,0 +1 @@ ++printf-alt0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-11-15 00:51:49.323334999 +0000 +@@ -1 +1 @@ +-3.1.2-p3 ++3.1.2-p4 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-11-15 00:51:49.323334999 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p3" ++#define MPFR_VERSION_STRING "3.1.2-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -1040,7 +1040,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'e', 'E', 'g', or 'G'. ++ number P when spec.spec is 'e', 'E', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field > INT_MAX */ +@@ -1167,7 +1167,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'f', 'F', 'g', or 'G'. ++ number P when spec.spec is 'f', 'F', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field of number_parts is greater than INT_MAX */ +@@ -1559,7 +1559,7 @@ + /* fractional part */ + { + np->point = MPFR_DECIMAL_POINT; +- np->fp_trailing_zeros = (spec.spec == 'g' && spec.spec == 'G') ? ++ np->fp_trailing_zeros = (spec.spec == 'g' || spec.spec == 'G') ? + spec.prec - 1 : spec.prec; + } + else if (spec.alt) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-11-15 00:51:49.323334999 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p3"; ++ return "3.1.2-p4"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -456,10 +456,16 @@ + check_sprintf ("1.999900 ", "%-#10.7RG", x); + check_sprintf ("1.9999 ", "%-10.7RG", x); + mpfr_set_ui (x, 1, MPFR_RNDN); ++ check_sprintf ("1.", "%#.1Rg", x); ++ check_sprintf ("1. ", "%-#5.1Rg", x); ++ check_sprintf (" 1.0", "%#5.2Rg", x); + check_sprintf ("1.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("1", "%.30Rg", x); + mpfr_set_ui (x, 0, MPFR_RNDN); +- check_sprintf ("0.000000000000000000000000000000", "%#.30Rg", x); ++ check_sprintf ("0.", "%#.1Rg", x); ++ check_sprintf ("0. ", "%-#5.1Rg", x); ++ check_sprintf (" 0.0", "%#5.2Rg", x); ++ check_sprintf ("0.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("0", "%.30Rg", x); + + /* following tests with precision 53 bits */ +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-12-01 11:07:49.751331625 +0000 +@@ -0,0 +1 @@ ++custom_init_set +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-12-01 11:07:49.747331585 +0000 +@@ -1 +1 @@ +-3.1.2-p4 ++3.1.2-p5 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-12-01 11:07:49.747331585 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p4" ++#define MPFR_VERSION_STRING "3.1.2-p5" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +@@ -861,7 +861,7 @@ + _t = (mpfr_kind_t) _k; \ + _s = 1; \ + } else { \ +- _t = (mpfr_kind_t) -k; \ ++ _t = (mpfr_kind_t) - _k; \ + _s = -1; \ + } \ + _e = _t == MPFR_REGULAR_KIND ? (e) : \ +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-12-01 11:07:49.747331585 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p4"; ++ return "3.1.2-p5"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 21:56:49.697059857 +0000 +@@ -0,0 +1 @@ ++li2-return +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 21:56:49.697059857 +0000 +@@ -1 +1 @@ +-3.1.2-p5 ++3.1.2-p6 +diff -Naurd mpfr-3.1.2-a/src/li2.c mpfr-3.1.2-b/src/li2.c +--- mpfr-3.1.2-a/src/li2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/li2.c 2014-04-15 21:56:49.653058661 +0000 +@@ -630,5 +630,5 @@ + return mpfr_check_range (y, inexact, rnd_mode); + } + +- MPFR_ASSERTN (0); /* should never reach this point */ ++ MPFR_RET_NEVER_GO_HERE (); + } +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 21:56:49.697059857 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p5" ++#define MPFR_VERSION_STRING "3.1.2-p6" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 21:56:49.697059857 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p5"; ++ return "3.1.2-p6"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:04:57.162288198 +0000 +@@ -0,0 +1 @@ ++exp3 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:04:57.162288198 +0000 +@@ -1 +1 @@ +-3.1.2-p6 ++3.1.2-p7 +diff -Naurd mpfr-3.1.2-a/src/exp3.c mpfr-3.1.2-b/src/exp3.c +--- mpfr-3.1.2-a/src/exp3.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp3.c 2014-04-15 22:04:57.126287230 +0000 +@@ -283,7 +283,7 @@ + } + } + +- if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDD, MPFR_RNDZ, ++ if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDN, MPFR_RNDZ, + MPFR_PREC(y) + (rnd_mode == MPFR_RNDN))) + { + inexact = mpfr_set (y, shift_x > 0 ? t : tmp, rnd_mode); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:04:57.162288198 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p6" ++#define MPFR_VERSION_STRING "3.1.2-p7" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:04:57.162288198 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p6"; ++ return "3.1.2-p7"; + } +diff -Naurd mpfr-3.1.2-a/tests/texp.c mpfr-3.1.2-b/tests/texp.c +--- mpfr-3.1.2-a/tests/texp.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/texp.c 2014-04-15 22:04:57.126287230 +0000 +@@ -150,6 +150,22 @@ + exit (1); + } + ++ mpfr_set_prec (x, 118); ++ mpfr_set_str_binary (x, "0.1110010100011101010000111110011000000000000000000000000000000000000000000000000000000000000000000000000000000000000000E-86"); ++ mpfr_set_prec (y, 118); ++ mpfr_exp_2 (y, x, MPFR_RNDU); ++ mpfr_exp_3 (x, x, MPFR_RNDU); ++ if (mpfr_cmp (x, y)) ++ { ++ printf ("mpfr_exp_2 and mpfr_exp_3 differ for prec=118\n"); ++ printf ("mpfr_exp_2 gives "); ++ mpfr_out_str (stdout, 2, 0, y, MPFR_RNDN); ++ printf ("\nmpfr_exp_3 gives "); ++ mpfr_out_str (stdout, 2, 0, x, MPFR_RNDN); ++ printf ("\n"); ++ exit (1); ++ } ++ + mpfr_clear (x); + mpfr_clear (y); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:20:32.243481506 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:22:32.418722707 +0000 +@@ -0,0 +1 @@ ++gmp6-compat +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:21:45.225450147 +0000 +@@ -1 +1 @@ +-3.1.2-p7 ++3.1.2-p8 +diff -Naurd mpfr-3.1.2-a/configure mpfr-3.1.2-b/configure +--- mpfr-3.1.2-a/configure 2013-03-13 15:38:20.000000000 +0000 ++++ mpfr-3.1.2-b/configure 2014-04-15 22:21:38.821277476 +0000 +@@ -14545,26 +14545,30 @@ + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + +-if test "$use_gmp_build" = yes ; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for valid GMP_NUMB_BITS" >&5 +-$as_echo_n "checking for valid GMP_NUMB_BITS... " >&6; } +- if test "$cross_compiling" = yes; then : ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency" >&5 ++$as_echo_n "checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency... " >&6; } ++if test "$cross_compiling" = yes; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: can't test" >&5 + $as_echo "can't test" >&6; } + else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + + int + main () + { + +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + + ; + return 0; +@@ -14577,14 +14581,14 @@ + + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } +- as_fn_error $? "GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options." "$LINENO" 5 ++ as_fn_error $? "GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS)." "$LINENO" 5 + fi + rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext + fi + +-fi + + + if test "$dont_link_with_gmp" = yes ; then +diff -Naurd mpfr-3.1.2-a/configure.ac mpfr-3.1.2-b/configure.ac +--- mpfr-3.1.2-a/configure.ac 2013-03-13 15:37:46.000000000 +0000 ++++ mpfr-3.1.2-b/configure.ac 2013-03-13 15:37:46.000000000 +0000 +@@ -435,23 +435,29 @@ + ]) + fi + +-dnl Check for valid GMP_NUMB_BITS and BYTES_PER_MP_LIMB ++dnl Check for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency. ++dnl Problems may occur if gmp.h was generated with some ABI ++dnl and is used with another ABI (or if nails are used). + dnl This test doesn't need to link with libgmp (at least it shouldn't). +-if test "$use_gmp_build" = yes ; then +- AC_MSG_CHECKING(for valid GMP_NUMB_BITS) +- AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++AC_MSG_CHECKING(for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency) ++AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + ]], [[ +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + ]])], [AC_MSG_RESULT(yes)], [ + AC_MSG_RESULT(no) +- AC_MSG_ERROR([GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options.])], ++ AC_MSG_ERROR([GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS).])], + [AC_MSG_RESULT([can't test])]) +-fi + + + dnl We really need to link using libtool. But it is impossible with the current +diff -Naurd mpfr-3.1.2-a/src/init2.c mpfr-3.1.2-b/src/init2.c +--- mpfr-3.1.2-a/src/init2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/init2.c 2014-04-15 22:21:06.220398489 +0000 +@@ -30,11 +30,11 @@ + + /* Check if we can represent the number of limbs + * associated to the maximum of mpfr_prec_t*/ +- MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/BYTES_PER_MP_LIMB) ); ++ MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/MPFR_BYTES_PER_MP_LIMB) ); + +- /* Check for correct GMP_NUMB_BITS and BYTES_PER_MP_LIMB */ +- MPFR_ASSERTN( GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ); ++ /* Check for correct GMP_NUMB_BITS and MPFR_BYTES_PER_MP_LIMB */ ++ MPFR_ASSERTN( GMP_NUMB_BITS == MPFR_BYTES_PER_MP_LIMB * CHAR_BIT ++ && sizeof(mp_limb_t) == MPFR_BYTES_PER_MP_LIMB ); + + MPFR_ASSERTN (mp_bits_per_limb == GMP_NUMB_BITS); + +diff -Naurd mpfr-3.1.2-a/src/mpfr-gmp.h mpfr-3.1.2-b/src/mpfr-gmp.h +--- mpfr-3.1.2-a/src/mpfr-gmp.h 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-gmp.h 2014-04-15 22:21:06.220398489 +0000 +@@ -72,7 +72,6 @@ + #endif + + /* Define some macros */ +-#define BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + #define MP_LIMB_T_MAX (~(mp_limb_t)0) + +@@ -96,19 +95,19 @@ + #define SHRT_HIGHBIT SHRT_MIN + + /* MP_LIMB macros */ +-#define MPN_ZERO(dst, n) memset((dst), 0, (n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) ++#define MPN_ZERO(dst, n) memset((dst), 0, (n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) + #define MPN_COPY(dst,src,n) \ + do \ + { \ + if ((dst) != (src)) \ + { \ + MPFR_ASSERTD ((char *) (dst) >= (char *) (src) + \ +- (n) * BYTES_PER_MP_LIMB || \ ++ (n) * MPFR_BYTES_PER_MP_LIMB || \ + (char *) (src) >= (char *) (dst) + \ +- (n) * BYTES_PER_MP_LIMB); \ +- memcpy ((dst), (src), (n) * BYTES_PER_MP_LIMB); \ ++ (n) * MPFR_BYTES_PER_MP_LIMB); \ ++ memcpy ((dst), (src), (n) * MPFR_BYTES_PER_MP_LIMB); \ + } \ + } \ + while (0) +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2014-04-15 22:21:06.220398489 +0000 +@@ -191,7 +191,7 @@ + # endif + #endif + +- ++#define MPFR_BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + /****************************************************** + ******************** Check GMP *********************** +@@ -930,7 +930,7 @@ + #define MPFR_SET_ALLOC_SIZE(x, n) \ + ( ((mp_size_t*) MPFR_MANT(x))[-1] = n) + #define MPFR_MALLOC_SIZE(s) \ +- ( sizeof(mpfr_size_limb_t) + BYTES_PER_MP_LIMB * ((size_t) s) ) ++ ( sizeof(mpfr_size_limb_t) + MPFR_BYTES_PER_MP_LIMB * ((size_t) s) ) + #define MPFR_SET_MANT_PTR(x,p) \ + (MPFR_MANT(x) = (mp_limb_t*) ((mpfr_size_limb_t*) p + 1)) + #define MPFR_GET_REAL_PTR(x) \ +@@ -964,7 +964,7 @@ + #endif + + #define MPFR_TMP_LIMBS_ALLOC(N) \ +- ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * BYTES_PER_MP_LIMB)) ++ ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * MPFR_BYTES_PER_MP_LIMB)) + + /* temporary allocate 1 limb at xp, and initialize mpfr variable x */ + /* The temporary var doesn't have any size field, but it doesn't matter +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:21:45.225450147 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p7" ++#define MPFR_VERSION_STRING "3.1.2-p8" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/mul.c mpfr-3.1.2-b/src/mul.c +--- mpfr-3.1.2-a/src/mul.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mul.c 2014-04-15 22:21:06.224398597 +0000 +@@ -106,7 +106,7 @@ + MPFR_ASSERTD(tn <= k); + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK(marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +@@ -301,7 +301,7 @@ + MPFR_ASSERTD (tn <= k); /* tn <= k, thus no int overflow */ + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK (marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +diff -Naurd mpfr-3.1.2-a/src/stack_interface.c mpfr-3.1.2-b/src/stack_interface.c +--- mpfr-3.1.2-a/src/stack_interface.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/stack_interface.c 2014-04-15 22:21:06.220398489 +0000 +@@ -26,7 +26,7 @@ + size_t + mpfr_custom_get_size (mpfr_prec_t prec) + { +- return MPFR_PREC2LIMBS (prec) * BYTES_PER_MP_LIMB; ++ return MPFR_PREC2LIMBS (prec) * MPFR_BYTES_PER_MP_LIMB; + } + + #undef mpfr_custom_init +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:21:45.225450147 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p7"; ++ return "3.1.2-p8"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:15:25.617269178 +0000 +@@ -0,0 +1 @@ ++div-overflow +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:15:25.529266797 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:15:25.617269178 +0000 +@@ -1 +1 @@ +-3.1.2-p8 ++3.1.2-p9 +diff -Naurd mpfr-3.1.2-a/src/div.c mpfr-3.1.2-b/src/div.c +--- mpfr-3.1.2-a/src/div.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/div.c 2014-06-30 15:15:25.585268312 +0000 +@@ -750,7 +750,9 @@ + truncate_check_qh: + if (qh) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + goto truncate; +@@ -765,7 +767,9 @@ + inex = 1; /* always here */ + if (mpn_add_1 (q0p, q0p, q0size, MPFR_LIMB_ONE << sh)) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:15:25.613269070 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p8" ++#define MPFR_VERSION_STRING "3.1.2-p9" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:15:25.613269070 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p8"; ++ return "3.1.2-p9"; + } +diff -Naurd mpfr-3.1.2-a/tests/tdiv.c mpfr-3.1.2-b/tests/tdiv.c +--- mpfr-3.1.2-a/tests/tdiv.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tdiv.c 2014-06-30 15:15:25.585268312 +0000 +@@ -1104,6 +1104,96 @@ + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) + #include "tgeneric.c" + ++static void ++test_extreme (void) ++{ ++ mpfr_t x, y, z; ++ mpfr_exp_t emin, emax; ++ mpfr_prec_t p[4] = { 8, 32, 64, 256 }; ++ int xi, yi, zi, j, r; ++ unsigned int flags, ex_flags; ++ ++ emin = mpfr_get_emin (); ++ emax = mpfr_get_emax (); ++ ++ mpfr_set_emin (MPFR_EMIN_MIN); ++ mpfr_set_emax (MPFR_EMAX_MAX); ++ ++ for (xi = 0; xi < 4; xi++) ++ { ++ mpfr_init2 (x, p[xi]); ++ mpfr_setmax (x, MPFR_EMAX_MAX); ++ MPFR_ASSERTN (mpfr_check (x)); ++ for (yi = 0; yi < 4; yi++) ++ { ++ mpfr_init2 (y, p[yi]); ++ mpfr_setmin (y, MPFR_EMIN_MIN); ++ for (j = 0; j < 2; j++) ++ { ++ MPFR_ASSERTN (mpfr_check (y)); ++ for (zi = 0; zi < 4; zi++) ++ { ++ mpfr_init2 (z, p[zi]); ++ RND_LOOP (r) ++ { ++ mpfr_clear_flags (); ++ mpfr_div (z, x, y, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_OVERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (x); ++ printf ("b = "); ++ mpfr_dump (y); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ mpfr_clear_flags (); ++ mpfr_div (z, y, x, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_UNDERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (y); ++ printf ("b = "); ++ mpfr_dump (x); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ } ++ mpfr_clear (z); ++ } /* zi */ ++ mpfr_nextabove (y); ++ } /* j */ ++ mpfr_clear (y); ++ } /* yi */ ++ mpfr_clear (x); ++ } /* xi */ ++ ++ set_emin (emin); ++ set_emax (emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1130,6 +1220,7 @@ + test_20070603 (); + test_20070628 (); + test_generic (2, 800, 50); ++ test_extreme (); + + tests_end_mpfr (); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:17:53.417270314 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:17:53.413270206 +0000 +@@ -1 +1 @@ +-3.1.2-p9 ++3.1.2-p10 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:17:53.413270206 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p9" ++#define MPFR_VERSION_STRING "3.1.2-p10" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -884,14 +884,18 @@ + first digit, we want the exponent for radix two and the decimal + point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN /4); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > (MPFR_EXP_MIN + 3) / 4); + exp = (exp - 1) * 4; + } + else + /* EXP is the exponent for decimal point BEFORE the first digit, we + want the exponent for decimal point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > MPFR_EXP_MIN); + --exp; + } + } +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:17:53.413270206 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p9"; ++ return "3.1.2-p10"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -1184,6 +1184,69 @@ + check_emax_aux (MPFR_EMAX_MAX); + } + ++static void ++check_emin_aux (mpfr_exp_t e) ++{ ++ mpfr_t x; ++ char *s1, s2[256]; ++ int i; ++ mpfr_exp_t emin; ++ mpz_t ee; ++ ++ MPFR_ASSERTN (e >= LONG_MIN); ++ emin = mpfr_get_emin (); ++ set_emin (e); ++ ++ mpfr_init2 (x, 16); ++ mpz_init (ee); ++ ++ mpfr_setmin (x, e); ++ mpz_set_si (ee, e); ++ mpz_sub_ui (ee, ee, 1); ++ ++ i = mpfr_asprintf (&s1, "%Ra", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "0x1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ i = mpfr_asprintf (&s1, "%Rb", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ mpfr_clear (x); ++ mpz_clear (ee); ++ set_emin (emin); ++} ++ ++static void ++check_emin (void) ++{ ++ check_emin_aux (-15); ++ check_emin_aux (mpfr_get_emin ()); ++ check_emin_aux (MPFR_EMIN_MIN); ++} ++ + int + main (int argc, char **argv) + { +@@ -1203,6 +1266,7 @@ + decimal (); + mixed (); + check_emax (); ++ check_emin (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + locale_da_DK (); +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-12-04 01:41:57.339791833 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-12-04 01:41:57.339791833 +0000 +@@ -1 +1 @@ +-3.1.2-p10 ++3.1.2-p11 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-12-04 01:41:57.335791790 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p10" ++#define MPFR_VERSION_STRING "3.1.2-p11" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/strtofr.c mpfr-3.1.2-b/src/strtofr.c +--- mpfr-3.1.2-a/src/strtofr.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/strtofr.c 2014-12-04 01:41:57.287791246 +0000 +@@ -473,8 +473,10 @@ + /* prec bits corresponds to ysize limbs */ + ysize_bits = ysize * GMP_NUMB_BITS; + /* and to ysize_bits >= prec > MPFR_PREC (x) bits */ +- y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 1); +- y += ysize; /* y has (ysize+1) allocated limbs */ ++ /* we need to allocate one more limb to work around bug ++ https://gmplib.org/list-archives/gmp-bugs/2013-December/003267.html */ ++ y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 2); ++ y += ysize; /* y has (ysize+2) allocated limbs */ + + /* pstr_size is the number of characters we read in pstr->mant + to have at least ysize full limbs. +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-12-04 01:41:57.339791833 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p10"; ++ return "3.1.2-p11"; + } -- GitLab From 2aa2adf21c052863684bdcf72ca43b3d0d8225d9 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 13 Apr 2015 15:57:08 +0200 Subject: [PATCH 594/911] Support Spark 1.3.0 --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 26 ++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb new file mode 100644 index 0000000000..7f97113c7d --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.3.0' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] +source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] + +java = 'Java' +javaver = '1.7.0_40' + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['bin', 'lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' -- GitLab From 404cce4fa83211c0b592fa7694fd9cf33b297006 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 14 Apr 2015 13:55:22 +0200 Subject: [PATCH 595/911] added easyconfig for newer mathematica versions --- .../m/Mathematica/Mathematica-10.0.2.eb | 14 ++++++++++++++ .../m/Mathematica/Mathematica-10.1.0.eb | 14 ++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb new file mode 100644 index 0000000000..cb33bf4bb0 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.0.2' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%s_LINUX.sh' % version] + +license_server = 'license.example.com' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb new file mode 100644 index 0000000000..79b9255141 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.1.0' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%s_LINUX.sh' % version] + +license_server = 'license.example.com' + +moduleclass = 'math' -- GitLab From bd259ad02ba9ce9b9e7380edd4f2f8e954190f80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Apr 2015 22:10:58 +0200 Subject: [PATCH 596/911] include fftw dep in Cray toolchains --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 2 ++ easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 2 ++ easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 2 ++ easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 2 ++ 6 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index f09961bd60..45d88cae31 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index ff0774c751..78c6b82ec4 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index d2d1520bce..f5228016b8 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index afc8c6010c..0577186f67 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 6cb4679750..9f906e92b4 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.0')] + moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index f24f574b3f..bcd630f2e9 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,4 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('fftw', '3.3.4.2')] + moduleclass = 'toolchain' -- GitLab From e70bb2853bdde3680953ea2038fbc6507cfd6f18 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 13:27:21 +0200 Subject: [PATCH 597/911] Remove check of bin dir since we check a file in bin anyway. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 7f97113c7d..5c8d510430 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -18,7 +18,7 @@ dependencies = [(java, javaver)] sanity_check_paths = { 'files': ['bin/spark-shell'], - 'dirs': ['bin', 'lib', 'python'] + 'dirs': ['lib', 'python'] } modextrapaths = {'PYTHONPATH': 'python'} -- GitLab From 9c618b599a4aae422aa055285ee02d41f078baf9 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 13:57:17 +0200 Subject: [PATCH 598/911] Update java dep version. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 5c8d510430..4a9f913b52 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -12,7 +12,7 @@ sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] java = 'Java' -javaver = '1.7.0_40' +javaver = '1.7.0_76' dependencies = [(java, javaver)] -- GitLab From 4359a869a93472ebaceb82bd0298f2dd424bb0f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 14:13:00 +0200 Subject: [PATCH 599/911] collapse deps --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 4a9f913b52..d635db080f 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -11,10 +11,7 @@ toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] -java = 'Java' -javaver = '1.7.0_76' - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.7.0_76')] sanity_check_paths = { 'files': ['bin/spark-shell'], -- GitLab From 4bd6b21cf3ef92004b71798ced797cce9e455f1a Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 20 Apr 2015 15:09:09 +0200 Subject: [PATCH 600/911] Fix sources. --- easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 4a9f913b52..15aa2288da 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -9,7 +9,11 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'dummy', 'version': ''} sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] -source_urls = ['http://www.apache.org/dyn/closer.cgi/spark/%(namelower)s-%(version)s'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] java = 'Java' javaver = '1.7.0_76' -- GitLab From 288967c089c19a8599a71336b858fc40b79f049f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:12:00 +0200 Subject: [PATCH 601/911] include petsc_arch spec in SLEPc 3.5.3 easyconfig --- .../easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb index 2253b31148..0f01678e28 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -16,4 +16,6 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('PETSc', '3.5.3', versionsuffix)] +petsc_arch = 'arch-linux2-c-opt' + moduleclass = 'numlib' -- GitLab From 5c18bb7e6a8b9198c2ce892b271cc6c86465f916 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:33:31 +0200 Subject: [PATCH 602/911] fix remarks --- easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb | 2 +- easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb index ef2bf9ff97..cea8ae91c9 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb @@ -17,6 +17,6 @@ source_urls = [ patches = ['METIS_IDXTYPEWIDTH.patch'] -builddependencies = [('CMake', '3.0.0')] +builddependencies = [('CMake', '3.2.1')] moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch index 363f95c19f..0689e81b9f 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch @@ -1,3 +1,5 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py --- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 +++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 -- GitLab From 73ead9e2d22f40790446a1b2ded92a34575693b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 16:35:34 +0200 Subject: [PATCH 603/911] use %(version)s template --- easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb | 2 +- easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb | 2 +- easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb | 2 +- easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch | 2 ++ 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb index cb33bf4bb0..e1bdcca9da 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb index 79b9255141..0093f6a4c2 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb index 2d148e7a75..aafd02cf83 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch index 363f95c19f..0689e81b9f 100644 --- a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch +++ b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch @@ -1,3 +1,5 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py --- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 +++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 -- GitLab From 4255429a0b3bd98bd547cfa009089c6a5ebe2da3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 17:41:51 +0200 Subject: [PATCH 604/911] add CMake as build dep to getdp/gmsh easyconfigs --- .../c/CMake/CMake-3.2.2-intel-2015a.eb | 22 +++++++++++++++++++ .../g/getdp/getdp-2.5.0-intel-2015a.eb | 2 ++ .../g/gmsh/gmsh-2.9.1-intel-2015a.eb | 2 ++ 3 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000..d971d9f7a0 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb index 1a8738bd04..32895add69 100644 --- a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://geuz.org/getdp/src/'] sources = ['%(name)s-%(version)s-source.tgz'] +builddependencies = [('CMake', '3.2.2')] + dependencies = [ ('GSL', '1.16'), ('PETSc', '3.5.3', versionsuffix), diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb index 00701f2eb2..40e96ab54b 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://geuz.org/gmsh/src/'] sources = ['%(name)s-%(version)s-source.tgz'] +builddependencies = [('CMake', '3.2.2')] + separate_build_dir = True configopts = '-DENABLE_FLTK=0' -- GitLab From fcb028610093a89c404bb865e01557c8bd46243d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 21:03:39 +0200 Subject: [PATCH 605/911] fix getdp easyconfig filename --- ...5.0-intel-2015a.eb => getdp-2.5.0-intel-2015a-Python-2.7.9.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/getdp/{getdp-2.5.0-intel-2015a.eb => getdp-2.5.0-intel-2015a-Python-2.7.9.eb} (100%) diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 100% rename from easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a.eb rename to easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb -- GitLab From 7b6b3008dc49190e0bc2e48f3914661ade0a6448 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 22:05:21 +0200 Subject: [PATCH 606/911] fix sanity check paths for getdp --- .../g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb index 32895add69..bf0165977f 100644 --- a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb @@ -23,4 +23,9 @@ dependencies = [ separate_build_dir = True +sanity_check_paths = { + 'files': ['bin/getdp'], + 'dirs': ['share'], +} + moduleclass = 'math' -- GitLab From 0d53fd727044b2a5de8c7449d51de680e09c6f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 22:53:55 +0200 Subject: [PATCH 607/911] add working easyconfigs for HPL, zlib, Szip with CrayGNU 5.1.29 toolchain --- .../h/HPL/HPL-2.1-CrayGNU-5.1.29.eb | 18 +++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.1.29.eb | 23 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb | 22 ++++++++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..806d976659 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..5a2850640d --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..737b571621 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From cd71dfbddb7f53bf75478689ebe433bd0236b20e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2015 23:02:52 +0200 Subject: [PATCH 608/911] add easyconfig for Libint 1.1.4 with CrayGNU 5.1.29 toolchain --- .../l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..7d4d9128c9 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' -- GitLab From 485182e90af909ae96d86bdf5dbfcff5b49c88bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 16:11:51 +0200 Subject: [PATCH 609/911] specify fftw dep in Cray toolchain easyconfigs as an external dep --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 2 +- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 2 +- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index 45d88cae31..f5df8a066a 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 78c6b82ec4..524d8e18e6 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index f5228016b8..cf8d95ff05 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 0577186f67..b811ad7ed5 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 9f906e92b4..8e4b5fe50e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.0')] +dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index bcd630f2e9..b460d5e453 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,6 +8,6 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw', '3.3.4.2')] +dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] moduleclass = 'toolchain' -- GitLab From 8b46e6671a2b1d719b649e3df568125326d7da7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 19:51:06 +0200 Subject: [PATCH 610/911] {tools}[GCC/4.9.2] parallel 20150322 --- .../p/parallel/parallel-20150322-GCC-4.9.2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb new file mode 100644 index 0000000000..5819c52290 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20150322' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/parallel'] + +dependencies = [ + ('Perl', '5.20.1', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 3430ac8b491a4dbf2cda7bb17f9fe397b8cbbbb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Apr 2015 19:54:02 +0200 Subject: [PATCH 611/911] bump Perl version in parallel dep to latest --- .../p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb | 19 +++++++++++++++++++ .../p/parallel/parallel-20150322-GCC-4.9.2.eb | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000..a79c30c3b2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb @@ -0,0 +1,19 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb index 5819c52290..d8b12a2b08 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/parallel'] dependencies = [ - ('Perl', '5.20.1', '-bare'), + ('Perl', '5.20.2', '-bare'), ] sanity_check_paths = { -- GitLab From 2528867b9d244f4bab88d7d73c983e885b4498b8 Mon Sep 17 00:00:00 2001 From: Petar Forai Date: Wed, 22 Apr 2015 01:48:23 +0200 Subject: [PATCH 612/911] Added initial GROMACS 4.6.5 support for CrayGNU. Need to add -mt and -hybrid suffixes. --- .../g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..e8c3fd1883 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.5' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.1.3', '', True)] + +runtest = False + +moduleclass = 'bio' -- GitLab From 29f05410639f3894651b8075469659144a2e6e8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 09:39:33 +0200 Subject: [PATCH 613/911] add easyconfig for GROMACS + ncurses/CMake deps with CrayGNU 5.1.29 --- .../c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb | 23 ++++++++++++ .../GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 37 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 22 +++++++++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..68df962efa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb new file mode 100644 index 0000000000..c7618bc1f3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..64defc00e8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' -- GitLab From 511854dff8266600d50b2d75a13e1ef055197ed4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 09:40:42 +0200 Subject: [PATCH 614/911] remove GROMACS 4.6.5 with CrayGNU --- .../g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb deleted file mode 100644 index e8c3fd1883..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-CrayGNU-5.1.29.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University -# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ -# George Tsouloupas , Kenneth Hoste -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html -## -name = 'GROMACS' -version = '4.6.5' - -homepage = 'http://www.gromacs.org' -description = """GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" - -toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] - -builddependencies = [('CMake', '3.1.3', '', True)] - -runtest = False - -moduleclass = 'bio' -- GitLab From 3adbc1318e829bef3ba5a8a2fe40c01deead9fd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Wed, 22 Apr 2015 09:47:17 +0200 Subject: [PATCH 615/911] Toolchain intel-2014.06 including HPL-2.1 --- .../h/HPL/HPL-2.1-intel-2014.06.eb | 18 +++++++++++++++ .../i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb | 21 +++++++++++++++++ .../imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb | 22 ++++++++++++++++++ ...4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb | 19 +++++++++++++++ .../easyconfigs/i/intel/intel-2014.06.eb | 23 +++++++++++++++++++ 5 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2014.06.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb new file mode 100644 index 0000000000..38c3e337e3 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000..6927105428 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '5.5.0' +versionsuffix = '-GCC-4.8.3' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '5.192' +compver = '2013.%s' % suff + +dependencies = [ # version/released + ('icc', compver, versionsuffix), # 28 Apr 2014 + ('ifort', compver, versionsuffix), # 28 Apr 2014 + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, versionsuffix))), # 06 Mar 2014 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000..e04b151136 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.0.5.192' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '5.5.0-GCC-4.8.3'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +interfaces = True + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb new file mode 100644 index 0000000000..00ee030d34 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.1.036' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2013.5.192-GCC-4.8.3'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb new file mode 100644 index 0000000000..57c2903c57 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2014.06' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '5.192' +compver = '2013.%s' % suff + +gccsuff = '-GCC-4.8.3' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.0.5.192', '', ('iimpi', '5.5.0%s' % gccsuff)), +] + +moduleclass = 'toolchain' -- GitLab From cf377e97fa10de64eb15963e45e25c8ceaae4888 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 12:07:43 +0200 Subject: [PATCH 616/911] include PrgEnv and cray-libsci deps in CrayGNU toolchains --- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 6 +++++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index cf8d95ff05..9f424cdc02 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -8,6 +8,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), + ('cray-libsci/13.0.1', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index b811ad7ed5..37804fbb5c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -8,6 +8,10 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), + ('cray-libsci/13.0.3', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' -- GitLab From ba093636f1a248850f323619b8988204dd966172 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 14:14:35 +0200 Subject: [PATCH 617/911] enable pic option in expat easyconfigs --- easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb | 1 + easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb | 1 + 18 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb index e10b56409e..5ec94cc902 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb index 32e37ffc4e..ff49fa9059 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb index a5482a0de8..e94cc361d0 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb index 77192999ec..faee47738e 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb index 7548d8a264..292f27fff3 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgoolf', 'version': '1.1.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb index 35e32ef7da..e68977279b 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb index 1381b2b8cd..600e38e8b5 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb index 1df1944fe7..5bf2380173 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb index 23118879c5..1e273d6bd7 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb index 207aea5fd5..7fee445ae4 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb index ccfb1c69db..c409db262d 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb index 3d951c24c9..988d22cea6 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb index 6fe54d636d..40d2dd346f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb index f59fe3f2c0..659d23c4d0 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb index 7717261400..c97465c9f1 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb index 45acf6dd3e..7960b1c2df 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb index f76c746c5e..1c0523995a 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb index 0eb1188648..084ab12246 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 05e3d12dda5b6d5862b21144d11e0af3ee50bc9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 17:47:55 +0200 Subject: [PATCH 618/911] add easyconfigs for CP2K + deps with CrayGNU/5.1.29 --- .../b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb | 22 +++++++++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb | 38 +++++++++++++++++++ .../f/flex/flex-2.5.39-CrayGNU-5.1.29.eb | 14 +++++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb | 32 ++++++++++++++++ .../m/M4/M4-1.4.17-CrayGNU-5.1.29.eb | 23 +++++++++++ 5 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..96873ab500 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..e1f9bdb729 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..a6d2ced89c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..548d650cde --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..de4b325756 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From b99801a68b103fa5037f4a15aaad321dd0c2bd0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 17:57:56 +0200 Subject: [PATCH 619/911] fix sources/source_urls in Octave easyconfig --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 131eedc724..f4320d6460 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -8,8 +8,8 @@ description = """GNU Octave is a high-level interpreted language, primarily inte toolchain = {'name': 'foss', 'version': '2015a'} -sources = [GNU_SOURCE] -source_urls = ['http://ftpmirror.gnu.org/octave/'] +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] configopts = '--with-blas="${LIBBLAS}"' -- GitLab From 4e6b0a299a1645227e03f8f7520846553a1465dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 20:54:44 +0200 Subject: [PATCH 620/911] {math}[intel/2015a] Octave 3.8.2 --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 4 +-- .../o/Octave/Octave-3.8.2-intel-2015a.eb | 29 +++++++++++++++++ .../o/Octave/Octave-3.8.2_intel.patch | 32 +++++++++++++++++++ 3 files changed, 63 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index f4320d6460..da90d7cb9f 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -11,14 +11,14 @@ toolchain = {'name': 'foss', 'version': '2015a'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -configopts = '--with-blas="${LIBBLAS}"' - dependencies = [ ('PCRE', '8.36'), ('ncurses', '5.9'), ('libreadline', '6.3'), ] +configopts = '--with-blas="${LIBBLAS}"' + sanity_check_paths = { 'files': ['bin/octave'], 'dirs': [] diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb new file mode 100644 index 0000000000..a7b0eeec4a --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '3.8.2' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Octave-%(version)s_intel.patch'] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +configopts = '--with-blas="${LIBBLAS}"' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch new file mode 100644 index 0000000000..3bc21ba24d --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -0,0 +1,32 @@ +avoid "declaration is incompatible with previous" style error message +cfr. http://lists.gnu.org/archive/html/help-octave/2011-10/msg00438.html +by Kenneth Hoste (HPC-UGent) +--- octave-3.8.2/libgnu/stdio.in.h.orig 2015-04-22 20:12:39.436847845 +0200 ++++ octave-3.8.2/libgnu/stdio.in.h 2015-04-22 20:15:20.800889451 +0200 +@@ -633,7 +633,7 @@ + _GL_FUNCDECL_RPL (getchar, int, (void)); + _GL_CXXALIAS_RPL (getchar, int, (void)); + # else +-_GL_CXXALIAS_SYS (getchar, int, (void)); ++//_GL_CXXALIAS_SYS (getchar, int, (void)); + # endif + _GL_CXXALIASWARN (getchar); + #endif +@@ -907,7 +907,7 @@ + _GL_FUNCDECL_RPL (putchar, int, (int c)); + _GL_CXXALIAS_RPL (putchar, int, (int c)); + # else +-_GL_CXXALIAS_SYS (putchar, int, (int c)); ++//_GL_CXXALIAS_SYS (putchar, int, (int c)); + # endif + _GL_CXXALIASWARN (putchar); + #endif +@@ -1261,7 +1261,7 @@ + /* Need to cast, because on Solaris, the second parameter is + __va_list args + and GCC's fixincludes did not change this to __gnuc_va_list. */ +-_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); ++//_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); + # endif + _GL_CXXALIASWARN (vprintf); + #endif -- GitLab From 9281c89c26232fbe8b18dcc1d2366de0aaaffd48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 21:34:22 +0200 Subject: [PATCH 621/911] fix patch for building Octave with Intel compilers, add sanity check command --- .../o/Octave/Octave-3.8.2-foss-2015a.eb | 2 + .../o/Octave/Octave-3.8.2-intel-2015a.eb | 2 + .../o/Octave/Octave-3.8.2_intel.patch | 55 +++++++++---------- 3 files changed, 29 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index da90d7cb9f..2bf046bbd9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -24,4 +24,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [('octave', '--eval "1+2"')] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb index a7b0eeec4a..a4fb263cdc 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [('octave', '--eval "1+2"')] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch index 3bc21ba24d..20560be7e6 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -1,32 +1,27 @@ -avoid "declaration is incompatible with previous" style error message -cfr. http://lists.gnu.org/archive/html/help-octave/2011-10/msg00438.html -by Kenneth Hoste (HPC-UGent) ---- octave-3.8.2/libgnu/stdio.in.h.orig 2015-04-22 20:12:39.436847845 +0200 -+++ octave-3.8.2/libgnu/stdio.in.h 2015-04-22 20:15:20.800889451 +0200 -@@ -633,7 +633,7 @@ - _GL_FUNCDECL_RPL (getchar, int, (void)); - _GL_CXXALIAS_RPL (getchar, int, (void)); - # else --_GL_CXXALIAS_SYS (getchar, int, (void)); -+//_GL_CXXALIAS_SYS (getchar, int, (void)); - # endif - _GL_CXXALIASWARN (getchar); +fix build issue with Intel compilers that manifests itself as: +../../libgnu/stdio.h(948): error: declaration is incompatible with previous "getchar" (declared at line 542 of "/usr/include/stdio.h") + _GL_CXXALIAS_SYS (getchar, int, (void)); + ^ +see http://octave.1599824.n4.nabble.com/Build-issues-with-libgnu-tt4666148.html#a4666416 +patch available via https://savannah.gnu.org/bugs/index.php?43171 +--- octave-3.8.2/libgnu/fcntl.in.h ++++ octave-3.8.2/libgnu//fcntl.in.h +@@ -34,7 +34,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include #endif -@@ -907,7 +907,7 @@ - _GL_FUNCDECL_RPL (putchar, int, (int c)); - _GL_CXXALIAS_RPL (putchar, int, (int c)); - # else --_GL_CXXALIAS_SYS (putchar, int, (int c)); -+//_GL_CXXALIAS_SYS (putchar, int, (int c)); - # endif - _GL_CXXALIASWARN (putchar); - #endif -@@ -1261,7 +1261,7 @@ - /* Need to cast, because on Solaris, the second parameter is - __va_list args - and GCC's fixincludes did not change this to __gnuc_va_list. */ --_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); -+//_GL_CXXALIAS_SYS_CAST (vprintf, int, (const char *format, va_list args)); - # endif - _GL_CXXALIASWARN (vprintf); + #@INCLUDE_NEXT@ @NEXT_FCNTL_H@ +@@ -53,7 +53,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include #endif + /* The include_next requires a split double-inclusion guard. */ + -- GitLab From 5e877df0dacccfa40d615e938848de522483e927 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 21:48:53 +0200 Subject: [PATCH 622/911] complete patch for building Octave with Intel --- .../o/Octave/Octave-3.8.2_intel.patch | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch index 20560be7e6..ec623d4749 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -25,3 +25,27 @@ patch available via https://savannah.gnu.org/bugs/index.php?43171 #endif /* The include_next requires a split double-inclusion guard. */ +--- octave-3.8.2/liboctave/cruft/misc/quit.h.orig 2015-04-22 21:47:08.614133593 +0200 ++++ octave-3.8.2/liboctave/cruft/misc/quit.h 2015-04-22 21:47:24.584562436 +0200 +@@ -23,16 +23,16 @@ + #if !defined (octave_quit_h) + #define octave_quit_h 1 + +-#ifdef __cplusplus +-#include +-extern "C" { +-#endif +- + #include + + #include + #include + ++#ifdef __cplusplus ++#include ++extern "C" { ++#endif ++ + #if defined (__WIN32__) && ! defined (_POSIX_VERSION) + + #define WIN32_LEAN_AND_MEAN -- GitLab From 3ad51d6e3c3eb177dd97e9f202bd822bc63907ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 22:26:02 +0200 Subject: [PATCH 623/911] add easyconfigs for Python/numpy/scipy with CrayGNU 5.1.29 --- ...numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.1.29-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 107 ++++++++++++++++++ ...cipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb | 19 ++++ 4 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000..49b27458ee --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb new file mode 100644 index 0000000000..2ec3cb1dc8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..4ef1c682d1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000..d6c03f828c --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' -- GitLab From fd0f971d2ce6b217255a2a757d738f18d6e50cda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 23:29:04 +0200 Subject: [PATCH 624/911] add missing bzip2 easyconfig with CrayGNU 5.1.29 --- .../b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..a04591dede --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' -- GitLab From c0f36ba76e8fce6cb7239b7dc0b2aa7f280c5cd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2015 23:29:41 +0200 Subject: [PATCH 625/911] add missing libreadline easyconfig with CrayGNU 5.1.29 --- .../libreadline-6.3-CrayGNU-5.1.29.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..8b8b71eae5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' -- GitLab From 2d387c0a2898473c987ad093100f56dcdf4c36a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lum=C3=ADr=20Jasiok?= Date: Thu, 23 Apr 2015 09:37:26 +0200 Subject: [PATCH 626/911] OpenCV-2.4.9-intel-2014.06 anddependencies --- .../a/ant/ant-1.9.3-Java-1.7.0_79.eb | 26 +++++ .../b/bzip2/bzip2-1.0.6-intel-2014.06.eb | 15 +++ .../c/CMake/CMake-3.0.0-intel-2014.06.eb | 22 +++++ .../f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb | 28 ++++++ .../g/GLib/GLib-2.40.0-intel-2014.06.eb | 21 +++++ .../g/gettext/gettext-0.19.2-intel-2014.06.eb | 18 ++++ .../j/JUnit/JUnit-4.11-Java-1.7.0_79.eb | 25 +++++ .../j/JasPer/JasPer-1.900.1-intel-2014.06.eb | 21 +++++ easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb | 15 +++ .../l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb | 19 ++++ .../l/libffi/libffi-3.1-intel-2014.06.eb | 23 +++++ .../libjpeg-turbo-1.3.1-intel-2014.06.eb | 24 +++++ .../l/libpng/libpng-1.6.12-intel-2014.06.eb | 19 ++++ .../libreadline-6.3-intel-2014.06.eb | 27 ++++++ .../n/NASM/NASM-2.11.05-intel-2014.06.eb | 19 ++++ .../n/ncurses/ncurses-5.9-intel-2014.06.eb | 15 +++ .../o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 76 +++++++++++++++ .../p/Python/Python-2.7.8-intel-2014.06.eb | 94 +++++++++++++++++++ .../z/zlib/zlib-1.2.8-intel-2014.06.eb | 24 +++++ 19 files changed, 531 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb new file mode 100644 index 0000000000..e1662e8bf2 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.9.3' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb new file mode 100644 index 0000000000..567328a2d6 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb new file mode 100644 index 0000000000..447079089d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb new file mode 100644 index 0000000000..36569d20af --- /dev/null +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ffmpeg' +version = '2.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.05'), + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server'] ] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb new file mode 100644 index 0000000000..0b2f10e82d --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.40.0-intel-2014.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.40.0' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/glib/%(version_major_minor)s/'] +sources = ['glib-%(version)s.tar.xz'] + +dependencies = [ + ('libffi', '3.1'), + ('gettext', '0.19.2'), +] +builddependencies = [('Python', '2.7.8')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb new file mode 100644 index 0000000000..238843b206 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb new file mode 100644 index 0000000000..4c4751893b --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb @@ -0,0 +1,25 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.11' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb new file mode 100644 index 0000000000..41dba8410e --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb new file mode 100644 index 0000000000..d7b280abb2 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_79' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb new file mode 100644 index 0000000000..987c5b0636 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb new file mode 100644 index 0000000000..1db00ffb5e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +homepage = 'http://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to various calling +conventions. This allows a programmer to call any function specified by a call interface description at run-time.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb new file mode 100644 index 0000000000..c76e470179 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb new file mode 100644 index 0000000000..e5160148db --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb new file mode 100644 index 0000000000..7154c323ba --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb new file mode 100644 index 0000000000..2a7e58d385 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb new file mode 100644 index 0000000000..e1045e7b9f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb new file mode 100644 index 0000000000..9bed0737f0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.9' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'opt': True, 'optarch': True} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +osdependencies = ['gtk2-devel'] + +builddependencies = [ + ('CMake', '3.0.0'), +] + +python = 'Python' +pythonver = '2.7.8' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +java = 'Java' +javaver = '1.7.0_79' + +dependencies = [ + (python, pythonver), + ('zlib', '1.2.8'), + ('ffmpeg', '2.4'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('LibTIFF', '4.0.3'), + ('JasPer', '1.900.1'), + (java, javaver ,'', True), + ('ant', '1.9.3', '-%s-%s' % (java,javaver), True), + ('GLib', '2.40.0') +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.so'] + + [ 'bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade'] ], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb new file mode 100644 index 0000000000..db0f00951f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -0,0 +1,94 @@ +name = 'Python' +version = '2.7.8' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb new file mode 100644 index 0000000000..7873060724 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 495f273d92617554442f773a673707cfeaea0403 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 09:52:44 +0200 Subject: [PATCH 627/911] Updated checksum --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 7a65f31c78..85c24b1b81 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -29,7 +29,7 @@ sources = [ patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ - '37cdc2eb0adf92e421c0841748ac1471', # gcc-5.1.0.tar.bz2 + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz -- GitLab From 3a22caad5a4aafd57c8db00ad2d88d20c9bcbf30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2015 09:54:21 +0200 Subject: [PATCH 628/911] sync with easyconfigs in develop where needed --- .../l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb | 16 +++++++++++++++- .../l/libffi/libffi-3.1-intel-2014.06.eb | 2 +- .../n/NASM/NASM-2.11.05-intel-2014.06.eb | 11 +++++++++++ .../p/Python/Python-2.7.8-intel-2014.06.eb | 13 ++++++++++--- .../z/zlib/zlib-1.2.8-intel-2014.06.eb | 2 -- 5 files changed, 37 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb index 987c5b0636..e29ed51d54 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb @@ -1,3 +1,14 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## easyblock = 'ConfigureMake' name = 'LibTIFF' @@ -6,7 +17,10 @@ version = '4.0.3' homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" -source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] sources = ['tiff-%(version)s.tar.gz'] toolchain = {'name': 'intel', 'version': '2014.06'} diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb index 1db00ffb5e..4f8e9bd62b 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb @@ -16,7 +16,7 @@ source_urls = [ sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { - 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], 'dirs': [], } diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb index 2a7e58d385..8eacf467e7 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb @@ -1,3 +1,14 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## easyblock = 'ConfigureMake' name = 'NASM' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index db0f00951f..54d5edce60 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -22,8 +22,11 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons ] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + # order is important! # Version updated 08/JULY/2014 exts_list = [ @@ -49,7 +52,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { - 'source_urls': ['https://mpi4py.googlecode.com/files/'], + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], @@ -63,6 +66,9 @@ exts_list = [ ('Cython', '0.20.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], @@ -81,6 +87,9 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), ('paramiko', '1.14.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], }), @@ -89,6 +98,4 @@ exts_list = [ }), ] -osdependencies = [('openssl-devel', 'libssl-dev')] - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb index 7873060724..24f9e69fb8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb @@ -14,8 +14,6 @@ toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -preconfigopts = 'LDSHARED="$CC -shared"' - sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 9f8ec0262d4e374fa6a57f40dc8b9b6b68d1c1a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2015 10:13:52 +0200 Subject: [PATCH 629/911] style fix in Octave easyconfigs --- easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb index 2bf046bbd9..eeea60d967 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ] -configopts = '--with-blas="${LIBBLAS}"' +configopts = '--with-blas="$LIBBLAS"' sanity_check_paths = { 'files': ['bin/octave'], diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb index a4fb263cdc..2b1159f006 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -19,7 +19,7 @@ dependencies = [ ('libreadline', '6.3'), ] -configopts = '--with-blas="${LIBBLAS}"' +configopts = '--with-blas="$LIBBLAS"' sanity_check_paths = { 'files': ['bin/octave'], -- GitLab From c3296f64fab24fd62f35f533e1814ba9afa8d359 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:27:45 +0200 Subject: [PATCH 630/911] Update GCC easyconfig --- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 85c24b1b81..8a37c34c77 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -23,7 +23,6 @@ sources = [ 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.3.tar.gz', - 'isl-0.14.tar.bz2', ] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] @@ -33,14 +32,11 @@ checksums = [ 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] -#withisl = True - # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From 90f959d537610594d36dd1f3bd37cfdd044f32f2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:27:56 +0200 Subject: [PATCH 631/911] Add GCC with ISL and 3 stage build --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 53 ++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb new file mode 100644 index 0000000000..49c83175bd --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb @@ -0,0 +1,53 @@ +name = "GCC" +version = '5.1.0' +versionsuffix = 'ISL' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +sanity_check_paths = { + 'files': ['bin/gcc'], + 'dirs': ["."] +} + +moduleclass = 'compiler' -- GitLab From fa38bc69b483bcff92c4d4882700de0954f8cc56 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 13:35:19 +0200 Subject: [PATCH 632/911] Updated version suffix --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb index 49c83175bd..acd0ece277 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb @@ -1,6 +1,6 @@ name = "GCC" version = '5.1.0' -versionsuffix = 'ISL' +versionsuffix = '-ISL' homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, -- GitLab From 981ae913f660d72ed08edb7589eb97273a5117ee Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 23 Apr 2015 16:06:02 +0200 Subject: [PATCH 633/911] Only build a ISL enabled version of GCC --- easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb | 53 -------------------- easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb | 4 ++ 2 files changed, 4 insertions(+), 53 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb deleted file mode 100644 index acd0ece277..0000000000 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-ISL.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = "GCC" -version = '5.1.0' -versionsuffix = '-ISL' - -homepage = 'http://gcc.gnu.org/' -description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, - as well as libraries for these languages (libstdc++, libgcj,...).""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -mpfr_version = '3.1.2' - -source_urls = [ - 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror - 'http://ftpmirror.gnu.org/gmp', # idem for GMP - 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR - 'http://www.multiprecision.org/mpc/download', # MPC official - 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies -] - -sources = [ - SOURCELOWER_TAR_BZ2, - 'gmp-6.0.0a.tar.bz2', - 'mpfr-%s.tar.gz' % mpfr_version, - 'mpc-1.0.3.tar.gz', - 'isl-0.14.tar.bz2', -] - -patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] - -checksums = [ - 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 - 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 - '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 - '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch -] - -languages = ['c', 'c++', 'fortran'] - -withisl = True - -# building GCC sometimes fails if make parallelism is too high, so let's limit it -maxparallel = 4 - -sanity_check_paths = { - 'files': ['bin/gcc'], - 'dirs': ["."] -} - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 8a37c34c77..4968008ae8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -23,6 +23,7 @@ sources = [ 'gmp-6.0.0a.tar.bz2', 'mpfr-%s.tar.gz' % mpfr_version, 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', ] patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] @@ -32,11 +33,14 @@ checksums = [ 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch ] languages = ['c', 'c++', 'fortran'] +withisl = True + # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From c83c8a1aa6eecac035536643e20914e3c85314b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 10:33:53 +0200 Subject: [PATCH 634/911] load cray-libsci versionless --- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 3 ++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index 9f424cdc02..b105aa0520 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - ('cray-libsci/13.0.1', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) + ('cray-libsci', EXTERNAL_MODULE), ('fftw/3.3.4.0', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 37804fbb5c..05afff31a0 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - ('cray-libsci/13.0.3', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) + ('cray-libsci', EXTERNAL_MODULE), # loaded by PrgEnv-gnu ('fftw/3.3.4.2', EXTERNAL_MODULE), ] -- GitLab From a49ebcb5cb34aa948f311f2b7801ce63f762dd8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 15:41:02 +0200 Subject: [PATCH 635/911] bump to latest versions (IPython 3.1.0), add Pygments dep for IPython --- ...IPython-3.1.0-intel-2015a-Python-2.7.9.eb} | 7 ++-- ...Q-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb} | 4 +-- ...Q-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb | 31 ------------------ ...Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 30 +++++++++++++++++ ...pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb | 32 +++++++++++++++++++ ...equests-2.6.2-intel-2015a-Python-2.7.9.eb} | 6 ++-- .../util-linux-2.22.2-intel-2015a.eb | 29 ----------------- ...l-2015a.eb => ZeroMQ-3.2.5-intel-2015a.eb} | 6 ++-- 8 files changed, 74 insertions(+), 71 deletions(-) rename easybuild/easyconfigs/i/IPython/{IPython-3.0.0-intel-2015a-Python-2.7.9.eb => IPython-3.1.0-intel-2015a-Python-2.7.9.eb} (88%) rename easybuild/easyconfigs/p/PyZMQ/{PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb => PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb} (94%) delete mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb create mode 100644 easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb rename easybuild/easyconfigs/r/requests/{requests-2.6.0-intel-2015a-Python-2.7.9.eb => requests-2.6.2-intel-2015a-Python-2.7.9.eb} (80%) delete mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb rename easybuild/easyconfigs/z/ZeroMQ/{ZeroMQ-3.2.2-intel-2015a.eb => ZeroMQ-3.2.5-intel-2015a.eb} (93%) diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb similarity index 88% rename from easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index bda10584b8..377e678904 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.0.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'IPython' -version = '3.0.0' +version = '3.1.0' homepage = 'http://ipython.org/index.html' description = """IPython provides a rich architecture for interactive computing with: @@ -24,8 +24,9 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), ('pysqlite', '2.6.3', versionsuffix), - ('PyZMQ', '14.5.0', '%s-zmq3' % versionsuffix), - ('requests', '2.6.0', versionsuffix) + ('PyZMQ', '14.6.0', '%s-zmq3' % versionsuffix), + ('requests', '2.6.2', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), ] # override extensions sanity check, default filter that imports a Python module doesn't work here diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb similarity index 94% rename from easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb rename to easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb index b297340fc3..182cf6eed5 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.5.0-intel-2015a-Python-2.7.9-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'PyZMQ' -version = '14.5.0' +version = '14.6.0' homepage = 'http://www.zeromq.org/bindings:python' description = """Python bindings for ZeroMQ""" @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' pythonshortversion = ".".join(pythonversion.split(".")[0:2]) -zmqversion = '3.2.2' +zmqversion = '3.2.5' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb deleted file mode 100644 index 022cf3fe3b..0000000000 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-intel-2015a-Python-2.7.9-zmq3.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'PyZMQ' -version = '2.2.0.1' - -homepage = 'http://www.zeromq.org/bindings:python' -description = """Python bindings for ZeroMQ""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -python = 'Python' -pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) -zmqversion = '3.2.2' - -versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) - -dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), -] - -options = {'modulename': 'zmq'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..c6557db043 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..cbbee774d8 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb similarity index 80% rename from easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb rename to easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb index 4a577a2051..c746104f6f 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.6.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'requests' -version = '2.6.0' +version = '2.6.2' homepage = 'https://pypi.python.org/pypi/requests/2.6.0' description = """Python http for humans""" @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +pyshortver = ".".join(pythonversion.split(".")[0:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -23,7 +23,7 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pythonshortversion, version, pythonshortversion) ], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb deleted file mode 100644 index 7cdce40ba2..0000000000 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-intel-2015a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'util-linux' -version = '2.22.2' - -homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' -description = """Set of Linux utilities""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] -sources = [SOURCELOWER_TAR_GZ] - -# disable account related utilities (they need OS dependant pam-devel files) -# disable wall and friends (requires group changing permissions for install user) -# install systemd service files in install dir -configopts = '--disable-chfn-chsh --disable-login --disable-su ' -configopts += '--disable-wall --disable-use-tty-group ' -configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' -configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " - -dependencies = [('ncurses', '5.9')] - -sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb similarity index 93% rename from easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb rename to easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb index 537584a82a..19243eab21 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'ZeroMQ' -version = '3.2.2' +version = '3.2.5' homepage = 'http://www.zeromq.org/' description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. @@ -16,7 +16,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://download.zeromq.org/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['ZeroMQ-%(version)s_icc.patch'] +patches = ['ZeroMQ-3.2.2_icc.patch'] # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' @@ -25,7 +25,7 @@ configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2'), + ('util-linux', '2.26.1'), ] sanity_check_paths = { -- GitLab From 77d9f566d3b11b2445277589eba80aacf845a598 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2015 15:46:50 +0200 Subject: [PATCH 636/911] minor style fixes --- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb | 4 ++-- .../p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb | 5 ++--- .../p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb | 3 +-- .../r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb | 3 +-- 4 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb index 9ac5fd9480..bb2adb94d7 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -12,8 +12,8 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] -sources = ['%s-%s.tar.gz' % ('libpgm', version)] +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb index 182cf6eed5..e38ac2e143 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) zmqversion = '3.2.5' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) @@ -27,8 +27,7 @@ options = {'modulename': 'zmq'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb index c6557db043..06251d7872 100644 --- a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -27,4 +27,3 @@ sanity_check_paths = { } moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb index c746104f6f..c8c3ba9720 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.9' -pyshortver = ".".join(pythonversion.split(".")[0:2]) +pyshortver = '.'.join(pythonversion.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pythonversion) @@ -27,4 +27,3 @@ sanity_check_paths = { } moduleclass = 'devel' - -- GitLab From dac9ed1317d25a0ef9bb73f54dcd6d23357698d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 01:38:53 +0200 Subject: [PATCH 637/911] don't include cray-libsci as direct toolchain component --- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb | 5 ++++- easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb | 5 ++++- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb | 4 +--- easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb | 4 +--- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb | 5 ++++- easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb | 5 ++++- 6 files changed, 18 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb index f5df8a066a..766d96d756 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb index 524d8e18e6..7a2e621e24 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb index b105aa0520..b3e7499933 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -9,9 +9,7 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) - ('cray-libsci', EXTERNAL_MODULE), + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci ('fftw/3.3.4.0', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb index 05afff31a0..4015746894 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -9,9 +9,7 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module. toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), - # cray-libsci is intentionally loaded with specifying a version, loaded by PrgEnv-gnu (version is site-specific) - ('cray-libsci', EXTERNAL_MODULE), # loaded by PrgEnv-gnu + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci ('fftw/3.3.4.2', EXTERNAL_MODULE), ] diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb index 8e4b5fe50e..7c17b80f7e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.0', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb index b460d5e453..edaac85f54 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -8,6 +8,9 @@ description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel modul toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('fftw/3.3.4.2', EXTERNAL_MODULE)] +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] moduleclass = 'toolchain' -- GitLab From 0ec82f30b35190fcb0b0c6044892a96c7a9b5865 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 14:21:29 +0200 Subject: [PATCH 638/911] add HPL easyconfigs using Cray toolchains --- .../h/HPL/HPL-2.1-CrayCCE-5.1.29.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.25.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.1.29.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.25.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.1.29.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.25.eb | 18 +++++++++++++++ .../easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch | 11 ++++++++++ 7 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb new file mode 100644 index 0000000000..a7abc8534e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb new file mode 100644 index 0000000000..109c7ddafc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..806d976659 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..b4acf0c1bc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb new file mode 100644 index 0000000000..c8cac688c8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.1.29'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb new file mode 100644 index 0000000000..0344d227a5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.25'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch new file mode 100644 index 0000000000..d0e0a51bc5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch @@ -0,0 +1,11 @@ +--- hpl-2.1/makes/Make.ptest.orig 2015-04-25 13:46:18.668624435 +0200 ++++ hpl-2.1/makes/Make.ptest 2015-04-25 13:47:20.958060830 +0200 +@@ -73,7 +73,7 @@ + ( $(CP) ../HPL.dat $(BINdir) ) + # + dexe.grd: $(HPL_pteobj) $(HPLlib) +- $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) ++ LINKER=`which ld` $(CC) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) + $(MAKE) $(BINdir)/HPL.dat + $(TOUCH) dexe.grd + # -- GitLab From e902fa555ec2d11b51bd154740345d2087ea36bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Apr 2015 14:29:08 +0200 Subject: [PATCH 639/911] fix HPL patch + add description --- easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch index d0e0a51bc5..799444d4e2 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch @@ -1,3 +1,5 @@ +Cray compiler don't like having $LINKER set to a non-absolute path +author: Kenneth Hoste (HPC-UGent) --- hpl-2.1/makes/Make.ptest.orig 2015-04-25 13:46:18.668624435 +0200 +++ hpl-2.1/makes/Make.ptest 2015-04-25 13:47:20.958060830 +0200 @@ -73,7 +73,7 @@ @@ -5,7 +7,7 @@ # dexe.grd: $(HPL_pteobj) $(HPLlib) - $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) -+ LINKER=`which ld` $(CC) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) ++ LINKER=`which ld` $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) $(MAKE) $(BINdir)/HPL.dat $(TOUCH) dexe.grd # -- GitLab From 77df251fcd68b611bb4e93f021d1452ce83de448 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:19:35 +0200 Subject: [PATCH 640/911] use proper Bundle easyblock for biodeps/PRACE --- .../easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 0a0256d97d..428ecbe9cf 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb index d8d026cace..6fcc534d72 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 878f45a16d..34a00add44 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb index 63eda1f427..1091497ff7 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 061dd6e110..849c3d613e 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index 84d13bb360..63cc6c8164 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' -- GitLab From 7cce6b48a59220705d011495b069f79d1d6f35c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:25:05 +0200 Subject: [PATCH 641/911] bump version to 2.1.0 and update release notes --- RELEASE_NOTES | 39 ++++++++++++++++++++++++++++++++++++--- setup.py | 4 ++-- 2 files changed, 38 insertions(+), 5 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b504cb01ce..b83a7af107 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,16 +3,49 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 581 different software packages, -32 different (compiler) toolchains and 6 software bundles. +The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 608 different software packages, +33 different (compiler) toolchains and 8 software bundles. +v2.1.0 (April 28th 2015) +------------------------ + +- added example easyconfig files for 27 new software packages: + AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530), + mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036), + Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536), + seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369), + Xmipp (#1489) +- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE + - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3, PETSc/SLEPc v3.5.3, WIEN2k v14.1 +- various other enhancements, including: + - include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540) + - include SQLite as dependency in Python v2.7.9 easyconfigs (#1468) + - set $LD_PRELOAD for Hoard and jemalloc (#1470) + - fix homepage in SCOTCH easyconfigs (#1485) + - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) + - enable pic option in expat easyconfigs (#1562) +- various bug fixes, including: + - adding missing zlib dependency in all Tcl easyconfig files (#1344) + - fix homepage in FLUENT easyconfigs (#1472) + - use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511) + - stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512) + - replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532) + - stop relying on $MKLROOT in ROOT easyconfigs (#1537) + - use proper Bundle easyblock for biodeps/PRACE (#1566) v2.0.0 (March 6th 2015) ----------------------- feature + bugfix release - added example easyconfig files for 29 new software packages: - bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) + bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), + fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), + jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), + rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), + ZPAQ (#1242) - added easyconfigs for new (common) toolchains foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) - added new software bundle: Autotools (#1385) diff --git a/setup.py b/setup.py index e23ed2d782..5b55ee3e55 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2013 Ghent University +# Copyright 2012-2015 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "2.1.0dev" +VERSION = '2.1.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 91460c6b94ed03715d96d93760f19ee04974fcca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 16:52:27 +0200 Subject: [PATCH 642/911] add easyconfig for WRF + deps with CrayGNU --- .../j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb | 21 ++++++++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb | 39 ++++++++++++++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 41 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..feca7c584a --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000..6245093966 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'shared': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb new file mode 100644 index 0000000000..3806e63de1 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' -- GitLab From b8d75d3267feaad5e1e28db4577e8f1d383b3be1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:18:16 +0200 Subject: [PATCH 643/911] added http://www.bioconductor.org/packages/release/bioc/src/contrib/ as download url for bioconductor packages --- easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb | 4 +++- easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb | 4 +++- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 1 + easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 1 + easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 1 + 17 files changed, 45 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb index 8468c6029d..d91d0ca1fd 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb index 84d3f3e99e..517c6d157a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb index 70126d1ce6..b2152142eb 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb index 3a90cc17eb..9414cfc682 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb index 201aa6b636..4b3f70cab0 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb index 65f22fa5a8..4434fbdf2a 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb index 2672165c50..174451bf44 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb index 2f2b2a553e..cc29570d01 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb index 2d510cfe36..4b201ba947 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb index 3bc73c713b..5280f5e5c7 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb index 580cc3effd..8fababc358 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb index 1bda6f96bc..549134c6cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb index ba677bcf6d..e7c9c708cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb @@ -31,7 +31,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb index 37633fc50a..91ba061891 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb @@ -32,7 +32,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index e60a4bb6fd..d92fd5ff79 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index a73e438a8c..d111c454b9 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index 99a39db56a..a5cec405ac 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -34,6 +34,7 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', -- GitLab From 87026420edafa0ed4ca97bfc48ff6d1700adca52 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:23:49 +0200 Subject: [PATCH 644/911] updated urls for data and experiments data --- easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 2 ++ easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index d92fd5ff79..bcd67f42d0 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index d111c454b9..467f0009f8 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index a5cec405ac..813bbd8f5d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -35,6 +35,8 @@ ext_options = { bioconductor_options = { 'source_urls': [ 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', -- GitLab From 0c375816933c4bc1edb21de240aff26d2fb6a7e4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sun, 26 Apr 2015 17:33:48 +0200 Subject: [PATCH 645/911] added 3.1.3 easyconfigs --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 384 ++++++++++++++++++ .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 383 +++++++++++++++++ 2 files changed, 767 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb new file mode 100644 index 0000000000..ad11c875f8 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -0,0 +1,384 @@ +name = 'R' +version = '3.1.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.0', ext_options), + ('gtools', '3.4.1', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.4', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.2', ext_options), + ('markdown', '0.7.4', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '4.4', ext_options), + ('RANN', '2.4.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.6-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.5.5', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', 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('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-5', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-33', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '1.9-8', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('knitr', '1.9', ext_options), + ('statmod', '1.4.20', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('affyio', '1.34.0', bioconductor_options), + ('BiocInstaller', '1.16.2', bioconductor_options), + ('preprocessCore', '1.28.0', bioconductor_options), + ('affy', '1.44.0', bioconductor_options), + ('GO.db', '3.0.0', bioconductor_options), + ('limma', '3.22.7', bioconductor_options), + ('RBGL', '1.42.0', bioconductor_options), + ('org.Hs.eg.db', '3.0.0', bioconductor_options), + ('AnnotationForge', '1.8.2', bioconductor_options), + ('KEGG.db', '3.0.0', bioconductor_options), + ('annaffy', '1.38.0', bioconductor_options), + ('gcrma', '2.38.0', bioconductor_options), + ('oligoClasses', '1.28.0', bioconductor_options), + ('edgeR', '3.8.6', bioconductor_options), + ('PFAM.db', '3.0.0', bioconductor_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('baySeq', '2.0.50', bioconductor_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('qvalue', '1.43.0', bioconductor_options), + ('impute', '1.40.0', bioconductor_options), + ('matrixStats', '0.14.0', ext_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.20.0', bioconductor_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('hgu133plus2.db', '3.0.0', bioconductor_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.14', ext_options), + ('kohonen', '2.0.15', ext_options), + ('base64', '1.1', ext_options), + ('illuminaio', '0.8.0', bioconductor_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('bumphunter', '1.6.0', bioconductor_options), + ('multtest', '2.22.0', bioconductor_options), + ('siggenes', '1.40.0', bioconductor_options), + ('nleqslv', '2.6', ext_options), + ('DynDoc', '1.44.0', bioconductor_options), + ('genoset', '1.20.0', bioconductor_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('multtest', '2.22.0', bioconductor_options), + ('NOISeq', '2.8.0', bioconductor_options), + ('openxlsx', '2.4.0', ext_options), + ('Rgraphviz', '2.10.0', bioconductor_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('reshape', '0.8.5', ext_options), + ('RNASeqPower', '1.6.0', bioconductor_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('Rsubread', '1.16.1', bioconductor_options), +] + +moduleclass = 'lang' -- GitLab From 4c44a3dead34859d7935cd66ca44050fa455cf1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 20:26:47 +0200 Subject: [PATCH 646/911] include PR #1568 --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b83a7af107..2282d108e0 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -27,6 +27,7 @@ v2.1.0 (April 28th 2015) - fix homepage in SCOTCH easyconfigs (#1485) - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) - enable pic option in expat easyconfigs (#1562) + - extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568) - various bug fixes, including: - adding missing zlib dependency in all Tcl easyconfig files (#1344) - fix homepage in FLUENT easyconfigs (#1472) -- GitLab From 17301a204cb5c1c0e10ee7e914b8a47cf8d1b3ae Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 20:34:29 +0200 Subject: [PATCH 647/911] R-3.2.0-goolf-1.7.20-bare.eb --- .../libjpeg-turbo-1.4.0-goolf-1.7.20.eb | 24 +++++++++++++++++ .../l/libpng/libpng-1.6.16-goolf-1.7.20.eb | 19 +++++++++++++ .../libreadline-6.3-goolf-1.7.20.eb | 27 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-goolf-1.7.20.eb | 15 +++++++++++ .../r/R/R-3.2.0-goolf-1.7.20-bare.eb | 27 +++++++++++++++++++ 5 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000..4197b7c635 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/libjpeg-turbo/' +description = """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG +compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb new file mode 100644 index 0000000000..4132ab6f67 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000..5449121e0b --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb new file mode 100644 index 0000000000..a62ac8f668 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb new file mode 100644 index 0000000000..d1098337a7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From c5624f2f880159ee7d66a5dc2ff4e05b41306e5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 20:53:43 +0200 Subject: [PATCH 648/911] fix tests w.r.t. external modules and Cray toolchains --- test/easyconfigs/easyconfigs.py | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5d7ca77279..4516a938ed 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -50,6 +50,7 @@ from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, proce from easybuild.tools import config from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version +from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies @@ -66,7 +67,9 @@ class EasyConfigTest(TestCase): config.init(eb_go.options, eb_go.get_options_by_section('config')) build_options = { 'check_osdeps': False, + 'external_modules_metadata': {}, 'force': True, + 'optarch': 'test', 'robot_path': get_paths_for("easyconfigs")[0], 'suffix_modules_path': GENERAL_CLASS, 'valid_module_classes': config.module_classes(), @@ -75,8 +78,14 @@ class EasyConfigTest(TestCase): config.init_build_options(build_options=build_options) config.set_tmpdir() del eb_go - + + # mock 'exist' and 'load' methods of modules tool, which are used for 'craype' external module + modtool = modules_tool() + modtool.exist = lambda m: [True]*len(m) + modtool.load = lambda m: True + log = fancylogger.getLogger("EasyConfigTest", fname=False) + # make sure a logger is present for main main._log = log ordered_specs = None @@ -93,6 +102,15 @@ class EasyConfigTest(TestCase): for spec in specs: self.parsed_easyconfigs.extend(process_easyconfig(spec)) + # filter out external modules + for ec in self.parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + for dep in ec['unresolved_deps'][:]: + if dep.get('external_module', False): + ec['unresolved_deps'].remove(dep) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) def test_dep_graph(self): -- GitLab From d6b1c83d0a70d80bccfe1a787b99d0cb18319df8 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:00:51 +0200 Subject: [PATCH 649/911] added NASM-2.11.06-goolf-1.7.20.eb --- .../n/NASM/NASM-2.11.06-goolf-1.7.20.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb new file mode 100644 index 0000000000..8ece8f5082 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' -- GitLab From e8aa3700033275de4681eee55e4d20cd1271756f Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:01:47 +0200 Subject: [PATCH 650/911] changed java version to latest in 1.7.x branch --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index d1098337a7..764ce77013 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_79', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From bc48592638f68af71e4c9d2acd19e9c0e95d056d Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:07:12 +0200 Subject: [PATCH 651/911] added Java-1.7.0_80.eb --- easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb new file mode 100644 index 0000000000..9acb602fa1 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_80' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] + +moduleclass = 'lang' -- GitLab From 31327acc8bc46fae1fea637a2e1f68ad169273e5 Mon Sep 17 00:00:00 2001 From: Generic user for software management Date: Sun, 26 Apr 2015 21:23:43 +0200 Subject: [PATCH 652/911] bump java to 1.7.80 --- easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 764ce77013..ed4f2cd8f4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -19,7 +19,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_79', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] exts_list = [] -- GitLab From faa0b4476b12d727d2affcbff8243cb151e7458e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:24:55 +0200 Subject: [PATCH 653/911] {lang}[foss,intel/2015a] R 3.2.0 -bare --- .../r/R/R-3.2.0-foss-2015a-bare.eb | 27 +++++++++++++++++++ .../r/R/R-3.2.0-intel-2015a-bare.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb new file mode 100644 index 0000000000..db8d624ca1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb new file mode 100644 index 0000000000..db8d624ca1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.16'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' -- GitLab From 375755453436b11f29fc3335ce3279a32af04bcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:30:36 +0200 Subject: [PATCH 654/911] also mention R v3.2.0 --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2282d108e0..04333d14ff 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -19,7 +19,7 @@ v2.1.0 (April 28th 2015) - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... - including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3, PETSc/SLEPc v3.5.3, WIEN2k v14.1 + including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 - various other enhancements, including: - include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540) - include SQLite as dependency in Python v2.7.9 easyconfigs (#1468) -- GitLab From 2dfba5a330f4b2a07a42565163342b800b570ba3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2015 22:36:55 +0200 Subject: [PATCH 655/911] fix toolchain in R easyconfig --- easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb index db8d624ca1..84e71410fa 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -5,7 +5,7 @@ versionsuffix = '-bare' homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -toolchain = {'name': 'intel', 'version': '2015a'} +toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCE_TAR_GZ] source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] -- GitLab From cf2b5fee068415b589f0d9527298265dd6061607 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2015 09:07:35 +0200 Subject: [PATCH 656/911] enable retain_all_deps when resolving dependencies in easyconfig tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4516a938ed..838f4a2957 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -111,7 +111,7 @@ class EasyConfigTest(TestCase): if dep.get('external_module', False): ec['unresolved_deps'].remove(dep) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From ae9df0b0abcbe10010b17f04f2fc7150f67d318a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2015 10:12:58 +0200 Subject: [PATCH 657/911] bump version of libpng in R 3.2.0 easyconfigs --- .../l/libpng/libpng-1.6.17-foss-2015a.eb | 19 +++++++++++++++++++ .../l/libpng/libpng-1.6.17-goolf-1.7.20.eb | 19 +++++++++++++++++++ .../l/libpng/libpng-1.6.17-intel-2015a.eb | 19 +++++++++++++++++++ .../r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- 6 files changed, 60 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb new file mode 100644 index 0000000000..2519d4c46d --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb new file mode 100644 index 0000000000..8e90204af6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb new file mode 100644 index 0000000000..afab7cb441 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb index 84e71410fa..6cf2221cfd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb index ed4f2cd8f4..d8c3392f6a 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb index db8d624ca1..f4f7ec9970 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb @@ -17,7 +17,7 @@ configopts += " --with-recommended-packages=no" dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), - ('libpng', '1.6.16'), # for plotting in R + ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] -- GitLab From 3af0e7c932393ffdd18b5915d2fc087280fb0986 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 10:27:27 +0200 Subject: [PATCH 658/911] fix date and counts in release notes --- RELEASE_NOTES | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 04333d14ff..737619aa4f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,12 +3,13 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,344 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,617 easyconfig files, for 608 different software packages, 33 different (compiler) toolchains and 8 software bundles. -v2.1.0 (April 28th 2015) +v2.1.0 (April 30th 2015) ------------------------ +feature + bugfix release - added example easyconfig files for 27 new software packages: AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530), mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036), -- GitLab From d952c5b7d9d733b1ef5d8a90d7f4d9ea828432db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2015 10:45:47 +0200 Subject: [PATCH 659/911] fix long line --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 737619aa4f..84c44e6c5f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -49,7 +49,8 @@ feature + bugfix release rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) - added easyconfigs for new (common) toolchains - foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) + foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), + intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) - added new software bundle: Autotools (#1385) - various other enhancements, including: - don't define $LDSHARED in zlib easyconfigs (#1350) -- GitLab From 9276b84095c3561e9114abfda2155cdcd8656124 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 28 Apr 2015 17:10:06 +0200 Subject: [PATCH 660/911] Adjusted Cube download URL and tweaked build Requires https://github.com/hpcugent/easybuild-easyblocks/pull/552 --- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index a097385484..cd8e278f30 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -20,19 +20,21 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] patches = ['Cube-4.2_fix-Qt-version-check.patch'] dependencies = [('Qt', '4.8.4')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" - sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } +# If all prerequisites for the Cube Java reader are available on the system, +# parallel builds will fail. Alternatively, disable the Java reader using +# configopts = "--without-java-reader" +maxparallel = 1 + moduleclass = 'perf' -- GitLab From d8c294bcd0f997894d59d977a998c975727b5f6d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 28 Apr 2015 18:31:22 +0200 Subject: [PATCH 661/911] Adjusted Scalasca URL --- .../s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb index 1f62732cc1..b4c09a0c49 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb @@ -26,9 +26,8 @@ dependencies = [ ('OTF2', '1.2.1'), ] -# http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist/scalasca-2.0.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] sanity_check_paths = { 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], -- GitLab From 1b9d0beacdeccd8e77ac617239aae93598f7afa4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 07:46:01 +0200 Subject: [PATCH 662/911] include link to EB@Cray wiki page --- RELEASE_NOTES | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 84c44e6c5f..31240be8e3 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -18,6 +18,7 @@ feature + bugfix release Xmipp (#1489) - added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) + - see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray - added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 @@ -27,7 +28,7 @@ feature + bugfix release - set $LD_PRELOAD for Hoard and jemalloc (#1470) - fix homepage in SCOTCH easyconfigs (#1485) - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) - - enable pic option in expat easyconfigs (#1562) + - enable pic toolchain option in expat easyconfigs (#1562) - extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568) - various bug fixes, including: - adding missing zlib dependency in all Tcl easyconfig files (#1344) -- GitLab From a67f2a824517e5587b88992dfb75135988593f00 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 29 Apr 2015 10:18:54 +0200 Subject: [PATCH 663/911] Try to fix build issue by patching `configure` Provide updated easyconfig for Cube 4.3 (which should be used anyhow) --- .../c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 19 +- .../c/Cube/Cube-4.2_fix-with-qt-check.patch | 209 ++++++++++++++++++ .../c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb | 40 ++++ 3 files changed, 261 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index cd8e278f30..b578e14673 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,6 +1,7 @@ # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr +# Authors:: Markus Geimer # License:: New BSD # # This work is based from experiences from the UNITE project @@ -23,18 +24,22 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -patches = ['Cube-4.2_fix-Qt-version-check.patch'] +patches = [ + 'Cube-4.2_fix-Qt-version-check.patch', + 'Cube-4.2_fix-with-qt-check.patch', +] dependencies = [('Qt', '4.8.4')] +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + sanity_check_paths = { 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], 'dirs': ["include/cube", "include/cubew"], } -# If all prerequisites for the Cube Java reader are available on the system, -# parallel builds will fail. Alternatively, disable the Java reader using -# configopts = "--without-java-reader" -maxparallel = 1 - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch new file mode 100644 index 0000000000..5ea89bb644 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch @@ -0,0 +1,209 @@ +--- build-backend/configure.orig 2013-08-02 13:20:33.000000000 +0200 ++++ build-backend/configure 2015-04-29 09:56:00.891697331 +0200 +@@ -19819,6 +19819,8 @@ $as_echo "$at_darwin" >&6; } + + # Find qmake. + ++ if test "x$QT_PATH" == "x"; then : ++ + for ac_prog in qmake-qt4 qmake + do + # Extract the first word of "$ac_prog", so it can be a program name with args. +@@ -19867,6 +19869,57 @@ done + test -n "$QMAKE" || QMAKE="missing" + + ++else ++ ++ for ac_prog in qmake ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_QMAKE+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $QMAKE in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_QMAKE="$QMAKE" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$QT_PATH:$QT_DIR:$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_QMAKE="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++QMAKE=$ac_cv_path_QMAKE ++if test -n "$QMAKE"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $QMAKE" >&5 ++$as_echo "$QMAKE" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$QMAKE" && break ++done ++test -n "$QMAKE" || QMAKE="missing" ++ ++ ++fi + if test x"$QMAKE" = xmissing; then + as_fn_error $? "Cannot find qmake in your PATH. Try to specify the exact path using the option --with-qt= or to switch off the compilation of gui using option --without-gui." "$LINENO" 5 + break +@@ -20309,7 +20362,59 @@ $as_echo "$at_cv_qt_build" >&6; } + + # Find moc (Meta Object Compiler). + +- for ac_prog in moc-qt4 moc ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in moc-qt4 moc ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_MOC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $MOC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_MOC="$MOC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_MOC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++MOC=$ac_cv_path_MOC ++if test -n "$MOC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MOC" >&5 ++$as_echo "$MOC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$MOC" && break ++done ++test -n "$MOC" || MOC="missing" ++ ++ ++else ++ ++ for ac_prog in moc + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20356,6 +20461,8 @@ fi + done + test -n "$MOC" || MOC="missing" + ++ ++fi + if test x"$MOC" = xmissing; then + as_fn_error $? "Cannot find moc (Meta Object Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break +@@ -20364,7 +20471,59 @@ test -n "$MOC" || MOC="missing" + + # Find uic (User Interface Compiler). + +- for ac_prog in uic-qt4 uic ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in uic-qt4 uic ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_UIC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $UIC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_UIC="$UIC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_UIC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++UIC=$ac_cv_path_UIC ++if test -n "$UIC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $UIC" >&5 ++$as_echo "$UIC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$UIC" && break ++done ++test -n "$UIC" || UIC="missing" ++ ++ ++else ++ ++ for ac_prog in uic + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20411,6 +20570,8 @@ fi + done + test -n "$UIC" || UIC="missing" + ++ ++fi + if test x"$UIC" = xmissing; then + as_fn_error $? "Cannot find uic (User Interface Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000..0a2aec777e --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Authors:: Markus Geimer +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.3" + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +dependencies = [('Qt', '4.8.4')] + +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support is has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + +sanity_check_paths = { + 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' -- GitLab From 0a8c2c2c2df86ed790eee92024a2dc1ce8ac08fb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 29 Apr 2015 11:17:57 +0200 Subject: [PATCH 664/911] Add comment that patches are no longer required for Cube 4.2.2 and up --- easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index b578e14673..941a048ad1 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -24,6 +24,7 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +# Backported fixes included in Cube 4.2.2 and up patches = [ 'Cube-4.2_fix-Qt-version-check.patch', 'Cube-4.2_fix-with-qt-check.patch', -- GitLab From 454e95a3227952c3e1d4743bf5882af4644e303e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:25:43 +0200 Subject: [PATCH 665/911] dummy --- easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb new file mode 100644 index 0000000000..e69de29bb2 -- GitLab From 995c8f51d24a0ee8950f96471e01d87b18d54226 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 29 Apr 2015 12:34:10 +0200 Subject: [PATCH 666/911] HMMER 3.1b2 with intel-2015a --- .../h/HMMER/HMMER-3.1b2-intel-2015a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index e69de29bb2..5255f85ddc 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.janelia.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] +source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", + "esl-alimap", "esl-cluster", "esl-mask"]], + 'dirs': [] +} + +runtest = 'check' + +moduleclass = 'bio' -- GitLab From 5da3932cb8ae56f330d05e98c9406cc155a4d4a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2015 22:36:23 +0200 Subject: [PATCH 667/911] include PR #1574 in release notes --- RELEASE_NOTES | 2 ++ 1 file changed, 2 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 31240be8e3..9cda838d2c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -38,6 +38,8 @@ feature + bugfix release - replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532) - stop relying on $MKLROOT in ROOT easyconfigs (#1537) - use proper Bundle easyblock for biodeps/PRACE (#1566) + - make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574) + - add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574) v2.0.0 (March 6th 2015) ----------------------- -- GitLab From 1272d0e0570333f0a362b1d8dbe751cc64cfb14a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 08:54:20 +0200 Subject: [PATCH 668/911] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9cda838d2c..c00535497a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,617 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,618 easyconfig files, for 608 different software packages, 33 different (compiler) toolchains and 8 software bundles. v2.1.0 (April 30th 2015) -- GitLab From 80e714ed681c330694fbf27ab62462db2ab04ce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 13:36:11 +0200 Subject: [PATCH 669/911] bump version to v2.1.x --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5b55ee3e55..e89248dca4 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.0' +VERSION = '2.1.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 172dc89ec881e00da3be3a32b133013bc46769b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 16:06:57 +0200 Subject: [PATCH 670/911] bump version to v2.2.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e89248dca4..9e5dd5137c 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.1dev' +VERSION = '2.2.0dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 0a603f9b0f666e4127d34e8b6b1686c27979ee7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 671/911] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From bd4e4c8b7189166116c41cced62fd385e1872741 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 672/911] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From f7adb79305616713b1d28b24b466e84669642750 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 4 May 2015 09:49:11 +0200 Subject: [PATCH 673/911] BLAST+ with foss 2015a --- .../BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..37178f8aa5 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = "2.2.30" +versionsuffix = '-Python-2.7.9' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + -- GitLab From 64389a02f3dfaec9bf1cb98ea088df5d96e98d36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2015 00:34:47 +0300 Subject: [PATCH 674/911] {geo}[foss/2015a] WRF 3.6.1 --- .../b/Bison/Bison-3.0.2-foss-2015a.eb | 22 ++++++++++ .../c/CMake/CMake-3.0.0-foss-2015a.eb | 22 ++++++++++ .../c/cURL/cURL-7.37.1-foss-2015a.eb | 27 +++++++++++++ .../d/Doxygen/Doxygen-1.8.7-foss-2015a.eb | 18 +++++++++ .../f/flex/flex-2.5.39-foss-2015a.eb | 14 +++++++ .../h/HDF5/HDF5-1.8.13-foss-2015a.eb | 25 ++++++++++++ .../j/JasPer/JasPer-1.900.1-foss-2015a.eb | 21 ++++++++++ .../easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb | 23 +++++++++++ .../netCDF-Fortran-4.4.0-foss-2015a.eb | 17 ++++++++ .../n/netCDF/netCDF-4.3.2-foss-2015a.eb | 31 ++++++++++++++ .../t/tcsh/tcsh-6.18.01-foss-2015a.eb | 38 ++++++++++++++++++ .../w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb | 40 +++++++++++++++++++ 12 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb new file mode 100644 index 0000000000..0b270e9381 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb new file mode 100644 index 0000000000..c55a48656c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb new file mode 100644 index 0000000000..0ba45ba9e5 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb new file mode 100644 index 0000000000..6fae2382dd --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +homepage = 'http://www.doxygen.org' +description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb new file mode 100644 index 0000000000..f9226ff5f3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb new file mode 100644 index 0000000000..f79d365b61 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.13' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb new file mode 100644 index 0000000000..02cb1d4f4c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb new file mode 100644 index 0000000000..411820a76b --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb new file mode 100644 index 0000000000..d623122642 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'netCDF-Fortran' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000..8319de8066 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -0,0 +1,31 @@ +name = 'netCDF' +version = '4.3.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb new file mode 100644 index 0000000000..4b5f7237ff --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb new file mode 100644 index 0000000000..5e773ca4e8 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_netCDF-Fortran_separate_path.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' -- GitLab From 638cc7d093d42f9d64b55820f73c2dd75391b28a Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Tue, 5 May 2015 16:00:36 +0200 Subject: [PATCH 675/911] Adding the easyconfigs for ictce-7.3.5 --- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 17 ++++++++++++++ .../i/iccifort/iccifort-2015.3.187.eb | 16 ++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 21 ++++++++++++++++++ .../easyconfigs/i/ifort/ifort-2015.3.187.eb | 17 ++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 18 +++++++++++++++ .../i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 22 +++++++++++++++++++ .../impi-5.0.3.048-iccifort-2015.3.187.eb | 19 ++++++++++++++++ 7 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb new file mode 100644 index 0000000000..55dec91be5 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb new file mode 100644 index 0000000000..8387432380 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version), + ('ifort', version), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb new file mode 100644 index 0000000000..6190ed2906 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '3.187' +compver = '2015.%s' % suff + +dependencies = [ # version/released + ('icc', compver), # Apr 13th 2015 + ('ifort', compver), # Apr 13th 2015 + ('impi', '5.0.3.048', '', ('iccifort', compver)), # Feb 10th 2015 + ('imkl', '11.2.%s' % suff, '', ('iimpi', version)), # Apr 13th 2015 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb new file mode 100644 index 0000000000..8253a3390b --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb new file mode 100644 index 0000000000..b0fe67cb26 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.3.187' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '5.0.3.048', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb new file mode 100644 index 0000000000..807b5f2004 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.3.5'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..5e0972d8f3 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 26de6e35ca028edfc16dbf44ec58e1858b45e426 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:36:05 +0200 Subject: [PATCH 676/911] Boost 1.58 for intel/2015a --- .../Boost-1.58.0-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..a209577bba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3568cde808c6d65622e0581414372da7c1ffd687 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:37:17 +0200 Subject: [PATCH 677/911] Boost 1.58.0 for foss/2015a --- .../Boost-1.58.0-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bbef8b760b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From abee1f0f0dd2f23cdb08bb9aaeb504a80ea11d6f Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Wed, 6 May 2015 11:31:15 +0200 Subject: [PATCH 678/911] Adding HPL 2.1 with ictce-7.3.5 --- .../easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb new file mode 100644 index 0000000000..55ab924d7d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From 633e68830ef8be546092e0d16857af624dfe44b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2015 15:59:13 +0300 Subject: [PATCH 679/911] enable usempi in GROMACS Cray easyconfig, the easyblock enables MPI support on it --- .../easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb index c7618bc1f3..1aa3886405 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -19,6 +19,7 @@ description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz source_urls = [ -- GitLab From b9f89c0d31ee7e48beac5dcb6e6383313d9ed13d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 680/911] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 8ab052fa8bfff470f7e635ae25fc48d555dcfaa9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 681/911] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From c834c42978d09f4ada1be3fc9ef552c6c74d6f5b Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:42:44 +0200 Subject: [PATCH 682/911] added even newer cutadapt --- ...cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1c463c28a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.8.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From c1a99608bf96df972dc4e1b30ee639db3bae71f5 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:56:11 +0200 Subject: [PATCH 683/911] fixed filename --- ...b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.5-intel2014b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} (100%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb similarity index 100% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb -- GitLab From 955ec3e9a236d4fc3fd0687ea16ccc79d1e8eb6e Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 10:19:56 +0200 Subject: [PATCH 684/911] fixed remarks --- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 9be9435a32..8a431e4a45 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 1c463c28a1..737e7e93bb 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } moduleclass = 'bio' - -- GitLab From 9bb645985ef91f8119d1f8e860e01050f8c4a3c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 11:14:44 +0200 Subject: [PATCH 685/911] add easyconfig for networkx --- ...networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6ae1e74b7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.9.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'tools' -- GitLab From 21ae64206431c783930c3a153769ea138f950518 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 15:23:36 +0200 Subject: [PATCH 686/911] add easyconfig for scikit-learn v0.16.1 --- ...t-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..8b997036dd --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' -- GitLab From 76564b498593ea34b852f40d935011b16ef293ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 22:06:49 +0200 Subject: [PATCH 687/911] list tcsh as build dep in WRF built with CrayGNU, rather than providing it as a build dep --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index 3806e63de1..aecb28f087 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -16,7 +16,10 @@ source_urls = [ ] # csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] +# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) +# ncurses related issue? rebuild tcsh without EB-provided ncurses? +#builddependencies = [('tcsh', '6.18.01')] +osdependencies = ['tcsh'] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From ba29611f7e2ffd4e6bd2232ff367088395e06a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 11:37:19 +0200 Subject: [PATCH 688/911] add easyconfig for Platanus (binary) --- .../p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb new file mode 100644 index 0000000000..c7b0660395 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -0,0 +1,20 @@ +easyblock = 'Binary' + +name = 'Platanus' +version = '1.2.1' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] +sources = ['platanus'] +checksums = ['02cf92847ec704d010a54df293b9c60a'] + +sanity_check_paths = { + 'files': ['platanus'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From a66a1e81e0bb6298a540ec3e86b23c8e48785836 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 14:39:33 +0200 Subject: [PATCH 689/911] fix versionsuffix in Platanus easyconfig --- easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb index c7b0660395..2fa31617c3 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -2,6 +2,7 @@ easyblock = 'Binary' name = 'Platanus' version = '1.2.1' +versionsuffix = '-linux-x86_64' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" -- GitLab From 85fedfc05c73a04c7d63b0bc8bf6f86894cbc518 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 May 2015 14:42:47 +0200 Subject: [PATCH 690/911] added python 3.4.3 intel 2015a --- .../p/Python/Python-3.4.3-intel-2015a.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb new file mode 100644 index 0000000000..d0fad95102 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '3.4.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] -- GitLab From 6efa2756f2aa3c60766659f37892daa6eddb47c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 691/911] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From f8578e3c2d71882e2529fc3d359c034c74b2f276 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 692/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From d6c783a9bb34da485da46ea42fa3887340aa7026 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 693/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 038bff909bf6a5d4d345cd8eb2830ce76a4e1f3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:08:13 +0200 Subject: [PATCH 694/911] {bio}[intel/2015a] SaguaroGW --- .../SaguaroGW-20150315-intel-2015a.eb | 31 +++++++++++++++++++ .../SaguaroGW/SaguaroGW_icpc-drop-const.patch | 15 +++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb new file mode 100644 index 0000000000..e922e754a3 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SaguaroGW' +version = '20150315' + +homepage = 'http://sourceforge.net/projects/saguarogw/' +description = """Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, + or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in +the genome.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] +# SVN revision r29 +sources = ['%(namelower)s-code-29.zip'] + +patches = ['SaguaroGW_icpc-drop-const.patch'] + +buildopts = 'CPLUSPLUS="$CXX" CC="$CC" OPEN_MP=yes' + +files_to_copy = [(['checkLock', 'CactiCorrelate', 'ChromoPaintCacti', 'ClusterCacti', 'Fasta2HMMFeature', + 'Genotype2HMMFeature', 'FilterCacti', 'HMMClassify', 'HMMTrain', 'HeatMaps', 'LocalTrees', + 'Maf2HMMFeature', 'PullFromFasta', 'Saguaro', 'Saguaro2Phylip', 'VCF2HMMFeature'], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch new file mode 100644 index 0000000000..193b028341 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch @@ -0,0 +1,15 @@ +fix issue with Intel compilers: 'the object has cv-qualifiers that are not compatible with the member function' +author: Kenneth Hoste (Ghent University) +--- /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h.orig 2012-05-16 15:40:12.000000000 +0200 ++++ /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h 2015-05-12 21:54:40.830166431 +0200 +@@ -39,8 +39,8 @@ + string GetName() { return mName; } + string GetDescription() { return mDesc; } + +-friend bool operator< (const commandArg &lhs, +- const commandArg &rhs) ++friend bool operator< (commandArg &lhs, ++ commandArg &rhs) + { + if ( lhs.GetName() < rhs.GetName() ) + return true; -- GitLab From 8a4c1d8fab0c700d8b32108e1d40dd77289a7fa2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:09:26 +0200 Subject: [PATCH 695/911] add MD5sum for SaguaroGW source tarball --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index e922e754a3..994bf42a7a 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -14,6 +14,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] # SVN revision r29 sources = ['%(namelower)s-code-29.zip'] +checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 4a76afbf4b79f2881f62f7352ee47fcc2e05937d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 697/911] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From d87786a613a0fc99572a3bd415e11662073f0f0d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 698/911] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From 3bce5c75ec8ff9e05fbf0bfda372b549384fb88a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 699/911] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 74d3f2808207c46f434390cb41480c539671a58f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 700/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 0c3e0073a7d4fd768f2bbbc753ede3023134ab15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 701/911] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 004eb26fd47c91b8d1093bd7be9263b6369629cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 703/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From 9b3e2a9aef90b62b554a9d2f2428ee41fe239ec2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 09:51:36 +0200 Subject: [PATCH 705/911] drop source_urls that are not guaranteed to work --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 994bf42a7a..897d3c2fd1 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -11,8 +11,7 @@ the genome.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True} -source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] -# SVN revision r29 +# SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] -- GitLab From 2ec310d55af639adf4b321f603fa8eb459196c24 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 13 May 2015 12:06:31 +0200 Subject: [PATCH 706/911] added python 3.4.1 with intel 2015a toolchain --- .../p/Python/Python-3.4.1-intel-2015a.eb | 103 ++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb new file mode 100644 index 0000000000..5769376b00 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -0,0 +1,103 @@ +name = 'Python' +version = '3.4.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-3.4_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + # tarball has changed upstream, so make sure we get the right version by verifying the checksum + 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' -- GitLab From 7c14eff85d3a767241c9f1b6f12a1f02e44b1ac4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:07:27 +0200 Subject: [PATCH 707/911] remove checksum, tarball is generated on the fly and checksum changes --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 897d3c2fd1..6edbc50c07 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -13,7 +13,6 @@ toolchainopts = {'openmp': True} # SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] -checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From b814e63fbf2f108f325f3abf42fa0fb222f27917 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:14:58 +0200 Subject: [PATCH 708/911] bump extension versions in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d0fad95102..a2c2596145 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.9.1' -scipyversion = '0.14.1' +numpyversion = '1.9.2' +scipyversion = '0.15.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # package versions updated Jan 19th 2015 exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ - ('setuptools', '11.3.1', { + ('setuptools', '15.2', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '6.0.6', { + ('pip', '6.1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('nose', '1.3.4', { + ('nose', '1.3.6', { 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { @@ -56,32 +56,32 @@ exts_list = [ ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), - ('argparse', '1.2.1', { + ('argparse', '1.3.0', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.8', { + ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.21.2', { + ('Cython', '0.22', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.0', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), - ('deap', '1.0.1', { + ('deap', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '3.4.0', { + ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), - ('arff', '2.0.1', { + ('arff', '2.0.2', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), @@ -89,7 +89,7 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('ecdsa', '0.11', { + ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), ('paramiko', '1.15.2', { @@ -101,7 +101,7 @@ exts_list = [ ('netifaces', '0.10.4', { 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], }), - ('netaddr', '0.7.13', { + ('netaddr', '0.7.14', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] -- GitLab From bfc912718ffdaf2b07149143595abc3c3ad7ade1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:20:45 +0200 Subject: [PATCH 709/911] fix argparse source URL --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a2c2596145..eca8e6a7b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], -- GitLab From f4b269542e2687feab55a0a7e8b6a6e91534974b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:25:24 +0200 Subject: [PATCH 710/911] fix deap source template --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index eca8e6a7b9..9e5af7e518 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,6 +76,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.2', { -- GitLab From 8196de12be7227bd95d891f4b0229974abae8c3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:41:14 +0200 Subject: [PATCH 711/911] {system}[intel/2015a] OpenSSL 1.0.1m --- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 ++ .../OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch | 343 ++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch | 116 ++++++ 3 files changed, 483 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..7665ce0775 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch new file mode 100644 index 0000000000..e30b04902b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch @@ -0,0 +1,343 @@ +Fixes build with make -jx, where x is greater than 1 +based on patch for 1.0.1e by Armin K. +diff -ru openssl-1.0.1m.orig/crypto/Makefile openssl-1.0.1m/crypto/Makefile +--- openssl-1.0.1m.orig/crypto/Makefile 2015-03-19 14:38:24.000000000 +0100 ++++ openssl-1.0.1m/crypto/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -85,11 +85,11 @@ + @if [ -z "$(THIS)" ]; then $(MAKE) -f $(TOP)/Makefile reflect THIS=$@; fi + + subdirs: +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +- @target=files; $(RECURSIVE_MAKE) ++ +@target=files; $(RECURSIVE_MAKE) + + links: + @$(PERL) $(TOP)/util/mklink.pl ../include/openssl $(EXHEADER) +@@ -100,7 +100,7 @@ + # lib: $(LIB): are splitted to avoid end-less loop + lib: $(LIB) + @touch lib +-$(LIB): $(LIBOBJ) ++$(LIB): $(LIBOBJ) | subdirs + $(AR) $(LIB) $(LIBOBJ) + [ -z "$(FIPSLIBDIR)" ] || $(AR) $(LIB) $(FIPSLIBDIR)fipscanister.o + $(RANLIB) $(LIB) || echo Never mind. +@@ -111,7 +111,7 @@ + fi + + libs: +- @target=lib; $(RECURSIVE_MAKE) ++ +@target=lib; $(RECURSIVE_MAKE) + + install: + @[ -n "$(INSTALLTOP)" ] # should be set by top Makefile... +@@ -120,7 +120,7 @@ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + lint: + @target=lint; $(RECURSIVE_MAKE) +diff -ru openssl-1.0.1m.orig/engines/Makefile openssl-1.0.1m/engines/Makefile +--- openssl-1.0.1m.orig/engines/Makefile 2015-03-19 14:38:35.000000000 +0100 ++++ openssl-1.0.1m/engines/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -72,7 +72,7 @@ + + all: lib subdirs + +-lib: $(LIBOBJ) ++lib: $(LIBOBJ) | subdirs + @if [ -n "$(SHARED_LIBS)" ]; then \ + set -e; \ + for l in $(LIBNAMES); do \ +@@ -89,7 +89,7 @@ + + subdirs: + echo $(EDIRS) +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +@@ -128,7 +128,7 @@ + mv -f $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx.new $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx ); \ + done; \ + fi +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + tags: + ctags $(SRC) +diff -ru openssl-1.0.1m.orig/Makefile.org openssl-1.0.1m/Makefile.org +--- openssl-1.0.1m.orig/Makefile.org 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Makefile.org 2015-03-31 12:14:56.071786835 +0200 +@@ -273,17 +273,17 @@ + build_libs: build_crypto build_ssl build_engines + + build_crypto: +- @dir=crypto; target=all; $(BUILD_ONE_CMD) +-build_ssl: +- @dir=ssl; target=all; $(BUILD_ONE_CMD) +-build_engines: +- @dir=engines; target=all; $(BUILD_ONE_CMD) +-build_apps: +- @dir=apps; target=all; $(BUILD_ONE_CMD) +-build_tests: +- @dir=test; target=all; $(BUILD_ONE_CMD) +-build_tools: +- @dir=tools; target=all; $(BUILD_ONE_CMD) ++ +@dir=crypto; target=all; $(BUILD_ONE_CMD) ++build_ssl: build_crypto ++ +@dir=ssl; target=all; $(BUILD_ONE_CMD) ++build_engines: build_crypto ++ +@dir=engines; target=all; $(BUILD_ONE_CMD) ++build_apps: build_libs ++ +@dir=apps; target=all; $(BUILD_ONE_CMD) ++build_tests: build_libs ++ +@dir=test; target=all; $(BUILD_ONE_CMD) ++build_tools: build_libs ++ +@dir=tools; target=all; $(BUILD_ONE_CMD) + + all_testapps: build_libs build_testapps + build_testapps: +@@ -538,9 +538,9 @@ + dist_pem_h: + (cd crypto/pem; $(MAKE) -e $(BUILDENV) pem.h; $(MAKE) clean) + +-install: all install_docs install_sw ++install: install_docs install_sw + +-install_sw: ++install_dirs: + @$(PERL) $(TOP)/util/mkdir-p.pl $(INSTALL_PREFIX)$(INSTALLTOP)/bin \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR) \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines \ +@@ -549,12 +549,19 @@ + $(INSTALL_PREFIX)$(OPENSSLDIR)/misc \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/certs \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/private ++ @$(PERL) $(TOP)/util/mkdir-p.pl \ ++ $(INSTALL_PREFIX)$(MANDIR)/man1 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man3 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man5 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man7 ++ ++install_sw: install_dirs + @set -e; headerlist="$(EXHEADER)"; for i in $$headerlist;\ + do \ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @set -e; target=install; $(RECURSIVE_BUILD_CMD) ++ +@set -e; target=install; $(RECURSIVE_BUILD_CMD) + @set -e; liblist="$(LIBS)"; for i in $$liblist ;\ + do \ + if [ -f "$$i" ]; then \ +@@ -634,12 +641,7 @@ + done; \ + done + +-install_docs: +- @$(PERL) $(TOP)/util/mkdir-p.pl \ +- $(INSTALL_PREFIX)$(MANDIR)/man1 \ +- $(INSTALL_PREFIX)$(MANDIR)/man3 \ +- $(INSTALL_PREFIX)$(MANDIR)/man5 \ +- $(INSTALL_PREFIX)$(MANDIR)/man7 ++install_docs: install_dirs + @pod2man="`cd ./util; ./pod2mantest $(PERL)`"; \ + here="`pwd`"; \ + filecase=; \ +diff -ru openssl-1.0.1m.orig/Makefile.shared openssl-1.0.1m/Makefile.shared +--- openssl-1.0.1m.orig/Makefile.shared 2015-01-20 13:33:36.000000000 +0100 ++++ openssl-1.0.1m/Makefile.shared 2015-03-31 12:14:56.071786835 +0200 +@@ -105,6 +105,7 @@ + SHAREDFLAGS="$${SHAREDFLAGS:-$(CFLAGS) $(SHARED_LDFLAGS)}"; \ + LIBPATH=`for x in $$LIBDEPS; do echo $$x; done | sed -e 's/^ *-L//;t' -e d | uniq`; \ + LIBPATH=`echo $$LIBPATH | sed -e 's/ /:/g'`; \ ++ [ -e $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX ] && exit 0; \ + LD_LIBRARY_PATH=$$LIBPATH:$$LD_LIBRARY_PATH \ + $${SHAREDCMD} $${SHAREDFLAGS} \ + -o $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX \ +@@ -122,6 +123,7 @@ + done; \ + fi; \ + if [ -n "$$SHLIB_SOVER" ]; then \ ++ [ -e "$$SHLIB$$SHLIB_SUFFIX" ] || \ + ( $(SET_X); rm -f $$SHLIB$$SHLIB_SUFFIX; \ + ln -s $$prev $$SHLIB$$SHLIB_SUFFIX ); \ + fi; \ +diff -ru openssl-1.0.1m.orig/test/Makefile openssl-1.0.1m/test/Makefile +--- openssl-1.0.1m.orig/test/Makefile 2015-03-19 14:38:37.000000000 +0100 ++++ openssl-1.0.1m/test/Makefile 2015-03-31 12:16:53.684158416 +0200 +@@ -130,7 +130,7 @@ + tags: + ctags $(SRC) + +-tests: exe apps $(TESTS) ++tests: exe $(TESTS) + + apps: + @(cd ..; $(MAKE) DIRS=apps all) +@@ -388,118 +388,118 @@ + link_app.$${shlib_target} + + $(RSATEST)$(EXE_EXT): $(RSATEST).o $(DLIBCRYPTO) +- @target=$(RSATEST); $(BUILD_CMD) ++ +@target=$(RSATEST); $(BUILD_CMD) + + $(BNTEST)$(EXE_EXT): $(BNTEST).o $(DLIBCRYPTO) +- @target=$(BNTEST); $(BUILD_CMD) ++ +@target=$(BNTEST); $(BUILD_CMD) + + $(ECTEST)$(EXE_EXT): $(ECTEST).o $(DLIBCRYPTO) +- @target=$(ECTEST); $(BUILD_CMD) ++ +@target=$(ECTEST); $(BUILD_CMD) + + $(EXPTEST)$(EXE_EXT): $(EXPTEST).o $(DLIBCRYPTO) +- @target=$(EXPTEST); $(BUILD_CMD) ++ +@target=$(EXPTEST); $(BUILD_CMD) + + $(IDEATEST)$(EXE_EXT): $(IDEATEST).o $(DLIBCRYPTO) +- @target=$(IDEATEST); $(BUILD_CMD) ++ +@target=$(IDEATEST); $(BUILD_CMD) + + $(MD2TEST)$(EXE_EXT): $(MD2TEST).o $(DLIBCRYPTO) +- @target=$(MD2TEST); $(BUILD_CMD) ++ +@target=$(MD2TEST); $(BUILD_CMD) + + $(SHATEST)$(EXE_EXT): $(SHATEST).o $(DLIBCRYPTO) +- @target=$(SHATEST); $(BUILD_CMD) ++ +@target=$(SHATEST); $(BUILD_CMD) + + $(SHA1TEST)$(EXE_EXT): $(SHA1TEST).o $(DLIBCRYPTO) +- @target=$(SHA1TEST); $(BUILD_CMD) ++ +@target=$(SHA1TEST); $(BUILD_CMD) + + $(SHA256TEST)$(EXE_EXT): $(SHA256TEST).o $(DLIBCRYPTO) +- @target=$(SHA256TEST); $(BUILD_CMD) ++ +@target=$(SHA256TEST); $(BUILD_CMD) + + $(SHA512TEST)$(EXE_EXT): $(SHA512TEST).o $(DLIBCRYPTO) +- @target=$(SHA512TEST); $(BUILD_CMD) ++ +@target=$(SHA512TEST); $(BUILD_CMD) + + $(RMDTEST)$(EXE_EXT): $(RMDTEST).o $(DLIBCRYPTO) +- @target=$(RMDTEST); $(BUILD_CMD) ++ +@target=$(RMDTEST); $(BUILD_CMD) + + $(MDC2TEST)$(EXE_EXT): $(MDC2TEST).o $(DLIBCRYPTO) +- @target=$(MDC2TEST); $(BUILD_CMD) ++ +@target=$(MDC2TEST); $(BUILD_CMD) + + $(MD4TEST)$(EXE_EXT): $(MD4TEST).o $(DLIBCRYPTO) +- @target=$(MD4TEST); $(BUILD_CMD) ++ +@target=$(MD4TEST); $(BUILD_CMD) + + $(MD5TEST)$(EXE_EXT): $(MD5TEST).o $(DLIBCRYPTO) +- @target=$(MD5TEST); $(BUILD_CMD) ++ +@target=$(MD5TEST); $(BUILD_CMD) + + $(HMACTEST)$(EXE_EXT): $(HMACTEST).o $(DLIBCRYPTO) +- @target=$(HMACTEST); $(BUILD_CMD) ++ +@target=$(HMACTEST); $(BUILD_CMD) + + $(WPTEST)$(EXE_EXT): $(WPTEST).o $(DLIBCRYPTO) +- @target=$(WPTEST); $(BUILD_CMD) ++ +@target=$(WPTEST); $(BUILD_CMD) + + $(RC2TEST)$(EXE_EXT): $(RC2TEST).o $(DLIBCRYPTO) +- @target=$(RC2TEST); $(BUILD_CMD) ++ +@target=$(RC2TEST); $(BUILD_CMD) + + $(BFTEST)$(EXE_EXT): $(BFTEST).o $(DLIBCRYPTO) +- @target=$(BFTEST); $(BUILD_CMD) ++ +@target=$(BFTEST); $(BUILD_CMD) + + $(CASTTEST)$(EXE_EXT): $(CASTTEST).o $(DLIBCRYPTO) +- @target=$(CASTTEST); $(BUILD_CMD) ++ +@target=$(CASTTEST); $(BUILD_CMD) + + $(RC4TEST)$(EXE_EXT): $(RC4TEST).o $(DLIBCRYPTO) +- @target=$(RC4TEST); $(BUILD_CMD) ++ +@target=$(RC4TEST); $(BUILD_CMD) + + $(RC5TEST)$(EXE_EXT): $(RC5TEST).o $(DLIBCRYPTO) +- @target=$(RC5TEST); $(BUILD_CMD) ++ +@target=$(RC5TEST); $(BUILD_CMD) + + $(DESTEST)$(EXE_EXT): $(DESTEST).o $(DLIBCRYPTO) +- @target=$(DESTEST); $(BUILD_CMD) ++ +@target=$(DESTEST); $(BUILD_CMD) + + $(RANDTEST)$(EXE_EXT): $(RANDTEST).o $(DLIBCRYPTO) +- @target=$(RANDTEST); $(BUILD_CMD) ++ +@target=$(RANDTEST); $(BUILD_CMD) + + $(DHTEST)$(EXE_EXT): $(DHTEST).o $(DLIBCRYPTO) +- @target=$(DHTEST); $(BUILD_CMD) ++ +@target=$(DHTEST); $(BUILD_CMD) + + $(DSATEST)$(EXE_EXT): $(DSATEST).o $(DLIBCRYPTO) +- @target=$(DSATEST); $(BUILD_CMD) ++ +@target=$(DSATEST); $(BUILD_CMD) + + $(METHTEST)$(EXE_EXT): $(METHTEST).o $(DLIBCRYPTO) +- @target=$(METHTEST); $(BUILD_CMD) ++ +@target=$(METHTEST); $(BUILD_CMD) + + $(SSLTEST)$(EXE_EXT): $(SSLTEST).o $(DLIBSSL) $(DLIBCRYPTO) +- @target=$(SSLTEST); $(FIPS_BUILD_CMD) ++ +@target=$(SSLTEST); $(FIPS_BUILD_CMD) + + $(ENGINETEST)$(EXE_EXT): $(ENGINETEST).o $(DLIBCRYPTO) +- @target=$(ENGINETEST); $(BUILD_CMD) ++ +@target=$(ENGINETEST); $(BUILD_CMD) + + $(EVPTEST)$(EXE_EXT): $(EVPTEST).o $(DLIBCRYPTO) +- @target=$(EVPTEST); $(BUILD_CMD) ++ +@target=$(EVPTEST); $(BUILD_CMD) + + $(EVPEXTRATEST)$(EXE_EXT): $(EVPEXTRATEST).o $(DLIBCRYPTO) +- @target=$(EVPEXTRATEST); $(BUILD_CMD) ++ +@target=$(EVPEXTRATEST); $(BUILD_CMD) + + $(ECDSATEST)$(EXE_EXT): $(ECDSATEST).o $(DLIBCRYPTO) +- @target=$(ECDSATEST); $(BUILD_CMD) ++ +@target=$(ECDSATEST); $(BUILD_CMD) + + $(ECDHTEST)$(EXE_EXT): $(ECDHTEST).o $(DLIBCRYPTO) +- @target=$(ECDHTEST); $(BUILD_CMD) ++ +@target=$(ECDHTEST); $(BUILD_CMD) + + $(IGETEST)$(EXE_EXT): $(IGETEST).o $(DLIBCRYPTO) +- @target=$(IGETEST); $(BUILD_CMD) ++ +@target=$(IGETEST); $(BUILD_CMD) + + $(JPAKETEST)$(EXE_EXT): $(JPAKETEST).o $(DLIBCRYPTO) +- @target=$(JPAKETEST); $(BUILD_CMD) ++ +@target=$(JPAKETEST); $(BUILD_CMD) + + $(ASN1TEST)$(EXE_EXT): $(ASN1TEST).o $(DLIBCRYPTO) +- @target=$(ASN1TEST); $(BUILD_CMD) ++ +@target=$(ASN1TEST); $(BUILD_CMD) + + $(SRPTEST)$(EXE_EXT): $(SRPTEST).o $(DLIBCRYPTO) +- @target=$(SRPTEST); $(BUILD_CMD) ++ +@target=$(SRPTEST); $(BUILD_CMD) + + $(HEARTBEATTEST)$(EXE_EXT): $(HEARTBEATTEST).o $(DLIBCRYPTO) +- @target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) ++ +@target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) + + $(CONSTTIMETEST)$(EXE_EXT): $(CONSTTIMETEST).o +- @target=$(CONSTTIMETEST) $(BUILD_CMD) ++ +@target=$(CONSTTIMETEST) $(BUILD_CMD) + + #$(AESTEST).o: $(AESTEST).c + # $(CC) -c $(CFLAGS) -DINTERMEDIATE_VALUE_KAT -DTRACE_KAT_MCT $(AESTEST).c diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch new file mode 100644 index 0000000000..16ab3306c7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch @@ -0,0 +1,116 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) +diff -ru openssl-1.0.1m.orig/Configure openssl-1.0.1m/Configure +--- openssl-1.0.1m.orig/Configure 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Configure 2015-03-31 12:50:44.965133568 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1m.orig/crypto/aes/aes_x86core.c openssl-1.0.1m/crypto/aes/aes_x86core.c +--- openssl-1.0.1m.orig/crypto/aes/aes_x86core.c 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/aes/aes_x86core.c 2015-03-31 12:28:27.768182812 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/des/des_locl.h openssl-1.0.1m/crypto/des/des_locl.h +--- openssl-1.0.1m.orig/crypto/des/des_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/des/des_locl.h 2015-03-31 12:52:29.287245531 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/md32_common.h openssl-1.0.1m/crypto/md32_common.h +--- openssl-1.0.1m.orig/crypto/md32_common.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/md32_common.h 2015-03-31 12:53:03.737932332 +0200 +@@ -142,8 +142,10 @@ + */ + #undef ROTATE + #ifndef PEDANTIC +-# if defined(_MSC_VER) || defined(__ICC) ++# if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++# elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + # elif defined(__MWERKS__) + # if defined(__POWERPC__) + # define ROTATE(a,n) __rlwinm(a,n,0,31) +diff -ru openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h openssl-1.0.1m/crypto/rc5/rc5_locl.h +--- openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/rc5/rc5_locl.h 2015-03-31 12:51:52.976509433 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From ac878e9b4e53948f8642c68c4ee0690edf7be387 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 15:13:04 +0200 Subject: [PATCH 712/911] fix OpenSSL 1.0.1m patch name --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index 7665ce0775..a127a7e7bb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s-fix_parallel_build-1.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From e53a0c251081b0103aaa3eb3fb9d1172ae02bd2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 16:21:04 +0200 Subject: [PATCH 713/911] include patch for deap extension in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 1 + .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 9e5af7e518..c1fd1209b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -78,6 +78,7 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch new file mode 100644 index 0000000000..b88bba0d0c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch @@ -0,0 +1,13 @@ +README.md is not included in tarball, so comment out long description +author: Kenneth Hoste (Ghent University) +--- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 ++++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 +@@ -19,7 +19,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=read_md('README.md'), ++ #long_description=read_md('README.md'), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='https://www.github.com/deap', -- GitLab From 556e7f32fa5f0ac4a159e48a342d7cfa4dee91cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 May 2015 09:19:11 +0200 Subject: [PATCH 714/911] bump subversion for deap extension, drop unnecessary patch --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +-- .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 ------------- 2 files changed, 1 insertion(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c1fd1209b8..3265a5bd15 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,9 +76,8 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch deleted file mode 100644 index b88bba0d0c..0000000000 --- a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch +++ /dev/null @@ -1,13 +0,0 @@ -README.md is not included in tarball, so comment out long description -author: Kenneth Hoste (Ghent University) ---- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 -+++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 -@@ -19,7 +19,7 @@ - setup(name='deap', - version=deap.__revision__, - description='Distributed Evolutionary Algorithms in Python', -- long_description=read_md('README.md'), -+ #long_description=read_md('README.md'), - author='deap Development Team', - author_email='deap-users@googlegroups.com', - url='https://www.github.com/deap', -- GitLab From f1c2d8e210f7bf638900d83e5e610f97245434f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 10:13:15 +0200 Subject: [PATCH 715/911] add version 5.2.40 of Cray toolchains + HPL as test case --- .../easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb | 16 ++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb | 16 ++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.40.eb | 16 ++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.40.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.40.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.40.eb | 18 +++++++++++++++ 6 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b31f4b3a23 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dbbbbbd303 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..5937accfe4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b91a1eb499 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dcfcc5ca6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..8a33b68ad9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From f92c4e0cc27bb4f4f910ef6e85ffa1396cff06ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 13:36:11 +0200 Subject: [PATCH 716/911] bump version to v2.1.x --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5b55ee3e55..e89248dca4 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.0' +VERSION = '2.1.1dev' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 08bfd4bc0cd77f1ea1c4f126925c0b5fc725e4ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:18:35 +0200 Subject: [PATCH 717/911] add easyconfig file for EasyBuild v2.1.0 --- .../e/EasyBuild/EasyBuild-2.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000..d753a18457 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = "2.1.0" + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From 8eb13ee04f0d3faab28cffe163d3fd83db885d60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2015 21:19:52 +0200 Subject: [PATCH 718/911] style fix --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index d753a18457..b11b8ff6c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_EasyBuildMeta' name = 'EasyBuild' -version = "2.1.0" +version = '2.1.0' homepage = 'http://hpcugent.github.com/easybuild/' description = """EasyBuild is a software build and installation framework -- GitLab From 55bd896831aea6ec4fdef337370fe3ee8c3dc0ed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:36:05 +0200 Subject: [PATCH 719/911] Boost 1.58 for intel/2015a --- .../Boost-1.58.0-intel-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..a209577bba --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From c4571e54605eba98ff436db0a762a773dc23a8e9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 May 2015 18:37:17 +0200 Subject: [PATCH 720/911] Boost 1.58.0 for foss/2015a --- .../Boost-1.58.0-foss-2015a-Python-2.7.9.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..bbef8b760b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' -- GitLab From 3de5c8412dd0472f36a779f9e0651f057d8863e4 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Tue, 5 May 2015 16:00:36 +0200 Subject: [PATCH 721/911] Adding the easyconfigs for ictce-7.3.5 --- easybuild/easyconfigs/i/icc/icc-2015.3.187.eb | 17 ++++++++++++++ .../i/iccifort/iccifort-2015.3.187.eb | 16 ++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb | 21 ++++++++++++++++++ .../easyconfigs/i/ifort/ifort-2015.3.187.eb | 17 ++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb | 18 +++++++++++++++ .../i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb | 22 +++++++++++++++++++ .../impi-5.0.3.048-iccifort-2015.3.187.eb | 19 ++++++++++++++++ 7 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb new file mode 100644 index 0000000000..55dec91be5 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb new file mode 100644 index 0000000000..8387432380 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version), + ('ifort', version), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb new file mode 100644 index 0000000000..6190ed2906 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '3.187' +compver = '2015.%s' % suff + +dependencies = [ # version/released + ('icc', compver), # Apr 13th 2015 + ('ifort', compver), # Apr 13th 2015 + ('impi', '5.0.3.048', '', ('iccifort', compver)), # Feb 10th 2015 + ('imkl', '11.2.%s' % suff, '', ('iimpi', version)), # Apr 13th 2015 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb new file mode 100644 index 0000000000..8253a3390b --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb new file mode 100644 index 0000000000..b0fe67cb26 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.3.187' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '5.0.3.048', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb new file mode 100644 index 0000000000..807b5f2004 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.3.5'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb new file mode 100644 index 0000000000..5e0972d8f3 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message + passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for + Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" + +toolchain = {'name': 'iccifort', 'version': '2015.3.187'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 38226e59dc0659a6ccc047c7712d0f135eb193e8 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Wed, 6 May 2015 11:31:15 +0200 Subject: [PATCH 722/911] Adding HPL 2.1 with ictce-7.3.5 --- .../easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb new file mode 100644 index 0000000000..55ab924d7d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From e59e7fca0b6840ae516121c9eaa8d11669239568 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Aug 2014 13:46:16 +0200 Subject: [PATCH 723/911] added new cutadapt for intel --- .../cutadapt-1.5-intel2014b-Python-2.7.8.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..9be9435a32 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From dad3b10a50135f61257f379827de38173e6d5fe6 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:42:44 +0200 Subject: [PATCH 724/911] added even newer cutadapt --- ...cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..1c463c28a1 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.8.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/marcelm/cutadapt/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt',], + 'dirs': [], +} + +moduleclass = 'bio' + -- GitLab From 380614ad77ca07f62bb9f5911deb4688f0f18d51 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 09:56:11 +0200 Subject: [PATCH 725/911] fixed filename --- ...b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cutadapt/{cutadapt-1.5-intel2014b-Python-2.7.8.eb => cutadapt-1.5-intel-2014b-Python-2.7.8.eb} (100%) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb similarity index 100% rename from easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel2014b-Python-2.7.8.eb rename to easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb -- GitLab From cb0e0011875100a86535fd58d74ce3267a94a5e2 Mon Sep 17 00:00:00 2001 From: Jens Date: Mon, 11 May 2015 10:19:56 +0200 Subject: [PATCH 726/911] fixed remarks --- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 2 +- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 9be9435a32..8a431e4a45 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt','lib/python2.7/site-packages/cutadapt/_align.so',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 1c463c28a1..737e7e93bb 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -29,9 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/cutadapt',], + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], 'dirs': [], } moduleclass = 'bio' - -- GitLab From 3336fa693a4dfcb0c6b4600380bc025b6f4df6d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 11:14:44 +0200 Subject: [PATCH 727/911] add easyconfig for networkx --- ...networkx-1.9.1-intel-2015a-Python-2.7.9.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6ae1e74b7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.9.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'tools' -- GitLab From 8ce753e79e359f691d042787927bd5577cd1ae12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 15:23:36 +0200 Subject: [PATCH 728/911] add easyconfig for scikit-learn v0.16.1 --- ...t-learn-0.16.1-intel-2015a-Python-2.7.9.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..8b997036dd --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' -- GitLab From 93ce24c124f1004bc7bdb8efd5c8ee30afa64cc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 11:37:19 +0200 Subject: [PATCH 729/911] add easyconfig for Platanus (binary) --- .../p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb new file mode 100644 index 0000000000..c7b0660395 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -0,0 +1,20 @@ +easyblock = 'Binary' + +name = 'Platanus' +version = '1.2.1' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] +sources = ['platanus'] +checksums = ['02cf92847ec704d010a54df293b9c60a'] + +sanity_check_paths = { + 'files': ['platanus'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6980c64b72428c6e0adca021a9fbc6185b418473 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 14:39:33 +0200 Subject: [PATCH 730/911] fix versionsuffix in Platanus easyconfig --- easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb index c7b0660395..2fa31617c3 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -2,6 +2,7 @@ easyblock = 'Binary' name = 'Platanus' version = '1.2.1' +versionsuffix = '-linux-x86_64' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" -- GitLab From af2f8f3d2b1c2be50df9504f87821caff900c746 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:33:57 +0100 Subject: [PATCH 731/911] Added Boost for ictce-7.1.2 --- .../Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000..d29dcc1cda --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' -- GitLab From ff98ab8d207b04305ac22c6d72da668fbe523b1b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 12:34:59 +0100 Subject: [PATCH 732/911] Added GROMACS 5.0.2 --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000..5e23be1026 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.2' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' -- GitLab From 516a5a56a437d3ac1344c99558666f8778de53e5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 2 Dec 2014 13:50:39 +0100 Subject: [PATCH 733/911] Added forgotten Boost patch --- .../easyconfigs/b/Boost/boost-impi5.patch | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/boost-impi5.patch diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000..635da12964 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { -- GitLab From 1d203c06dc40e56f65458d55c8d102e1d499b5c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 21:57:32 +0200 Subject: [PATCH 734/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb index 5e23be1026..b6b649c1ec 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'ictce', 'version': '7.1.2'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 58b1fc72996bff6fb05a172f2f57f8c088a78886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:03:53 +0200 Subject: [PATCH 735/911] {bio}[intel/2015a] GROMACS 5.0.4 (mt, hybrid) --- .../GROMACS-5.0.4-intel-2015a-hybrid.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..954bb885eb --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000..ea167cc786 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.4' +versionsuffix = '-mt' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From b4d9eaf523881e8aef2fd1ae5c39fd9e42d6535d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 19:06:56 +0200 Subject: [PATCH 736/911] drop non-existing source URL, remove uncommented source tarball for regressiontests --- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb | 12 ++---------- .../g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb | 12 ++---------- 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb index 954bb885eb..0914af5ffd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb index ea167cc786..f0da8f6053 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb @@ -21,16 +21,8 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', - 'http://gerrit.gromacs.org/download/', -] - -sources = [ - SOURCELOWER_TAR_GZ, -# seems to have disappeared? -# 'regressiontests-5.0.2.tar.gz', -] +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.2.2'), -- GitLab From 36704f8219b0bf683665b5f2d33eb3c0a2b28424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:08:13 +0200 Subject: [PATCH 737/911] {bio}[intel/2015a] SaguaroGW --- .../SaguaroGW-20150315-intel-2015a.eb | 31 +++++++++++++++++++ .../SaguaroGW/SaguaroGW_icpc-drop-const.patch | 15 +++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb new file mode 100644 index 0000000000..e922e754a3 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'SaguaroGW' +version = '20150315' + +homepage = 'http://sourceforge.net/projects/saguarogw/' +description = """Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, + or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in +the genome.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] +# SVN revision r29 +sources = ['%(namelower)s-code-29.zip'] + +patches = ['SaguaroGW_icpc-drop-const.patch'] + +buildopts = 'CPLUSPLUS="$CXX" CC="$CC" OPEN_MP=yes' + +files_to_copy = [(['checkLock', 'CactiCorrelate', 'ChromoPaintCacti', 'ClusterCacti', 'Fasta2HMMFeature', + 'Genotype2HMMFeature', 'FilterCacti', 'HMMClassify', 'HMMTrain', 'HeatMaps', 'LocalTrees', + 'Maf2HMMFeature', 'PullFromFasta', 'Saguaro', 'Saguaro2Phylip', 'VCF2HMMFeature'], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch new file mode 100644 index 0000000000..193b028341 --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch @@ -0,0 +1,15 @@ +fix issue with Intel compilers: 'the object has cv-qualifiers that are not compatible with the member function' +author: Kenneth Hoste (Ghent University) +--- /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h.orig 2012-05-16 15:40:12.000000000 +0200 ++++ /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h 2015-05-12 21:54:40.830166431 +0200 +@@ -39,8 +39,8 @@ + string GetName() { return mName; } + string GetDescription() { return mDesc; } + +-friend bool operator< (const commandArg &lhs, +- const commandArg &rhs) ++friend bool operator< (commandArg &lhs, ++ commandArg &rhs) + { + if ( lhs.GetName() < rhs.GetName() ) + return true; -- GitLab From b6510084eabdbc338561400131cebb659f561810 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2015 22:09:26 +0200 Subject: [PATCH 738/911] add MD5sum for SaguaroGW source tarball --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index e922e754a3..994bf42a7a 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -14,6 +14,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] # SVN revision r29 sources = ['%(namelower)s-code-29.zip'] +checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 76089b1bea669044438b59ccc2670e6e4128e8c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 09:51:36 +0200 Subject: [PATCH 739/911] drop source_urls that are not guaranteed to work --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 994bf42a7a..897d3c2fd1 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -11,8 +11,7 @@ the genome.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'openmp': True} -source_urls = ['http://sourceforge.net/code-snapshots/svn/s/sa/saguarogw/code/'] -# SVN revision r29 +# SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] -- GitLab From 86dfb7262445cf3398eda3751c7b5d65904d281a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:07:27 +0200 Subject: [PATCH 740/911] remove checksum, tarball is generated on the fly and checksum changes --- .../easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb index 897d3c2fd1..6edbc50c07 100644 --- a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -13,7 +13,6 @@ toolchainopts = {'openmp': True} # SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) sources = ['%(namelower)s-code-29.zip'] -checksums = ['d8549fa4c8b69f5bcb50742c41f4fd4e'] patches = ['SaguaroGW_icpc-drop-const.patch'] -- GitLab From 8e6841ad5556e8c355ed664c1ff66184e5a71414 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:41:14 +0200 Subject: [PATCH 741/911] {system}[intel/2015a] OpenSSL 1.0.1m --- .../o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 24 ++ .../OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch | 343 ++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch | 116 ++++++ 3 files changed, 483 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000..7665ce0775 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s-fix_parallel_build-1.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch new file mode 100644 index 0000000000..e30b04902b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch @@ -0,0 +1,343 @@ +Fixes build with make -jx, where x is greater than 1 +based on patch for 1.0.1e by Armin K. +diff -ru openssl-1.0.1m.orig/crypto/Makefile openssl-1.0.1m/crypto/Makefile +--- openssl-1.0.1m.orig/crypto/Makefile 2015-03-19 14:38:24.000000000 +0100 ++++ openssl-1.0.1m/crypto/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -85,11 +85,11 @@ + @if [ -z "$(THIS)" ]; then $(MAKE) -f $(TOP)/Makefile reflect THIS=$@; fi + + subdirs: +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +- @target=files; $(RECURSIVE_MAKE) ++ +@target=files; $(RECURSIVE_MAKE) + + links: + @$(PERL) $(TOP)/util/mklink.pl ../include/openssl $(EXHEADER) +@@ -100,7 +100,7 @@ + # lib: $(LIB): are splitted to avoid end-less loop + lib: $(LIB) + @touch lib +-$(LIB): $(LIBOBJ) ++$(LIB): $(LIBOBJ) | subdirs + $(AR) $(LIB) $(LIBOBJ) + [ -z "$(FIPSLIBDIR)" ] || $(AR) $(LIB) $(FIPSLIBDIR)fipscanister.o + $(RANLIB) $(LIB) || echo Never mind. +@@ -111,7 +111,7 @@ + fi + + libs: +- @target=lib; $(RECURSIVE_MAKE) ++ +@target=lib; $(RECURSIVE_MAKE) + + install: + @[ -n "$(INSTALLTOP)" ] # should be set by top Makefile... +@@ -120,7 +120,7 @@ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + lint: + @target=lint; $(RECURSIVE_MAKE) +diff -ru openssl-1.0.1m.orig/engines/Makefile openssl-1.0.1m/engines/Makefile +--- openssl-1.0.1m.orig/engines/Makefile 2015-03-19 14:38:35.000000000 +0100 ++++ openssl-1.0.1m/engines/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -72,7 +72,7 @@ + + all: lib subdirs + +-lib: $(LIBOBJ) ++lib: $(LIBOBJ) | subdirs + @if [ -n "$(SHARED_LIBS)" ]; then \ + set -e; \ + for l in $(LIBNAMES); do \ +@@ -89,7 +89,7 @@ + + subdirs: + echo $(EDIRS) +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +@@ -128,7 +128,7 @@ + mv -f $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx.new $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx ); \ + done; \ + fi +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + tags: + ctags $(SRC) +diff -ru openssl-1.0.1m.orig/Makefile.org openssl-1.0.1m/Makefile.org +--- openssl-1.0.1m.orig/Makefile.org 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Makefile.org 2015-03-31 12:14:56.071786835 +0200 +@@ -273,17 +273,17 @@ + build_libs: build_crypto build_ssl build_engines + + build_crypto: +- @dir=crypto; target=all; $(BUILD_ONE_CMD) +-build_ssl: +- @dir=ssl; target=all; $(BUILD_ONE_CMD) +-build_engines: +- @dir=engines; target=all; $(BUILD_ONE_CMD) +-build_apps: +- @dir=apps; target=all; $(BUILD_ONE_CMD) +-build_tests: +- @dir=test; target=all; $(BUILD_ONE_CMD) +-build_tools: +- @dir=tools; target=all; $(BUILD_ONE_CMD) ++ +@dir=crypto; target=all; $(BUILD_ONE_CMD) ++build_ssl: build_crypto ++ +@dir=ssl; target=all; $(BUILD_ONE_CMD) ++build_engines: build_crypto ++ +@dir=engines; target=all; $(BUILD_ONE_CMD) ++build_apps: build_libs ++ +@dir=apps; target=all; $(BUILD_ONE_CMD) ++build_tests: build_libs ++ +@dir=test; target=all; $(BUILD_ONE_CMD) ++build_tools: build_libs ++ +@dir=tools; target=all; $(BUILD_ONE_CMD) + + all_testapps: build_libs build_testapps + build_testapps: +@@ -538,9 +538,9 @@ + dist_pem_h: + (cd crypto/pem; $(MAKE) -e $(BUILDENV) pem.h; $(MAKE) clean) + +-install: all install_docs install_sw ++install: install_docs install_sw + +-install_sw: ++install_dirs: + @$(PERL) $(TOP)/util/mkdir-p.pl $(INSTALL_PREFIX)$(INSTALLTOP)/bin \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR) \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines \ +@@ -549,12 +549,19 @@ + $(INSTALL_PREFIX)$(OPENSSLDIR)/misc \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/certs \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/private ++ @$(PERL) $(TOP)/util/mkdir-p.pl \ ++ $(INSTALL_PREFIX)$(MANDIR)/man1 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man3 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man5 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man7 ++ ++install_sw: install_dirs + @set -e; headerlist="$(EXHEADER)"; for i in $$headerlist;\ + do \ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @set -e; target=install; $(RECURSIVE_BUILD_CMD) ++ +@set -e; target=install; $(RECURSIVE_BUILD_CMD) + @set -e; liblist="$(LIBS)"; for i in $$liblist ;\ + do \ + if [ -f "$$i" ]; then \ +@@ -634,12 +641,7 @@ + done; \ + done + +-install_docs: +- @$(PERL) $(TOP)/util/mkdir-p.pl \ +- $(INSTALL_PREFIX)$(MANDIR)/man1 \ +- $(INSTALL_PREFIX)$(MANDIR)/man3 \ +- $(INSTALL_PREFIX)$(MANDIR)/man5 \ +- $(INSTALL_PREFIX)$(MANDIR)/man7 ++install_docs: install_dirs + @pod2man="`cd ./util; ./pod2mantest $(PERL)`"; \ + here="`pwd`"; \ + filecase=; \ +diff -ru openssl-1.0.1m.orig/Makefile.shared openssl-1.0.1m/Makefile.shared +--- openssl-1.0.1m.orig/Makefile.shared 2015-01-20 13:33:36.000000000 +0100 ++++ openssl-1.0.1m/Makefile.shared 2015-03-31 12:14:56.071786835 +0200 +@@ -105,6 +105,7 @@ + SHAREDFLAGS="$${SHAREDFLAGS:-$(CFLAGS) $(SHARED_LDFLAGS)}"; \ + LIBPATH=`for x in $$LIBDEPS; do echo $$x; done | sed -e 's/^ *-L//;t' -e d | uniq`; \ + LIBPATH=`echo $$LIBPATH | sed -e 's/ /:/g'`; \ ++ [ -e $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX ] && exit 0; \ + LD_LIBRARY_PATH=$$LIBPATH:$$LD_LIBRARY_PATH \ + $${SHAREDCMD} $${SHAREDFLAGS} \ + -o $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX \ +@@ -122,6 +123,7 @@ + done; \ + fi; \ + if [ -n "$$SHLIB_SOVER" ]; then \ ++ [ -e "$$SHLIB$$SHLIB_SUFFIX" ] || \ + ( $(SET_X); rm -f $$SHLIB$$SHLIB_SUFFIX; \ + ln -s $$prev $$SHLIB$$SHLIB_SUFFIX ); \ + fi; \ +diff -ru openssl-1.0.1m.orig/test/Makefile openssl-1.0.1m/test/Makefile +--- openssl-1.0.1m.orig/test/Makefile 2015-03-19 14:38:37.000000000 +0100 ++++ openssl-1.0.1m/test/Makefile 2015-03-31 12:16:53.684158416 +0200 +@@ -130,7 +130,7 @@ + tags: + ctags $(SRC) + +-tests: exe apps $(TESTS) ++tests: exe $(TESTS) + + apps: + @(cd ..; $(MAKE) DIRS=apps all) +@@ -388,118 +388,118 @@ + link_app.$${shlib_target} + + $(RSATEST)$(EXE_EXT): $(RSATEST).o $(DLIBCRYPTO) +- @target=$(RSATEST); $(BUILD_CMD) ++ +@target=$(RSATEST); $(BUILD_CMD) + + $(BNTEST)$(EXE_EXT): $(BNTEST).o $(DLIBCRYPTO) +- @target=$(BNTEST); $(BUILD_CMD) ++ +@target=$(BNTEST); $(BUILD_CMD) + + $(ECTEST)$(EXE_EXT): $(ECTEST).o $(DLIBCRYPTO) +- @target=$(ECTEST); $(BUILD_CMD) ++ +@target=$(ECTEST); $(BUILD_CMD) + + $(EXPTEST)$(EXE_EXT): $(EXPTEST).o $(DLIBCRYPTO) +- @target=$(EXPTEST); $(BUILD_CMD) ++ +@target=$(EXPTEST); $(BUILD_CMD) + + $(IDEATEST)$(EXE_EXT): $(IDEATEST).o $(DLIBCRYPTO) +- @target=$(IDEATEST); $(BUILD_CMD) ++ +@target=$(IDEATEST); $(BUILD_CMD) + + $(MD2TEST)$(EXE_EXT): $(MD2TEST).o $(DLIBCRYPTO) +- @target=$(MD2TEST); $(BUILD_CMD) ++ +@target=$(MD2TEST); $(BUILD_CMD) + + $(SHATEST)$(EXE_EXT): $(SHATEST).o $(DLIBCRYPTO) +- @target=$(SHATEST); $(BUILD_CMD) ++ +@target=$(SHATEST); $(BUILD_CMD) + + $(SHA1TEST)$(EXE_EXT): $(SHA1TEST).o $(DLIBCRYPTO) +- @target=$(SHA1TEST); $(BUILD_CMD) ++ +@target=$(SHA1TEST); $(BUILD_CMD) + + $(SHA256TEST)$(EXE_EXT): $(SHA256TEST).o $(DLIBCRYPTO) +- @target=$(SHA256TEST); $(BUILD_CMD) ++ +@target=$(SHA256TEST); $(BUILD_CMD) + + $(SHA512TEST)$(EXE_EXT): $(SHA512TEST).o $(DLIBCRYPTO) +- @target=$(SHA512TEST); $(BUILD_CMD) ++ +@target=$(SHA512TEST); $(BUILD_CMD) + + $(RMDTEST)$(EXE_EXT): $(RMDTEST).o $(DLIBCRYPTO) +- @target=$(RMDTEST); $(BUILD_CMD) ++ +@target=$(RMDTEST); $(BUILD_CMD) + + $(MDC2TEST)$(EXE_EXT): $(MDC2TEST).o $(DLIBCRYPTO) +- @target=$(MDC2TEST); $(BUILD_CMD) ++ +@target=$(MDC2TEST); $(BUILD_CMD) + + $(MD4TEST)$(EXE_EXT): $(MD4TEST).o $(DLIBCRYPTO) +- @target=$(MD4TEST); $(BUILD_CMD) ++ +@target=$(MD4TEST); $(BUILD_CMD) + + $(MD5TEST)$(EXE_EXT): $(MD5TEST).o $(DLIBCRYPTO) +- @target=$(MD5TEST); $(BUILD_CMD) ++ +@target=$(MD5TEST); $(BUILD_CMD) + + $(HMACTEST)$(EXE_EXT): $(HMACTEST).o $(DLIBCRYPTO) +- @target=$(HMACTEST); $(BUILD_CMD) ++ +@target=$(HMACTEST); $(BUILD_CMD) + + $(WPTEST)$(EXE_EXT): $(WPTEST).o $(DLIBCRYPTO) +- @target=$(WPTEST); $(BUILD_CMD) ++ +@target=$(WPTEST); $(BUILD_CMD) + + $(RC2TEST)$(EXE_EXT): $(RC2TEST).o $(DLIBCRYPTO) +- @target=$(RC2TEST); $(BUILD_CMD) ++ +@target=$(RC2TEST); $(BUILD_CMD) + + $(BFTEST)$(EXE_EXT): $(BFTEST).o $(DLIBCRYPTO) +- @target=$(BFTEST); $(BUILD_CMD) ++ +@target=$(BFTEST); $(BUILD_CMD) + + $(CASTTEST)$(EXE_EXT): $(CASTTEST).o $(DLIBCRYPTO) +- @target=$(CASTTEST); $(BUILD_CMD) ++ +@target=$(CASTTEST); $(BUILD_CMD) + + $(RC4TEST)$(EXE_EXT): $(RC4TEST).o $(DLIBCRYPTO) +- @target=$(RC4TEST); $(BUILD_CMD) ++ +@target=$(RC4TEST); $(BUILD_CMD) + + $(RC5TEST)$(EXE_EXT): $(RC5TEST).o $(DLIBCRYPTO) +- @target=$(RC5TEST); $(BUILD_CMD) ++ +@target=$(RC5TEST); $(BUILD_CMD) + + $(DESTEST)$(EXE_EXT): $(DESTEST).o $(DLIBCRYPTO) +- @target=$(DESTEST); $(BUILD_CMD) ++ +@target=$(DESTEST); $(BUILD_CMD) + + $(RANDTEST)$(EXE_EXT): $(RANDTEST).o $(DLIBCRYPTO) +- @target=$(RANDTEST); $(BUILD_CMD) ++ +@target=$(RANDTEST); $(BUILD_CMD) + + $(DHTEST)$(EXE_EXT): $(DHTEST).o $(DLIBCRYPTO) +- @target=$(DHTEST); $(BUILD_CMD) ++ +@target=$(DHTEST); $(BUILD_CMD) + + $(DSATEST)$(EXE_EXT): $(DSATEST).o $(DLIBCRYPTO) +- @target=$(DSATEST); $(BUILD_CMD) ++ +@target=$(DSATEST); $(BUILD_CMD) + + $(METHTEST)$(EXE_EXT): $(METHTEST).o $(DLIBCRYPTO) +- @target=$(METHTEST); $(BUILD_CMD) ++ +@target=$(METHTEST); $(BUILD_CMD) + + $(SSLTEST)$(EXE_EXT): $(SSLTEST).o $(DLIBSSL) $(DLIBCRYPTO) +- @target=$(SSLTEST); $(FIPS_BUILD_CMD) ++ +@target=$(SSLTEST); $(FIPS_BUILD_CMD) + + $(ENGINETEST)$(EXE_EXT): $(ENGINETEST).o $(DLIBCRYPTO) +- @target=$(ENGINETEST); $(BUILD_CMD) ++ +@target=$(ENGINETEST); $(BUILD_CMD) + + $(EVPTEST)$(EXE_EXT): $(EVPTEST).o $(DLIBCRYPTO) +- @target=$(EVPTEST); $(BUILD_CMD) ++ +@target=$(EVPTEST); $(BUILD_CMD) + + $(EVPEXTRATEST)$(EXE_EXT): $(EVPEXTRATEST).o $(DLIBCRYPTO) +- @target=$(EVPEXTRATEST); $(BUILD_CMD) ++ +@target=$(EVPEXTRATEST); $(BUILD_CMD) + + $(ECDSATEST)$(EXE_EXT): $(ECDSATEST).o $(DLIBCRYPTO) +- @target=$(ECDSATEST); $(BUILD_CMD) ++ +@target=$(ECDSATEST); $(BUILD_CMD) + + $(ECDHTEST)$(EXE_EXT): $(ECDHTEST).o $(DLIBCRYPTO) +- @target=$(ECDHTEST); $(BUILD_CMD) ++ +@target=$(ECDHTEST); $(BUILD_CMD) + + $(IGETEST)$(EXE_EXT): $(IGETEST).o $(DLIBCRYPTO) +- @target=$(IGETEST); $(BUILD_CMD) ++ +@target=$(IGETEST); $(BUILD_CMD) + + $(JPAKETEST)$(EXE_EXT): $(JPAKETEST).o $(DLIBCRYPTO) +- @target=$(JPAKETEST); $(BUILD_CMD) ++ +@target=$(JPAKETEST); $(BUILD_CMD) + + $(ASN1TEST)$(EXE_EXT): $(ASN1TEST).o $(DLIBCRYPTO) +- @target=$(ASN1TEST); $(BUILD_CMD) ++ +@target=$(ASN1TEST); $(BUILD_CMD) + + $(SRPTEST)$(EXE_EXT): $(SRPTEST).o $(DLIBCRYPTO) +- @target=$(SRPTEST); $(BUILD_CMD) ++ +@target=$(SRPTEST); $(BUILD_CMD) + + $(HEARTBEATTEST)$(EXE_EXT): $(HEARTBEATTEST).o $(DLIBCRYPTO) +- @target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) ++ +@target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) + + $(CONSTTIMETEST)$(EXE_EXT): $(CONSTTIMETEST).o +- @target=$(CONSTTIMETEST) $(BUILD_CMD) ++ +@target=$(CONSTTIMETEST) $(BUILD_CMD) + + #$(AESTEST).o: $(AESTEST).c + # $(CC) -c $(CFLAGS) -DINTERMEDIATE_VALUE_KAT -DTRACE_KAT_MCT $(AESTEST).c diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch new file mode 100644 index 0000000000..16ab3306c7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch @@ -0,0 +1,116 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) +diff -ru openssl-1.0.1m.orig/Configure openssl-1.0.1m/Configure +--- openssl-1.0.1m.orig/Configure 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Configure 2015-03-31 12:50:44.965133568 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1m.orig/crypto/aes/aes_x86core.c openssl-1.0.1m/crypto/aes/aes_x86core.c +--- openssl-1.0.1m.orig/crypto/aes/aes_x86core.c 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/aes/aes_x86core.c 2015-03-31 12:28:27.768182812 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/des/des_locl.h openssl-1.0.1m/crypto/des/des_locl.h +--- openssl-1.0.1m.orig/crypto/des/des_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/des/des_locl.h 2015-03-31 12:52:29.287245531 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/md32_common.h openssl-1.0.1m/crypto/md32_common.h +--- openssl-1.0.1m.orig/crypto/md32_common.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/md32_common.h 2015-03-31 12:53:03.737932332 +0200 +@@ -142,8 +142,10 @@ + */ + #undef ROTATE + #ifndef PEDANTIC +-# if defined(_MSC_VER) || defined(__ICC) ++# if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++# elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + # elif defined(__MWERKS__) + # if defined(__POWERPC__) + # define ROTATE(a,n) __rlwinm(a,n,0,31) +diff -ru openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h openssl-1.0.1m/crypto/rc5/rc5_locl.h +--- openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/rc5/rc5_locl.h 2015-03-31 12:51:52.976509433 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ -- GitLab From b031cab7df4eecc84a831a406496436d757b0e68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 15:13:04 +0200 Subject: [PATCH 742/911] fix OpenSSL 1.0.1m patch name --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb index 7665ce0775..a127a7e7bb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] patches = [ 'OpenSSL-%(version)s_icc-fixes.patch', - 'OpenSSL-%(version)s-fix_parallel_build-1.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', ] dependencies = [('zlib', '1.2.8')] -- GitLab From 2515a635d62a5d85ec1e267dbfbf72bfed64cac4 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 13 May 2015 12:06:31 +0200 Subject: [PATCH 743/911] added python 3.4.1 with intel 2015a toolchain --- .../p/Python/Python-3.4.1-intel-2015a.eb | 103 ++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb new file mode 100644 index 0000000000..5769376b00 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -0,0 +1,103 @@ +name = 'Python' +version = '3.4.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-3.4_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-%s-mkl.patch' % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + # tarball has changed upstream, so make sure we get the right version by verifying the checksum + 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' -- GitLab From ab0c00b9fdfb4ab34672f873afaadb66266a3697 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 12 May 2015 14:42:47 +0200 Subject: [PATCH 744/911] added python 3.4.3 intel 2015a --- .../p/Python/Python-3.4.3-intel-2015a.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb new file mode 100644 index 0000000000..d0fad95102 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '3.4.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] -- GitLab From 7c5a920698c566bf60d7a801d602972c7c9420dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:14:58 +0200 Subject: [PATCH 745/911] bump extension versions in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d0fad95102..a2c2596145 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.9.1' -scipyversion = '0.14.1' +numpyversion = '1.9.2' +scipyversion = '0.15.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.3'), ('ncurses', '5.9'), -# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # package versions updated Jan 19th 2015 exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ - ('setuptools', '11.3.1', { + ('setuptools', '15.2', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '6.0.6', { + ('pip', '6.1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('nose', '1.3.4', { + ('nose', '1.3.6', { 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { @@ -56,32 +56,32 @@ exts_list = [ ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), - ('argparse', '1.2.1', { + ('argparse', '1.3.0', { 'source_urls': ['http://argparse.googlecode.com/files/'], }), - ('pbr', '0.10.8', { + ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.21.2', { + ('Cython', '0.22', { 'source_urls': ['http://www.cython.org/release/'], }), ('six', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), - ('dateutil', '2.4.0', { + ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), - ('deap', '1.0.1', { + ('deap', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), - ('decorator', '3.4.0', { + ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], }), - ('arff', '2.0.1', { + ('arff', '2.0.2', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), @@ -89,7 +89,7 @@ exts_list = [ 'modulename': 'Crypto', 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], }), - ('ecdsa', '0.11', { + ('ecdsa', '0.13', { 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], }), ('paramiko', '1.15.2', { @@ -101,7 +101,7 @@ exts_list = [ ('netifaces', '0.10.4', { 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], }), - ('netaddr', '0.7.13', { + ('netaddr', '0.7.14', { 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] -- GitLab From 7e8feed77c7d66b2cbb1d6e639d06e20675752f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:20:45 +0200 Subject: [PATCH 746/911] fix argparse source URL --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index a2c2596145..eca8e6a7b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.11.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], -- GitLab From 709871afa62c5c125a7c6bd46b5af3781d25dbe4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 14:25:24 +0200 Subject: [PATCH 747/911] fix deap source template --- easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index eca8e6a7b9..9e5af7e518 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,6 +76,7 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.2', { -- GitLab From 0c3fc06d04290127ce15b3908e009778613dcc24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2015 16:21:04 +0200 Subject: [PATCH 748/911] include patch for deap extension in Python 3.4.3 easyconfig --- .../p/Python/Python-3.4.3-intel-2015a.eb | 1 + .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 9e5af7e518..c1fd1209b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -78,6 +78,7 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch new file mode 100644 index 0000000000..b88bba0d0c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch @@ -0,0 +1,13 @@ +README.md is not included in tarball, so comment out long description +author: Kenneth Hoste (Ghent University) +--- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 ++++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 +@@ -19,7 +19,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=read_md('README.md'), ++ #long_description=read_md('README.md'), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='https://www.github.com/deap', -- GitLab From 59a7685480a80ea6e0493b60d2a9c736a6189a1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 May 2015 09:19:11 +0200 Subject: [PATCH 749/911] bump subversion for deap extension, drop unnecessary patch --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +-- .../easyconfigs/p/Python/deap-1.0.2_no-README.patch | 13 ------------- 2 files changed, 1 insertion(+), 15 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c1fd1209b8..3265a5bd15 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -76,9 +76,8 @@ exts_list = [ 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { - 'source_tmpl': '%(name)s-%(version)s.post1.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'patches': ['deap-1.0.2_no-README.patch'], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch deleted file mode 100644 index b88bba0d0c..0000000000 --- a/easybuild/easyconfigs/p/Python/deap-1.0.2_no-README.patch +++ /dev/null @@ -1,13 +0,0 @@ -README.md is not included in tarball, so comment out long description -author: Kenneth Hoste (Ghent University) ---- deap-1.0.2/setup.py.orig 2015-05-13 15:58:21.188127136 +0200 -+++ deap-1.0.2/setup.py 2015-05-13 15:58:30.288556411 +0200 -@@ -19,7 +19,7 @@ - setup(name='deap', - version=deap.__revision__, - description='Distributed Evolutionary Algorithms in Python', -- long_description=read_md('README.md'), -+ #long_description=read_md('README.md'), - author='deap Development Team', - author_email='deap-users@googlegroups.com', - url='https://www.github.com/deap', -- GitLab From 04cb28e3bcf535261ee816ae0144b049ded5bb33 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 4 May 2015 09:49:11 +0200 Subject: [PATCH 750/911] BLAST+ with foss 2015a --- .../BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..37178f8aa5 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = "2.2.30" +versionsuffix = '-Python-2.7.9' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + -- GitLab From 38d140ef441956f834faef6efa12ef0cb2b843e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 10:13:15 +0200 Subject: [PATCH 751/911] add version 5.2.40 of Cray toolchains + HPL as test case --- .../easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb | 16 ++++++++++++++ .../easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb | 16 ++++++++++++++ .../c/CrayIntel/CrayIntel-5.2.40.eb | 16 ++++++++++++++ .../h/HPL/HPL-2.1-CrayCCE-5.2.40.eb | 22 +++++++++++++++++++ .../h/HPL/HPL-2.1-CrayGNU-5.2.40.eb | 18 +++++++++++++++ .../h/HPL/HPL-2.1-CrayIntel-5.2.40.eb | 18 +++++++++++++++ 6 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b31f4b3a23 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dbbbbbd303 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..5937accfe4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb new file mode 100644 index 0000000000..b91a1eb499 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayCCE', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..dcfcc5ca6e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb new file mode 100644 index 0000000000..8a33b68ad9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.1' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic + on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the + High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'CrayIntel', 'version': '5.2.40'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' -- GitLab From d5d049057b951e9fa52840ce987377b8d4e0a441 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2015 15:59:13 +0300 Subject: [PATCH 752/911] enable usempi in GROMACS Cray easyconfig, the easyblock enables MPI support on it --- .../easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb index c7618bc1f3..1aa3886405 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.1.29-mpi.eb @@ -19,6 +19,7 @@ description = """GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz source_urls = [ -- GitLab From 114232dd6b90b67f9f3bb61d9a032c2b9b5e8780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 14:45:13 +0200 Subject: [PATCH 753/911] only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 64defc00e8..23ac2489aa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -7,7 +7,7 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} +toolchainopts = {'pic': True, 'dynamic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb index 5a2850640d..dfcda740ab 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb @@ -7,7 +7,7 @@ homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' description = "Szip compression software, providing lossless compression of scientific data" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True, 'dynamic': True} +toolchainopts = {'pic': True, 'dynamic': True} source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb index 6245093966..b62190e55f 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb @@ -21,7 +21,7 @@ description = """Tcsh is an enhanced, but completely compatible version of the B mechanism, job control and a C-like syntax.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'shared': True, 'dynamic': True} +toolchainopts = {'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb index 737b571621..f6714bc2c1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb @@ -9,7 +9,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum computer hardware and operating system.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'shared': True} +toolchainopts = {'pic': True, 'dynamic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -- GitLab From a87232564c6f4ac0c48a03d46ed25abc6b6c06f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 15:18:33 +0200 Subject: [PATCH 755/911] clean up comments --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index aecb28f087..cfdc17ab69 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -15,11 +15,9 @@ source_urls = [ 'http://www.mmm.ucar.edu/wrf/src/', ] -# csh is used by WRF install scripts -# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) -# ncurses related issue? rebuild tcsh without EB-provided ncurses? -#builddependencies = [('tcsh', '6.18.01')] +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From 4dc228d977e87af658704efd36df9d4a30b3aa8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2015 22:06:49 +0200 Subject: [PATCH 756/911] list tcsh as build dep in WRF built with CrayGNU, rather than providing it as a build dep --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index 3806e63de1..aecb28f087 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -16,7 +16,10 @@ source_urls = [ ] # csh is used by WRF install scripts -builddependencies = [('tcsh', '6.18.01')] +# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) +# ncurses related issue? rebuild tcsh without EB-provided ncurses? +#builddependencies = [('tcsh', '6.18.01')] +osdependencies = ['tcsh'] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From fca31c50d3a4efc30b2f05a208a70c2eb8dc482a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 15:18:33 +0200 Subject: [PATCH 757/911] clean up comments --- .../easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb index aecb28f087..cfdc17ab69 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -15,11 +15,9 @@ source_urls = [ 'http://www.mmm.ucar.edu/wrf/src/', ] -# csh is used by WRF install scripts -# tcsh provided via EasyBuild may cause build to hang (in interactive configure?) -# ncurses related issue? rebuild tcsh without EB-provided ncurses? -#builddependencies = [('tcsh', '6.18.01')] +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] dependencies = [ ('JasPer', '1.900.1'), -- GitLab From ad84890dd55eb8282003990306ac64c1ad362726 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 17:33:21 +0200 Subject: [PATCH 758/911] add easyconfigs using CrayGNU/5.2.40 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.40.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.40.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.40.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.40-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.40.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb | 22 ++++ 20 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..67832ccafa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..58489cb68f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..275dc8cada --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..eea0ba5f73 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..470ec059e0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb new file mode 100644 index 0000000000..239ea564c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..cef32fd43d --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..4f2df44352 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..7264a9260e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..80df7f4320 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d1ac7167dc --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..af63de1cff --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..7d81f886bc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb new file mode 100644 index 0000000000..10c6659238 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..deac7ecaca --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d98933db4b --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..adb35688b3 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..171465e133 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb new file mode 100644 index 0000000000..4f97a28683 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..736d7b43ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 3fd381b1986243a3ba19d848b98c4246449750e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:47:47 +0200 Subject: [PATCH 759/911] update binutils to work with dummy --- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 7 ++--- .../easyconfigs/b/binutils/binutils-2.25.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb | 21 +++++++++++++++ 3 files changed, 52 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index e44a4bc4f7..8f92f6c007 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -11,12 +11,13 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'GCC', 'version': '4.9.2'} -dependencies = [ - ('zlib', '1.2.8'), -] +dependencies = [('zlib', '1.2.8')] + +configopts = '--with-sysroot' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb new file mode 100644 index 0000000000..8b1980cd7d --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [('zlib', '1.2.8')] + +configopts = '--with-sysroot' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb new file mode 100644 index 0000000000..50f8b33ec8 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From b7279aff404dced7a2306aeeecf7f96ece221900 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:48:32 +0200 Subject: [PATCH 760/911] Forgotten dependency --- easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 8f92f6c007..f91dda00cd 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} dependencies = [('zlib', '1.2.8')] +builddependencies = [('binutils', '2.25', '', True)] + configopts = '--with-sysroot' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', -- GitLab From 19fdbbcd774288f6c51a6336a0f689d350702968 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 16 May 2015 17:49:58 +0200 Subject: [PATCH 761/911] update gcc to use binutils --- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index cb9f3aa4f2..dd71a77ce5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' @@ -22,6 +22,8 @@ sources = [ 'mpc-1.0.2.tar.gz', ] +builddependencies = [('binutils', '2.25')] + patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ -- GitLab From cddd0c9e8349e8c14e1285413bd907ab663eb3af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 23:40:29 +0200 Subject: [PATCH 762/911] add easyconfigs using CrayGNU/5.2.25 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.25.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.25.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.25.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.25-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.25.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb | 42 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb | 22 ++++ 20 files changed, 608 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79f11b47fe --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..3f96190606 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..75190be28b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..43baa97a11 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e9455b96ac --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb new file mode 100644 index 0000000000..4a945e2af8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..606c94876c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e7bca79f1d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..6078f8b7e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79002b6ce4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..06f80557f1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..95c1010bbc --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..fa04b42299 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb new file mode 100644 index 0000000000..09917d5025 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..adcd0caa18 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..0772f31b94 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..be06b3e907 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..c678adaf68 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb new file mode 100644 index 0000000000..b4103d924f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..17db62ce98 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 977a898d0a0a34f670efb8eae3eb8eb8264462aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 17:33:21 +0200 Subject: [PATCH 763/911] add easyconfigs using CrayGNU/5.2.40 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.40.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.40.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.40.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.40-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.40.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb | 41 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb | 22 ++++ 20 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..67832ccafa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..58489cb68f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..275dc8cada --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..eea0ba5f73 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..470ec059e0 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb new file mode 100644 index 0000000000..239ea564c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..cef32fd43d --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..4f2df44352 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..7264a9260e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..80df7f4320 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d1ac7167dc --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..af63de1cff --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..7d81f886bc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb new file mode 100644 index 0000000000..10c6659238 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..deac7ecaca --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..d98933db4b --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000..adb35688b3 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..171465e133 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb new file mode 100644 index 0000000000..4f97a28683 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000..736d7b43ce --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 181bd951a6fd8505b74c2c275bc581ffe19a9148 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 23:40:29 +0200 Subject: [PATCH 764/911] add easyconfigs using CrayGNU/5.2.25 toolchain --- .../b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb | 22 ++++ .../b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb | 15 +++ .../c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb | 23 ++++ .../c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb | 38 +++++++ .../f/flex/flex-2.5.39-CrayGNU-5.2.25.eb | 14 +++ .../GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb | 38 +++++++ .../j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb | 21 ++++ .../l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb | 24 ++++ .../libreadline-6.3-CrayGNU-5.2.25.eb | 27 +++++ .../l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb | 32 ++++++ .../m/M4/M4-1.4.17-CrayGNU-5.2.25.eb | 23 ++++ .../n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb | 22 ++++ ...numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb | 26 +++++ .../Python-2.7.9-CrayGNU-5.2.25-bare.eb | 31 +++++ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 107 ++++++++++++++++++ .../s/Szip/Szip-2.1-CrayGNU-5.2.25.eb | 23 ++++ ...cipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb | 19 ++++ .../t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb | 39 +++++++ .../w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb | 42 +++++++ .../z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb | 22 ++++ 20 files changed, 608 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79f11b47fe --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..3f96190606 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb @@ -0,0 +1,15 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..75190be28b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..43baa97a11 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e9455b96ac --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb new file mode 100644 index 0000000000..4a945e2af8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '4.6.7' +versionsuffix = '-mpi' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..606c94876c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..e7bca79f1d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -0,0 +1,24 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..6078f8b7e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..79002b6ce4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..06f80557f1 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..95c1010bbc --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..fa04b42299 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb new file mode 100644 index 0000000000..09917d5025 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.9' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..adcd0caa18 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -0,0 +1,107 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..0772f31b94 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000..be06b3e907 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..c678adaf68 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb new file mode 100644 index 0000000000..b4103d924f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000..17db62ce98 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 2e364489f116e52784d5999acb4ed117fc5b0d5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 12:15:28 +0200 Subject: [PATCH 769/911] bump version to 2.1.1 and update release notes --- RELEASE_NOTES | 14 +++++++++++++- setup.py | 2 +- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c00535497a..d718187f88 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,21 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,618 easyconfig files, for 608 different software packages, +The latest version of easybuild-easyconfig provides 3,649 easyconfig files, for 611 different software packages, 33 different (compiler) toolchains and 8 software bundles. +v2.1.1 (May 18th 2015) +---------------------- + +bugfix release +- added example easyconfig files for 3 new software packages: + networkx (#1592), Platanus (#1597), SaguaroGW (#1600) +- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 +- various bug fixes, including: + - enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590) + v2.1.0 (April 30th 2015) ------------------------ diff --git a/setup.py b/setup.py index e89248dca4..7111a82776 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.1.1dev' +VERSION = '2.1.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From b4269fd81f4a535ab684aaf158614bc180a8cf7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 May 2015 16:06:08 +0200 Subject: [PATCH 770/911] include #1595, #1609 in v2.1.1 release notes --- RELEASE_NOTES | 2 ++ 1 file changed, 2 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d718187f88..8466fcf171 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -17,6 +17,8 @@ bugfix release including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 - various bug fixes, including: - enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590) + - use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595) + - only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609) v2.1.0 (April 30th 2015) ------------------------ -- GitLab From 2baae9592738f1fed3fa6e36fdca64d7090910c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 17 May 2015 09:44:45 +0200 Subject: [PATCH 771/911] includ PRs #1610 and #1611 in release notes --- RELEASE_NOTES | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8466fcf171..4f2bb65a95 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -13,6 +13,7 @@ bugfix release - added example easyconfig files for 3 new software packages: networkx (#1592), Platanus (#1597), SaguaroGW (#1600) - added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40 +- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611) - added additional easyconfigs for various supported software packages: version updates, different toolchains, ... including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 - various bug fixes, including: -- GitLab From 24dd63aaae7a34e34d0119be08d217eaf06b7e34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 09:02:48 +0200 Subject: [PATCH 772/911] fix easyconfigs count --- RELEASE_NOTES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 4f2bb65a95..b593156524 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 3,649 easyconfig files, for 611 different software packages, +The latest version of easybuild-easyconfig provides 3,689 easyconfig files, for 611 different software packages, 33 different (compiler) toolchains and 8 software bundles. v2.1.1 (May 18th 2015) -- GitLab From a04d50f343f8599e96d1bf8d68f4934cdadf502f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 13:50:25 +0200 Subject: [PATCH 773/911] {bio}[intel/2015a] MrBayes 3.2.5 --- .../m/MrBayes/MrBayes-3.2.5-intel-2015a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb new file mode 100644 index 0000000000..5836ec7f0f --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb @@ -0,0 +1,18 @@ +name = 'MrBayes' +version = '3.2.5' + +homepage = 'http://mrbayes.csit.fsu.edu' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] + +dependencies = [ + ('beagle-lib', '20141202'), + ('libreadline', '6.3'), +] + +moduleclass = 'bio' -- GitLab From 2b9145a950cdf0a5a90e027ced75f7130d08b2e7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 14:10:47 +0200 Subject: [PATCH 774/911] drop zlib dep in foss & gompi --- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 1 - easybuild/easyconfigs/g/gompi/gompi-2015.01.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index dfce67f25b..9c0f07775d 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -29,7 +29,6 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), (blaslib, blasver, blassuff, comp), diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb index e59112cb7f..1dd2af3813 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -16,7 +16,6 @@ comp = (compname, compver) # compiler toolchain dependencies dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), ] -- GitLab From 15e64083305ccf18fdeb24d6dc700aa5f3f3d327 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 14:13:14 +0200 Subject: [PATCH 775/911] forgotten toolchains --- easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 1 - easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb index f50cd40115..f8cc89cff5 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb @@ -16,7 +16,6 @@ comp = (compname, compver) # compiler toolchain dependencies dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), ] diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb index 0f2aea75a4..feeb6330ff 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb @@ -28,7 +28,6 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ comp, - ('zlib', '1.2.8', '', comp), ('binutils', '2.25', '', comp), ('OpenMPI', '1.8.4', '', comp), (blaslib, blasver, blassuff, comp), -- GitLab From 462c15dfe12a4805d0ef0a4342537242f4b112bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 16:10:12 +0200 Subject: [PATCH 776/911] static link with zlib in dummy binutils --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 8b1980cd7d..e3e98b2548 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,7 +11,11 @@ source_urls = [GNU_SOURCE] toolchain = {'name': 'dummy', 'version': ''} -dependencies = [('zlib', '1.2.8')] +builddependencies = [('zlib', '1.2.8')] + +# statically link with zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' configopts = '--with-sysroot' -- GitLab From a164a54aacab9104326fb3cd237753ba3e4830ed Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 18 May 2015 16:17:37 +0200 Subject: [PATCH 777/911] clearfy static linking zlib in binutils --- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index e3e98b2548..9a9d28a75d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'dummy', 'version': ''} builddependencies = [('zlib', '1.2.8')] -# statically link with zlib +# statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -- GitLab From 24863a480808fdfde716c66fdb0f88a332155c94 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 10:58:05 -0400 Subject: [PATCH 778/911] fixing version in sanity checks --- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index ec8aac5c94..7597335a90 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -20,11 +20,12 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] +# Due to the way versioning works now with ruby, the libraries and such are labelled major.minor.0 sanity_check_paths = { 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.%(version_major_minor)s.0', 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] + 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] } configopts = "--disable-install-doc --enable-shared" -- GitLab From ea7acab60f40e453856e5323a005a7256e82b90c Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 11:14:18 -0400 Subject: [PATCH 779/911] moving configopts to easyblock and updating other comments per PR comments --- easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index 7597335a90..d422f5a2f3 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -28,17 +28,12 @@ sanity_check_paths = { 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] } -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - -name_tmpl = '%(name)s-%(version)s.gem' ext_options = { 'source_urls': [ 'http://rubygems.org/downloads/', # gem archive ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s-%(version)s.gem', } exts_list = [ @@ -51,3 +46,5 @@ exts_list = [ ('clamp', '0.6.4', ext_options), ('fpm', '1.3.3', ext_options), ] + +moduleclass = 'lang' -- GitLab From b97ff1c4e5b44c4ea3f935b1d1ed1fbbcb67e668 Mon Sep 17 00:00:00 2001 From: Robert Schmidt Date: Mon, 18 May 2015 11:16:12 -0400 Subject: [PATCH 780/911] don't bother committing foss version --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 ------------------- .../r/Ruby/Ruby-2.1.5-intel-2014b.eb | 33 ------------------- 2 files changed, 66 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb deleted file mode 100644 index c585ab1d31..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb deleted file mode 100644 index 32eca44aae..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- -easyblock = 'ConfigureMake' - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'intel', 'version': '2014b'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' -- GitLab From d49bb8dfb55e1d67e8d8e192ee1fd1b22b33ea80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:32:14 +0200 Subject: [PATCH 781/911] {tools}[dummy] EasyBuild v2.1.1 --- .../e/EasyBuild/EasyBuild-2.1.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb new file mode 100644 index 0000000000..f6127ef3f7 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://pypi.python.org/packages/source/v/vsc-base/', + 'http://pypi.python.org/packages/source/e/easybuild-framework/', + 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.2.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' -- GitLab From ff52953b05070a498f1ce059ab60b203fc491505 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:44:18 +0200 Subject: [PATCH 782/911] use https source_urls in EasyBuild 2.1.1 easyconfig --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb index f6127ef3f7..632563276e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ -- GitLab From e079d27c019c59900735ddd457de4576d5f864b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 18:59:52 +0200 Subject: [PATCH 783/911] consistently use https for PyPI URLs in homepage/source_urls --- ...Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Cython-0.16-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb | 6 +++--- .../easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb | 8 ++++---- .../easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb | 8 ++++---- .../Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb | 2 +- ....4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb | 2 +- .../monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb | 2 +- .../PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb | 2 +- .../p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 10 +++++----- .../p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 10 +++++----- .../p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 10 +++++----- .../p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 10 +++++----- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.3-goolf-1.5.14.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-4.0.6.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 10 +++++----- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 10 +++++----- .../p/Python/Python-2.7.3-intel-2015a.eb | 10 +++++----- .../p/Python/Python-2.7.3-iomkl-4.6.13.eb | 10 +++++----- .../p/Python/Python-2.7.3-iqacml-3.7.3.eb | 10 +++++----- .../p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 10 +++++----- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 10 +++++----- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 10 +++++----- .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 10 +++++----- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 10 +++++----- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 10 +++++----- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 10 +++++----- .../p/Python/Python-2.7.8-foss-2014b.eb | 10 +++++----- .../p/Python/Python-2.7.8-goolf-1.5.14.eb | 14 +++++++------- .../p/Python/Python-2.7.8-ictce-7.1.2.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2014.06.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2014b.eb | 12 ++++++------ .../p/Python/Python-2.7.8-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 12 ++++++------ .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 12 ++++++------ .../p/Python/Python-2.7.9-foss-2015a.eb | 12 ++++++------ .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 12 ++++++------ .../p/Python/Python-2.7.9-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 6 +++--- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 6 +++--- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 6 +++--- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 6 +++--- .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 6 +++--- .../p/Python/Python-3.3.2-ictce-4.1.13.eb | 6 +++--- .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 6 +++--- .../p/Python/Python-3.4.1-intel-2014b.eb | 12 ++++++------ .../p/Python/Python-3.4.1-intel-2015a.eb | 12 ++++++------ .../p/Python/Python-3.4.3-intel-2015a.eb | 12 ++++++------ .../pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../pandas-0.16.0-intel-2015a-Python-2.7.9.eb | 2 +- ...check-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb | 6 ++---- .../paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb | 7 ++----- .../paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb | 6 ++---- ...13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb | 2 +- .../pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb | 2 +- ...ools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb | 4 ++-- .../setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb | 5 ++--- .../easyconfigs/s/setuptools/setuptools-1.4.2.eb | 4 ++-- .../stemming-1.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- 113 files changed, 377 insertions(+), 389 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 83aec1d936..01ad882b83 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index 892d56aaa1..fa53744e7c 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb index b81a538f5c..33197474ce 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb index 6e94f41099..5cd50bc1ae 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index 5d1302c3c1..f2fb277465 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index ebccd555bb..0e8ac631d0 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb index 3c845e9845..37ecdfbd48 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 544e217059..6ba8ee3375 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 6d9476ba0f..80955e4cc6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.2' -homepage = 'http://pypi.python.org/pypi/Cython/' +homepage = 'https://pypi.python.org/pypi/Cython/' description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 375a69f41e..6a13fbccbd 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index ceb0952d37..1fc508215c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index 335d94e6fb..aefe4f3461 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index 22d8fd70bd..aec17460aa 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index 99d04a46aa..12381b6467 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index e4ebd91d1b..a8ef6b164a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index 798cd20488..d2df7f1988 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index b7092a63e9..345d210d28 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index f8cd7d18f2..97720876b9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 1b3cf50b1a..0b5ba14c24 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index 8ceec790c8..0176f2b558 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index cfc44c499c..3ae286c658 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index 0f2a68be4b..b4fb5e015c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index d44b604d27..9025d6b24b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index 248cce692e..2ac7d84426 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index 83ed95495c..a7a958a3ca 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index 8f07608f03..26fbe953cd 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index 8d013d1941..84e658abed 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 4a22f26fd3..62ec508192 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index a94a92c657..f56094b5c0 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index 07838d8020..df9a262ab2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index fd30e9820c..9082a71a46 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index 39be41a74e..a2164fa02d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 1fe6136b55..8fa4a0a750 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index 629ec16acb..1774b8976c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index 15551872f9..d990801ac2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 4047b50760..97801124aa 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 2528629319..81d586f625 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index b11b8ff6c1..cb8c19e606 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb index 757c5d4553..4d3d248af6 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb @@ -13,8 +13,8 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.6' diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f06323716c..46c4f977e8 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb index 88fdc36fa5..e37ffbc4e2 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb index 4707146708..191856a900 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb index a801441c8b..9711dba080 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb index 1dfd105d74..d4224bd978 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'monty' version = '0.6.4' -homepage = 'http://pypi.python.org/pypi/monty/' +homepage = 'https://pypi.python.org/pypi/monty/' description = """Monty implements supplementary useful functions for Python that are not part of the standard library. Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton and cached_class, and many more.""" diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb index 7d2b055f0b..58d8cae9ee 100644 --- a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'monty' version = '0.6.4' -homepage = 'http://pypi.python.org/pypi/monty/' +homepage = 'https://pypi.python.org/pypi/monty/' description = """Monty implements supplementary useful functions for Python that are not part of the standard library. Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton and cached_class, and many more.""" diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb index bd74a7c6d1..580a294eee 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "PyYAML" version = "3.11" -homepage = "http://pypi.python.org/pypi/PyYAML/" +homepage = "https://pypi.python.org/pypi/PyYAML/" description = """PyYAML is a YAML parser and emitter for the Python programming language.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 5625804833..8bf00ee94a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index eea5ccfa5e..2ade7ad4f1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a6794c06c9..a73fef035d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index dc891b7530..2af2f0c181 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 51cfbe4606..0218dcafbd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 311b197edf..342b19c101 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index 80c8900b94..b883b3a7a7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index f847189fab..53fb8ff292 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index b2a76a28d3..c2cc52183e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 077f9d9e7e..994f20889f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 930a85f683..459199e8c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index f86e562788..3e4b4f03f3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 401dc6dd76..2e8be6d925 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index e19d9c8443..c6d6010f0e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 91d0cee83b..2da448273b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 31732a9f47..b7849aec58 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 3dd0016674..c17df2cb09 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -68,7 +68,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 47b8de7acf..9f5cd7d95f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,7 +46,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -62,7 +62,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index a9868e2f66..a24d0b3e6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index b3e31e4ea3..cee2b8e189 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index ec5e6c7a3a..751a483994 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -65,7 +65,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 4625232be8..8b46b16cd3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -65,7 +65,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 1496901c99..ed13d94285 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -53,7 +53,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -69,7 +69,7 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index ba61389fd5..8e7a62f6da 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 575fabb0e6..aaba09ba09 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index 8b621ebdee..d9f7ad0b77 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -67,7 +67,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 8ef1b28d6b..6e042b928d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,7 +48,7 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -64,7 +64,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://deap.googlecode.com/files/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 2dd2282def..09dc45c1e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,16 +48,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('six', '1.7.3', { - 'source_urls': ['http://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 478804a887..383b7d978b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -34,13 +34,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,13 +52,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -74,7 +74,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 54d5edce60..18aa12a4b8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 65ec137785..787f5ecab1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index ad901ece9f..16a9eea25f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -30,13 +30,13 @@ dependencies = [ # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index 4ef1c682d1..fdb44db0d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index adcd0caa18..bb0be0ac85 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index deac7ecaca..3950c920d4 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -31,13 +31,13 @@ buildopts = 'LINKCC="$CC -dynamic"' # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index d228f95a16..3273aa0399 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,13 +45,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index e667c4f618..9a1f9af5fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,13 +45,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 06dcabeb70..95f4d38205 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index ff366c2d52..033d183105 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index 1a46862919..c928dc3ca3 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index bfaa166f08..f523509a1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -29,14 +29,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index 92a41bf7e7..a47ee809f5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index c462546fe3..f23e383d17 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 51dd82cdf9..28d140c742 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index f1f4f3af6b..a66a2c142a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index b64218f00f..07f5694321 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 5769376b00..ba75d726f9 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index 3265a5bd15..c5e5b4ddcb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev')] exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ ('setuptools', '15.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,13 +48,13 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], @@ -73,7 +73,7 @@ exts_list = [ }), ('dateutil', '2.4.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 350eeb2738..7d470be431 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb index 683efb783b..644c39f1d8 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb index 9d8a5aeb67..236486c7f6 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb index b38ad74c90..934bb24741 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.12.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb index f0ae8b6a9f..36528b21fe 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.13.1" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb index d8f4627e56..a94b0b1e5d 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.16.0" -homepage = "http://pypi.python.org/pypi/pandas/" +homepage = "https://pypi.python.org/pypi/pandas/" description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.""" diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index dd8127de7f..05e281d1d7 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index c1a1ef52b4..67f7bc47b5 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -3,14 +3,12 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb index 9d393ee393..0f1fade586 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 295d530de8..5170a4d2bd 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -3,16 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb index 66535a0069..f140852405 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'iomkl', 'version': '4.6.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb index 8e35e9a845..5534c8acd7 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.0.13' -homepage = 'http://pypi.python.org/pypi/pymatgen' +homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.""" diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb index 73ac37040a..31bebaefdd 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'pymatgen' version = '3.0.13' -homepage = 'http://pypi.python.org/pypi/pymatgen' +homepage = 'https://pypi.python.org/pypi/pymatgen' description = """Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.""" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 5e2b080c59..637462ec29 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb index ca5228d480..517404e770 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb index d34f8f5f64..62aa6e2bbc 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb index 612cf670c0..82de605fe3 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb @@ -3,13 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index 87db02a9fa..f08e79381b 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -3,12 +3,12 @@ easyblock = "VersionIndependentPythonPackage" name = "setuptools" version = "1.4.2" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://pypi.python.org/packages/source/s/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb index 04c3e47988..241a1d5fbf 100644 --- a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "stemming" version = "1.0" -homepage = "http://pypi.python.org/pypi/stemming/" +homepage = "https://pypi.python.org/pypi/stemming/" description = """Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -- GitLab From 86662e26ed3675e7b71af0f4ccb419405765feea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2015 19:06:22 +0200 Subject: [PATCH 784/911] use PIPY_SOURCE as source URL where applicable --- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb | 4 ++-- .../c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb | 2 +- 14 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index 77441b5881..c519419dcf 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index e788568341..f278de669b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index cf67752ee4..a308b21130 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb index 3a32415096..a4f5169761 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index f9435f3efa..3303167a21 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb index 8a431e4a45..dbc8a13634 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -12,8 +12,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://pypi.python.org/packages/source/c/cutadapt/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index b165a51c0c..83a8d8a50d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index fbe7a035d3..f879b0939f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index a5093a2f21..60048badc4 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb index 737e7e93bb..a69f7bc2f8 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.9' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb index 467ed7ee6d..e1391aa56b 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb index d593001ecd..285c21b3f7 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb index 478d636658..411df518d3 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb index 172dead842..8894ccbab9 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From a6ab388623360535963811b931c41ba15464ea94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:20:02 +0200 Subject: [PATCH 785/911] add easyconfig for binary version of FDS --- .../easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb new file mode 100644 index 0000000000..f0c7225183 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FDS' +version = '6.0.1' +versionsuffix = '-no-OFED' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """ + Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and + heat transport from fires. +""" +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball +sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] + +dependencies = [('OpenMPI', '1.6.5-GCC-4.8.2-no-OFED')] + +skipsteps= ['configure', 'build'] + +sanity_check_paths = { + 'files': ['bin/fds', 'bin/fds_mpi'], + 'dirs': [], +} + +moduleclass = 'phys' -- GitLab From c52300e394b9cf0b7c924631155921ab7ee278f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:41:41 +0200 Subject: [PATCH 786/911] rename FDS patch file + style cleanup --- .../easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 9 ++++----- .../easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 12 ++++++------ ...{FDS_makefile.patch => FDS-r18915_makefile.patch} | 0 3 files changed, 10 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/f/FDS/{FDS_makefile.patch => FDS-r18915_makefile.patch} (100%) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index d49cfa69e6..5747ab3226 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -2,20 +2,19 @@ name = 'FDS' version = 'r18915' homepage = 'https://code.google.com/p/fds-smv/' -description = """ - Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and - heat transport from fires. -""" +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + # just run make in the install dir skipsteps = ['configure', 'install'] buildininstalldir = True -patches = ['FDS_makefile.patch'] modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb index ef3f6f0041..9710fba50f 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -2,19 +2,19 @@ name = 'FDS' version = 'r18915' homepage = 'https://code.google.com/p/fds-smv/' -description = """ - Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and - heat transport from fires. -""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + # just run make in the install dir skipsteps = ['configure', 'install'] buildininstalldir = True -patches = ['FDS_makefile.patch'] modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FDS/FDS_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch similarity index 100% rename from easybuild/easyconfigs/f/FDS/FDS_makefile.patch rename to easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch -- GitLab From 41b4371583caa928a9519cdaa614e4970ad46880 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 09:44:50 +0200 Subject: [PATCH 787/911] add missing 'easyblock' line --- easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb | 2 ++ easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index 5747ab3226..e84a122aeb 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'FDS' version = 'r18915' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb index 9710fba50f..78ff82e688 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'FDS' version = 'r18915' -- GitLab From b2a2986eb682f37726eee7a591584422cdabc52b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2015 15:52:28 +0200 Subject: [PATCH 788/911] {vis}[intel/2015a] frealign 9.09 --- .../frealign-9.09-intel-2015a-avx-mp.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb diff --git a/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb new file mode 100644 index 0000000000..a6b21fbfff --- /dev/null +++ b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'frealign' +version = '9.09' +versionsuffix = '-avx-mp' + +homepage = 'http://grigoriefflab.janelia.org/frealign' +description = """Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of + single particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = ['frealign_v%(version)s_150422.tar.gz'] + +start_dir = 'src' + +parallel = 1 + +# clean all included binaries first +prebuildopts = "rm ../bin/* && " +buildopts = "-f Makefile_linux_avx_intel_mp_static" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/resample_mp.exe', 'bin/merge_3d_mp.exe', 'bin/frealign_v%(version_major)s_mp.exe'], + 'dirs': [], +} + +moduleclass = 'vis' -- GitLab From 53337ee42f174c2358b16c68a3caf3022e462e1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 09:12:01 +0200 Subject: [PATCH 789/911] rework foss/2015.01 by introducing GNU subtoolchain --- .../Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb | 26 ++++++++++ .../Automake/Automake-1.15-GNU-4.9.2-2.25.eb | 33 ++++++++++++ ... binutils-2.25-GCC-4.9.2-binutils-2.25.eb} | 4 +- .../f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb | 34 ------------- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 14 ++--- .../g/GCC/GCC-4.9.2-binutils-2.25.eb | 45 ++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 2 - easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb | 20 ++++++++ easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb | 23 --------- .../easyconfigs/g/gompi/gompi-2015.01.eb | 12 ++--- easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb | 38 -------------- .../easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb | 18 ------- .../h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb | 23 +++++++++ .../l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb | 15 ++++++ .../m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb | 23 +++++++++ .../numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb | 31 +++++++++++ ...BLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb | 34 +++++++++++++ ...ompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 25 --------- .../zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 21 ++++++++ 20 files changed, 337 insertions(+), 155 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/b/binutils/{binutils-2.25-GCC-4.9.2.eb => binutils-2.25-GCC-4.9.2-binutils-2.25.eb} (85%) delete mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb create mode 100644 easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb delete mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..b57c1dcc83 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..f0e456c431 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb similarity index 85% rename from easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb rename to easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index f91dda00cd..9fe47929d3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -9,11 +9,11 @@ description = "binutils: GNU binary utilities" sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%(version)s'} dependencies = [('zlib', '1.2.8')] -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', version, '', True)] configopts = '--with-sysroot' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb deleted file mode 100644 index 080b817838..0000000000 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.9.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FFTW' -version = '3.3.4' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'gompi', 'version': '1.9.0'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [homepage] - -common_configopts = "--enable-threads --enable-openmp --with-pic" - -configopts = [ - common_configopts + " --enable-single --enable-sse2 --enable-mpi", - common_configopts + " --enable-long-double --enable-mpi", - common_configopts + " --enable-quad-precision", - common_configopts + " --enable-sse2 --enable-mpi", # default as last -] - -sanity_check_paths = { - 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + - ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + - ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb index 9c0f07775d..47df95ad70 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.01.eb @@ -9,9 +9,9 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, includi toolchain = {'name': 'dummy', 'version': 'dummy'} -comp_name = 'GCC' -comp_version = '4.9.2' -comp = (comp_name, comp_version) +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) blaslib = 'OpenBLAS' blasver = '0.2.13' @@ -28,10 +28,10 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions # For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), - (blaslib, blasver, blassuff, comp), + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..4985b9228e --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,45 @@ +name = "GCC" +version = '4.9.2' + +binutilsver = '2.25' +versionsuffix = '-binutils-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index dd71a77ce5..ebf339e6b0 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -22,8 +22,6 @@ sources = [ 'mpc-1.0.2.tar.gz', ] -builddependencies = [('binutils', '2.25')] - patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] checksums = [ diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..c1b036b3c1 --- /dev/null +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'GNU' +gccver = '4.9.2' +binutilsver = '2.25' +version = '%s-%s' % (gccver, binutilsver) + +homepage = 'http://gnu.org' +description = "Compiler-only toolchain with GCC and binutils." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # GCC built on top of (dummy-built) binutils + ('GCC', gccver, '-binutils-%s' % binutilsver), + # binutils built on top of GCC, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCC', '%s-binutils-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb b/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb deleted file mode 100644 index f8cc89cff5..0000000000 --- a/easybuild/easyconfigs/g/gompi/gompi-1.9.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompi' -version = '1.9.0' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compname = 'GCC' -compver = '4.9.2' -comp = (compname, compver) - -# compiler toolchain dependencies -dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb index 1dd2af3813..61953c785a 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb @@ -9,15 +9,15 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain, toolchain = {'name': 'dummy', 'version': 'dummy'} -compname = 'GCC' -compver = '4.9.2' -comp = (compname, compver) +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) # compiler toolchain dependencies dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb b/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb deleted file mode 100644 index feeb6330ff..0000000000 --- a/easybuild/easyconfigs/g/goolf/goolf-1.9.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = "Toolchain" - -name = 'goolf' -version = '1.9.0' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -comp_name = 'GCC' -comp_version = '4.9.2' -comp = (comp_name, comp_version) - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.5.0' - -# toolchain used to build goolf dependencies -comp_mpi_tc_name = 'gompi' -comp_mpi_tc_ver = "%s" % version -comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) - -# compiler toolchain depencies -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions -dependencies = [ - comp, - ('binutils', '2.25', '', comp), - ('OpenMPI', '1.8.4', '', comp), - (blaslib, blasver, blassuff, comp), - ('FFTW', '3.3.4', '', comp_mpi_tc), - ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb deleted file mode 100644 index e9fc6dc2e2..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-goolf-1.9.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'HPL' -version = '2.1' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic - on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the - High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'goolf', 'version': '1.9.0'} -toolchainopts = {'optarch': True, 'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..dfcbd3f2c0 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.0' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..9897d9bd11 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..e2764250bf --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.17' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..3ada055448 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Automake', '1.15'), + ('libtool', '2.4.2'), +] + +preconfigopts = './autogen.sh && ' + + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..1ff75dff8d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..14daf056ee --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.0')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb deleted file mode 100644 index e0aff023b0..0000000000 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.9.0-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'ScaLAPACK' -version = '2.0.2' - -homepage = 'http://www.netlib.org/scalapack/' -description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines - redesigned for distributed memory MIMD parallel computers.""" - -toolchain = {'name': 'gompi', 'version': '1.9.0'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TGZ] - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blassuff = '-LAPACK-3.5.0' - -versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) - -dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] - -## parallel build tends to fail, so disabling it -parallel = 1 - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000..64ff4fbec6 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 63c37d0acd168b26d30710221f45fc7da541f7cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 09:21:03 +0200 Subject: [PATCH 790/911] fix ScaLAPACK dep spec --- ...caLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb index 962d8049d0..cd879dacd3 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb @@ -17,7 +17,7 @@ blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -dependencies = [(blaslib, blasver, blassuff, ('GCC', '4.9.2'))] +dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.2-2.25'))] ## parallel build tends to fail, so disabling it parallel = 1 -- GitLab From 1009235604f4daa0eb83b0dd659c66d0f8ffe7d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:06:28 +0200 Subject: [PATCH 791/911] add Tk without X11 support --- .../t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..50b6df47b2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 206c5f6ff26612114751151767a7e9ebc9c2f220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:15:39 +0200 Subject: [PATCH 792/911] remove libX11 dep from no-X11 Tk easyconfig --- easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb index 50b6df47b2..39ccca9596 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -15,7 +15,6 @@ sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [ ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), ] configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' -- GitLab From 9f1645c4cc7b5494284c4c8b8b0531a5aa31f168 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:33:06 +0200 Subject: [PATCH 793/911] use --with-sysroot=/ in binutils easyconfigs --- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 3 ++- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 9fe47929d3..b93783f696 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,8 @@ dependencies = [('zlib', '1.2.8')] builddependencies = [('binutils', version, '', True)] -configopts = '--with-sysroot' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 9a9d28a75d..dee468601d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -17,7 +17,8 @@ builddependencies = [('zlib', '1.2.8')] preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -configopts = '--with-sysroot' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] -- GitLab From becefcb5a6635e5df687e18c59313044ddddd775 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 11:44:22 +0200 Subject: [PATCH 794/911] use no-X11 Tk as dep in R-extra easyconfig --- .../R-extra-20150323-intel-2015a-R-3.1.3.eb | 2 +- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 ------------------- .../easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb | 24 ------------------ 3 files changed, 1 insertion(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb delete mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb index 7ec2e95168..6cd16e2bf9 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), ('Tcl', '8.6.4'), - ('Tk', '8.6.4'), + ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb deleted file mode 100644 index b2673863fd..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb deleted file mode 100644 index de684154a7..0000000000 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tk' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building - a graphical user interface (GUI) in many different programming languages.""" - -toolchain = {'name': 'intel', 'version': '2015a'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('Tcl', version), - ('libX11', '1.6.3', '-Python-2.7.9'), -] - -configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' - -start_dir = 'unix' - -moduleclass = 'vis' -- GitLab From f0b88162888cec97df7788b437445f0f98efaa82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 12:00:37 +0200 Subject: [PATCH 795/911] readd Tcl 8.6.4 that is required as a dep --- .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' -- GitLab From ca15317769e216045f32651ab9e9b199fcbf3671 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 14:42:01 +0200 Subject: [PATCH 796/911] fix typo --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 838f4a2957..6efa3b178f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -244,7 +244,7 @@ def template_easyconfig_test(self, spec): # check easyconfig file name expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easconfig matches expected filename '%s'" % (spec, expected_fn) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) self.assertEqual(os.path.basename(spec), expected_fn, msg) name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) -- GitLab From 6c6c63d9e27c12d2ae6b99f88af11fbd8cf28637 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 13:41:12 +0200 Subject: [PATCH 797/911] WIP for R-bundles and devtools. Renaming the file and giving it a fix for the versionsuffix. Updated to reflect boegel's comment. --- ...s-20150520-intel-2015a-R-3.1.3-devtools.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb new file mode 100644 index 0000000000..cf38b2b642 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'R-bundles' +version = '20150520' +bundlename = 'devtools' +rver = '3.1.3' +versionsuffix = '-R-%s-%s' % (rver, bundlename) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.3.1', ext_options), + ('roxygen2', '4.1.1', ext_options), + ('git2r', '0.10.1', ext_options), + ('RCurl', '1.95-4.6', ext_options), + ('httr', '0.6.1', ext_options), + ('rversions', '1.0.0', ext_options), + ('devtools', '1.8.0', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'lang' + -- GitLab From 0ad26a61082a6538d145fa4a1bef534cc383bcbe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 15:48:17 +0200 Subject: [PATCH 798/911] update to OpenMPI 1.8.5 and OpenBLAS 0.2.14 (foss/2015.05) --- .../Autotools-20150215-GNU-4.9.2-2.25.eb | 17 +++++++ ...2015.01.eb => FFTW-3.3.4-gompi-2015.05.eb} | 2 +- easybuild/easyconfigs/f/foss/foss-2015.01.eb | 39 -------------- easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb | 2 +- .../easyconfigs/g/gompi/gompi-2015.01.eb | 23 --------- .../h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb | 23 --------- .../l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb | 15 ------ .../numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb | 6 +-- ...BLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 ------------------- .../o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb | 34 ------------- ...i-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb} | 4 +- 11 files changed, 22 insertions(+), 194 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-gompi-2015.01.eb => FFTW-3.3.4-gompi-2015.05.eb} (96%) delete mode 100644 easybuild/easyconfigs/f/foss/foss-2015.01.eb delete mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.01.eb delete mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb delete mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb => ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb} (89%) diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..25b293c3c4 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20150215' # date of the most recent change + +homepage = 'http://autotools.io' +description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb similarity index 96% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb index bcb190c092..0d9c4ae7b5 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.01.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb @@ -7,7 +7,7 @@ homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchain = {'name': 'gompi', 'version': '2015.05'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/foss/foss-2015.01.eb b/easybuild/easyconfigs/f/foss/foss-2015.01.eb deleted file mode 100644 index 47df95ad70..0000000000 --- a/easybuild/easyconfigs/f/foss/foss-2015.01.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = "Toolchain" - -name = 'foss' -version = '2015.01' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '4.9.2' -binutilsver = '2.25' -tcver = '%s-binutils-%s' % (gccver, binutilsver) - -blaslib = 'OpenBLAS' -blasver = '0.2.13' -blas = '%s-%s' % (blaslib, blasver) -blassuff = '-LAPACK-3.5.0' - -# toolchain used to build foss dependencies -comp_mpi_tc_name = 'gompi' -comp_mpi_tc_ver = "%s" % version -comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) - -# compiler toolchain depencies -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions -# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds -dependencies = [ - ('GCC', gccver, '-binutils-%s' % binutilsver), - ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), - (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), - ('FFTW', '3.3.4', '', comp_mpi_tc), - ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb index c1b036b3c1..61b0e08a72 100644 --- a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb @@ -5,7 +5,7 @@ gccver = '4.9.2' binutilsver = '2.25' version = '%s-%s' % (gccver, binutilsver) -homepage = 'http://gnu.org' +homepage = 'http://www.gnu.org/software/' description = "Compiler-only toolchain with GCC and binutils." toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb deleted file mode 100644 index 61953c785a..0000000000 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.01.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompi' -version = '2015.01' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -gccver = '4.9.2' -binutilsver = '2.25' -tcver = '%s-binutils-%s' % (gccver, binutilsver) - -# compiler toolchain dependencies -dependencies = [ - ('GCC', gccver, '-binutils-%s' % binutilsver), - ('binutils', binutilsver, '', ('GCC', tcver)), - ('OpenMPI', '1.8.4', '', ('GNU', '%s-%s' % (gccver, binutilsver))), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb deleted file mode 100644 index dfcbd3f2c0..0000000000 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.10.0' - -homepage = 'http://www.open-mpi.org/projects/hwloc/' -description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction - (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including - NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various - system attributes such as cache and memory information as well as the locality of I/O devices such as - network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering - information about modern computing hardware so as to exploit it accordingly and efficiently.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -dependencies = [('numactl', '2.0.10')] - -configopts = "--enable-libnuma=$EBROOTNUMACTL" - -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb deleted file mode 100644 index 9897d9bd11..0000000000 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,15 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libtool' -version = '2.4.2' - -homepage = 'http://www.gnu.org/software/libtool' -description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries - behind a consistent, portable interface.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [GNU_SOURCE] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb index 3ada055448..52f1df7369 100644 --- a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb @@ -15,14 +15,10 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] sources = [SOURCE_TAR_GZ] -builddependencies = [ - ('Automake', '1.15'), - ('libtool', '2.4.2'), -] +builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' - sanity_check_paths = { 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], 'dirs': ['share/man', 'include'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb deleted file mode 100644 index 1ff75dff8d..0000000000 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenBLAS' -version = '0.2.13' - -lapackver = '3.5.0' -versionsuffix = '-LAPACK-%s' % lapackver - -homepage = 'http://xianyi.github.com/OpenBLAS/' -description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] -source_urls = [ - # order matters, trying to download the LAPACK tarball from GitHub causes trouble - "http://www.netlib.org/lapack/", - "http://www.netlib.org/lapack/timing/", - "https://github.com/xianyi/OpenBLAS/archive/", -] - -patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), -] - -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' -installopts = "USE_THREAD=1 PREFIX=%(installdir)s" - -# extensive testing can be enabled by uncommenting the line below -#runtest = 'PATH=.:$PATH lapack-timing' - -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb deleted file mode 100644 index 14daf056ee..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GNU-4.9.2-2.25.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenMPI' -version = '1.8.4' - -homepage = 'http://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-2 implementation.""" - -toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - -dependencies = [('hwloc', '1.10.0')] - -configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' -configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support -configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading - -# needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] - -sanity_check_paths = { - 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + - ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], -} - -moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb similarity index 89% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb index cd879dacd3..e8390ed236 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.01-OpenBLAS-0.2.13-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -5,14 +5,14 @@ homepage = 'http://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '2015.01'} +toolchain = {'name': 'gompi', 'version': '2015.05'} toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' -blasver = '0.2.13' +blasver = '0.2.14' blassuff = '-LAPACK-3.5.0' versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) -- GitLab From 36303e1d582c3fd5e68fae3d6d28c3b3fdc60711 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 15:58:31 +0200 Subject: [PATCH 799/911] add missing easyconfigs --- .../easyconfigs/g/gompi/gompi-2015.05.eb | 23 +++++++++ .../l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb | 15 ++++++ ...BLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 51 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 34 +++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb new file mode 100644 index 0000000000..a9acbdd507 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..2985ab6f8a --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..23704a985e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.14' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..17455567fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.1')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", + "mpi", "ompitrace", "open-pal", + "open-rte", "vt", "vt-hyb", + "vt-mpi", "vt-mpi-unify"]] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' -- GitLab From 324627c42123041813559bf922af272a562e7d65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:06:20 +0200 Subject: [PATCH 800/911] add missing hwloc, also update HPL easyconfig for foss/2015.05 --- ...oss-2015.01.eb => HPL-2.1-foss-2015.05.eb} | 2 +- .../h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb | 23 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.1-foss-2015.01.eb => HPL-2.1-foss-2015.05.eb} (92%) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb similarity index 92% rename from easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb index 6e2eb261d6..6e7b16eb21 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.01.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'foss', 'version': '2015.01'} +toolchain = {'name': 'foss', 'version': '2015.05'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000..33b2aeafd6 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.1' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' -- GitLab From 217d5da8dc55d077a2acb7ba42db1a0ffc2896b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:15:07 +0200 Subject: [PATCH 801/911] add foss/2015.05 easyconfig --- easybuild/easyconfigs/f/foss/foss-2015.05.eb | 39 ++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2015.05.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2015.05.eb b/easybuild/easyconfigs/f/foss/foss-2015.05.eb new file mode 100644 index 0000000000..e468cc0b43 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015.05.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From afa60d29df4fe8302f4ec69816fa2cfbe8b0415f Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Wed, 20 May 2015 16:45:41 +0200 Subject: [PATCH 802/911] Roll back the cURL version since 7.41.0 is parked in a WIP PR. --- .../R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb index cf38b2b642..8cb259acf8 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -17,7 +17,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.41.0'), + ('cURL', '7.40.0'), ('libxml2', '2.9.2'), ] -- GitLab From 6947b4af64d910b5b3586d4a29c4a12a458384b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:54:47 +0200 Subject: [PATCH 803/911] don't fiddle with existing GCC-4.9.2.eb easyconfig --- easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index ebf339e6b0..cb9f3aa4f2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = {'name': 'dummy', 'version': 'dummy'} mpfr_version = '3.1.2' -- GitLab From 19101529562e7a25335428c780ab6320c6bcabbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 16:59:04 +0200 Subject: [PATCH 804/911] readd binutils easyconfig that was there already --- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb new file mode 100644 index 0000000000..e44a4bc4f7 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +dependencies = [ + ('zlib', '1.2.8'), +] + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 2acb0acb676ef4263c9e9b41c07626935db96886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 17:08:03 +0200 Subject: [PATCH 805/911] add --with-sysroot=/ to all binutils easyconfigs --- .../b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb | 7 +++++-- .../b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 7 +++++-- .../easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb | 5 ++++- .../easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb | 3 +++ .../easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb | 3 +++ .../easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 3 +++ 6 files changed, 23 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index 6d0b4d9315..09be4e2513 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 129afa50d1..037eea64d6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 98ff0c9aef..6eefeecf7f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -18,10 +18,13 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goolf', 'version': '1.4.10'} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 7e0429c8a1..f289f62f1b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb index 35ffa05491..90ee55811f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index e44a4bc4f7..080795bcde 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { -- GitLab From 948fa64a0701c1236890593168e3cf07d3e725a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 17:27:44 +0200 Subject: [PATCH 806/911] include Tcl and Tk as dependencies in R easyconfig --- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 ++ .../t/Tcl/Tcl-8.6.4-intel-2015a.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 19bdf89c03..fefd97519c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000..b2673863fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..39ccca9596 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 46e6b83f725bba2477cc26f82853bbe7b2d6376a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 18:22:29 +0200 Subject: [PATCH 807/911] Revert "don't bother committing foss version" This reverts commit b97ff1c4e5b44c4ea3f935b1d1ed1fbbcb67e668. --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 +++++++++++++++++++ .../r/Ruby/Ruby-2.1.5-intel-2014b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb new file mode 100644 index 0000000000..c585ab1d31 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb new file mode 100644 index 0000000000..32eca44aae --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-intel-2014b.eb @@ -0,0 +1,33 @@ +# With <3 for EasyBuild +# +# EasyConfig for Ruby 2.1: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Aaron Zauner +# ---------------------------------------------------------------------------- +easyblock = 'ConfigureMake' + +name = 'Ruby' +version = '2.1.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] + +sanity_check_paths = { + 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', + 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', + 'lib/libruby-static.a', 'lib/libruby.so'], + 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] +} + +configopts = "--disable-install-doc --enable-shared" + +moduleclass = 'lang' -- GitLab From c0e1547ae6e599aed6800950d34a54674ad0040c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 18:22:51 +0200 Subject: [PATCH 808/911] don't bother committing foss version (fixed) --- .../r/Ruby/Ruby-2.1.5-foss-2015a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb deleted file mode 100644 index c585ab1d31..0000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5-foss-2015a.eb +++ /dev/null @@ -1,33 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for Ruby 2.1: -# ---------------------------------------------------------------------------- -# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Aaron Zauner -# ---------------------------------------------------------------------------- - -name = 'Ruby' -version = '2.1.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] - -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.2.1.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/2.1.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-2.1.0'] -} - -configopts = "--disable-install-doc --enable-shared" - -moduleclass = 'lang' - -- GitLab From b6f710ac19644014cbec67d6e8c046af4b59ae0a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 18:49:43 +0200 Subject: [PATCH 809/911] add missing build dep for binutils in zlib --- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 64ff4fbec6..3f419579d9 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +builddependencies = [('binutils', '2.25', '', True)] + sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], 'dirs': [], -- GitLab From 76f35e21156e30e817fa9dc9a55e95ce559a8239 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 18:50:35 +0200 Subject: [PATCH 810/911] libtool was missing M4 dep --- easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb index 2985ab6f8a..f29d89e1c6 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb @@ -12,4 +12,6 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] +dependencies = [('M4', '1.4.17')] + moduleclass = 'lib' -- GitLab From 627201ca872c434956e141ea54f1ae6b115ce694 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 19:26:58 +0200 Subject: [PATCH 811/911] statically link zlib in binutils --- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index b93783f696..f316e5d537 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -6,18 +6,23 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -sources = [SOURCE_TAR_GZ] -source_urls = [GNU_SOURCE] - toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%(version)s'} -dependencies = [('zlib', '1.2.8')] +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] -builddependencies = [('binutils', version, '', True)] +builddependencies = [ + ('zlib', '1.2.8'), + ('binutils', version, '', True) +] # make sure that system libraries are also considered by ld configopts = '--with-sysroot=/' +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] -- GitLab From 38ce9f64b23d7bdf5de4d590e4670b7c42a5dbbc Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 May 2015 20:54:18 +0200 Subject: [PATCH 812/911] all binutils-2.25 link statically with zlib --- .../binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 6 +++--- .../easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb | 11 +++++++---- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 4 ++-- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index f316e5d537..cb9289d4be 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -16,13 +16,13 @@ builddependencies = [ ('binutils', version, '', True) ] -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' - # statically link with zlib, to avoid runtime dependency on zlib preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index 080795bcde..8aefcfeeee 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -6,20 +6,23 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +builddependencies = [('zlib', '1.2.8')] -dependencies = [ - ('zlib', '1.2.8'), -] +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' # make sure that system libraries are also considered by ld configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index dee468601d..3c7395c4a9 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -6,11 +6,11 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" +toolchain = {'name': 'dummy', 'version': ''} + sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'dummy', 'version': ''} - builddependencies = [('zlib', '1.2.8')] # statically link with zlib, to avoid runtime dependency on zlib -- GitLab From f6913e1ca0c1873885fc8c49f7b1435f485d090c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 20:57:29 +0200 Subject: [PATCH 813/911] flesh out FPM into a dedicated easyconfig, sanity_check_paths were moved to Ruby easyblock --- .../easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb | 17 +++++++++++++++++ easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb | 14 +------------- 2 files changed, 18 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb new file mode 100644 index 0000000000..a275aabe94 --- /dev/null +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb @@ -0,0 +1,17 @@ +easyblock = 'RubyGem' + +name = 'FPM' +version = '1.3.3' + +homepage = 'https://github.com/jordansissel/fpm' +description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease + and sanity.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', '2.1.5')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb index d422f5a2f3..a83d1888f2 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb @@ -20,19 +20,8 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] -# Due to the way versioning works now with ruby, the libraries and such are labelled major.minor.0 -sanity_check_paths = { - 'files': ['bin/ruby', 'bin/rake', 'bin/gem', 'bin/testrb', 'bin/erb', - 'bin/ri', 'bin/irb', 'bin/rdoc', 'lib/libruby.so.%(version_major_minor)s.0', - 'lib/libruby-static.a', 'lib/libruby.so'], - 'dirs': ['lib/ruby/%(version_major_minor)s.0', 'lib/ruby/gems', 'lib/pkgconfig', 'include/ruby-%(version_major_minor)s.0'] -} - - ext_options = { - 'source_urls': [ - 'http://rubygems.org/downloads/', # gem archive - ], + 'source_urls': ['http://rubygems.org/downloads/'], 'source_tmpl': '%(name)s-%(version)s.gem', } @@ -44,7 +33,6 @@ exts_list = [ ('backports', '3.6.4', ext_options), ('arr-pm', '0.0.9', ext_options), ('clamp', '0.6.4', ext_options), - ('fpm', '1.3.3', ext_options), ] moduleclass = 'lang' -- GitLab From 4dad61c9513cce50dd112e6e87c4ca4584e26049 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 21:16:37 +0200 Subject: [PATCH 814/911] bump versions: Ruby 2.1.6 + latest extension versions --- ...1.3.3-Ruby-2.1.5.eb => FPM-1.3.3-Ruby-2.1.6.eb} | 5 ++++- .../r/Ruby/{Ruby-2.1.5.eb => Ruby-2.1.6.eb} | 14 +++++++------- 2 files changed, 11 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/f/FPM/{FPM-1.3.3-Ruby-2.1.5.eb => FPM-1.3.3-Ruby-2.1.6.eb} (81%) rename easybuild/easyconfigs/r/Ruby/{Ruby-2.1.5.eb => Ruby-2.1.6.eb} (78%) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb similarity index 81% rename from easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb rename to easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index a275aabe94..b6d3efe3ac 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -3,6 +3,9 @@ easyblock = 'RubyGem' name = 'FPM' version = '1.3.3' +rubyver = '2.1.6' +versionsuffix = '-Ruby-%s' % rubyver + homepage = 'https://github.com/jordansissel/fpm' description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.""" @@ -12,6 +15,6 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://rubygems.org/downloads/'] sources = ['%(namelower)s-%(version)s.gem'] -dependencies = [('Ruby', '2.1.5')] +dependencies = [('Ruby', rubyver)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb similarity index 78% rename from easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb rename to easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb index a83d1888f2..b2e22e2b13 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.5.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb @@ -8,7 +8,7 @@ # ---------------------------------------------------------------------------- name = 'Ruby' -version = '2.1.5' +version = '2.1.6' homepage = 'https://www.ruby-lang.org' description = """Ruby is a dynamic, open source programming language with @@ -26,13 +26,13 @@ ext_options = { } exts_list = [ - ('ffi', '1.9.6', ext_options), - ('childprocess', '0.5.5', ext_options), - ('json', '1.8.2', ext_options), - ('cabin', '0.7.1', ext_options), + ('ffi', '1.9.8', ext_options), + ('childprocess', '0.5.6', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), ('backports', '3.6.4', ext_options), - ('arr-pm', '0.0.9', ext_options), - ('clamp', '0.6.4', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '0.6.5', ext_options), ] moduleclass = 'lang' -- GitLab From b78e23ea4e58b6aeb28fd761199985966487b8c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2015 22:03:41 +0200 Subject: [PATCH 815/911] include Tcl and Tk as dependencies in R foss/2015a easyconfig --- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 ++ .../easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb | 24 ++++++++++++++++++ 3 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index ad11c875f8..5d7d661a1f 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb new file mode 100644 index 0000000000..d1a6b6efb2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb new file mode 100644 index 0000000000..fee35bd216 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From f2d25bea1c5399f3d5b22e2f25f915ab2adac5ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:05:19 +0200 Subject: [PATCH 816/911] {vis}[intel/2015a] SPIDER 22.10 --- .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 41 +++++++++++ .../SPIDER-22.10_fix-syntax-ifort.patch | 71 +++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb new file mode 100644 index 0000000000..f9744a6899 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' +#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch new file mode 100644 index 0000000000..9857ea9f14 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -0,0 +1,71 @@ +--- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 ++++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 +@@ -88,7 +88,7 @@ + INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) + INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) + +- CHARACTER(LEN=1), ALLOCATABLE :: CVAL(:) ++ CHARACTER(LEN=:), ALLOCATABLE :: CVAL + + CHARACTER(LEN=24) :: CDATE + +@@ -290,7 +290,7 @@ + IF ( ICOUNT > ICVAL_LEN) THEN + IF (ALLOCATED(CVAL)) DEALLOCATE(CVAL) + ICVAL_LEN = ICOUNT +- ALLOCATE(CVAL(1)(ICVAL_LEN), STAT=IRTFLG) ++ ALLOCATE(CHARACTER(LEN=ICVAL_LEN) :: CVAL, STAT=IRTFLG) + + IF (IRTFLG .NE. 0) THEN + CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) +@@ -432,7 +432,7 @@ + GOTRESU = .TRUE. + + ELSEIF (ITAG == 306) THEN +- CDATE = CVAL(1)(1:22) ++ CDATE = CVAL(1:22) + c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', + c & CVAL(1)(1:ICOUNT) + GOTDATE = .TRUE. +--- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 ++++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 +@@ -269,7 +269,7 @@ + ENDIF + + C GREATER OF (0 AND (THE SMALLER OF RVAL AND 255)) +- IVAL = MAX(0,MIN(RVAL, 255.)) ++ IVAL = MAX(0.,MIN(RVAL, 255.)) + + IF (FLIP) THEN + IVAL = 255 - IVAL +--- spider/src/hisd.f.orig 2015-05-20 21:30:04.788208000 +0200 ++++ spider/src/hisd.f 2015-05-20 21:30:29.848221000 +0200 +@@ -146,9 +146,7 @@ + & 'OUTPUT DOC FILE (OR * IF NONE)',ISOLD,APPEND,MESSAGE, + & NEWFILE,IRTFLG) + +- WANTDOC = (IRTFLG == 0) +- +- IF (WANTDOC) THEN ++ IF (IRTFLG == 0) THEN + C OUTPUT TO DOC FILE + + C 123456789 123456789 123456789 123456789 123456789 +--- spider/src/star2doc.f.orig 2015-05-20 21:41:24.588241000 +0200 ++++ spider/src/star2doc.f 2015-05-20 21:41:50.069338858 +0200 +@@ -82,6 +82,7 @@ + CHARACTER(LEN=1) :: CDUM + INTEGER :: LUNDOCT,ILOC,IT,NLIST,ILAST + INTEGER :: IHI,I,IKEY,IRTFLG,LENREC,IVAR,ITOK ++ INTEGER :: NSPI + + LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM + LOGICAL :: ADDEXT,GETNAME +--- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +@@ -14,4 +14,4 @@ + .f.a: + $(COMP) $(FFLAGS) $< + $(AR) $(AFLAGS) $(LIB) $*.o +- @\rm $*.o ++# @\rm $*.o -- GitLab From b1b0d1ed44844db6e5e773b53ea20a18b485f6f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:06:21 +0200 Subject: [PATCH 817/911] fix path in SPIDER patch --- .../easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 9857ea9f14..3f36cf0b41 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -61,8 +61,8 @@ LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM LOGICAL :: ADDEXT,GETNAME ---- /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 -+++ /gpfs/scratch/projects/project_gpilot/vsc40023/software/SPIDER/22.10-intel-2015a/spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +--- spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 @@ -14,4 +14,4 @@ .f.a: $(COMP) $(FFLAGS) $< -- GitLab From a54658145a7cfe4633c9958ede6b2d7e44defd23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:40:43 +0200 Subject: [PATCH 818/911] add -mt and -mpi variants of SPIDER, extend patch --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 40 +++++++++++++++++++ .../s/SPIDER/SPIDER-22.10-intel-2015a.eb | 4 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 27 +++++++++++++ 4 files changed, 108 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb create mode 100644 easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb new file mode 100644 index 0000000000..051f460b6a --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mpi' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'usempi': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb new file mode 100644 index 0000000000..3638191610 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mt' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'openmp': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb index f9744a6899..cf9bac0479 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -27,9 +27,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -WB -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DSP_MP -c" LF="$F90FLAGS"' -#buildopts += 'FFLAGS="$F90FLAGS -DHAS_IEEE -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -DUSE_MPI -c" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 3f36cf0b41..57bb1f1a3d 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -69,3 +69,30 @@ $(AR) $(AFLAGS) $(LIB) $*.o - @\rm $*.o +# @\rm $*.o +--- spider/src/four_fq.f.orig 2015-05-21 10:37:01.109541000 +0200 ++++ spider/src/four_fq.f 2015-05-21 10:36:37.703908871 +0200 +@@ -1028,13 +1028,11 @@ + C BUTTERWORTH ELLIPTIC LOWPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + ELSEIF (IOPT == 12) THEN + C BUTTERWORTH ELLIPTIC HIGHPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + + ELSEIF (IOPT == 13) THEN +--- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 ++++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +@@ -1252,7 +1252,7 @@ + INCLUDE 'CMBLOCK.INC' + + INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG +- LOGICAL :: SAYIT ++ LOGICAL :: SAYIT, ENDFILE + + REAL, POINTER :: IPQ(:) + CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START -- GitLab From 0891d0214499d4bdbd11622f1a28da2bd075d69e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:41:25 +0200 Subject: [PATCH 819/911] make FDS patch compatible with recent versions --- easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch index d9c7c2a315..d7106bff9f 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch @@ -1,5 +1,5 @@ ---- makefile (revision 18916) -+++ makefile (working copy) +--- FDS_Compilation/makefile.orig (revision 18916) ++++ FDS_Compilation/makefile (working copy) @@ -29,9 +29,9 @@ # General Purpose Rules -- GitLab From 9519137d051e2f69640db52d87cfa9f5fdd412b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 10:42:06 +0200 Subject: [PATCH 820/911] {phys}[intel/2015a] FDS r17534 + rr22681 --- .../f/FDS/FDS-r17534-intel-2015a.eb | 32 +++++++++++++++++++ .../f/FDS/FDS-r17534_makefile.patch | 16 ++++++++++ .../f/FDS/FDS-r22681-intel-2015a.eb | 30 +++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch create mode 100644 easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb new file mode 100644 index 0000000000..2179b3462c --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r17534' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +parallel = 1 + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch new file mode 100644 index 0000000000..dea4f7695f --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch @@ -0,0 +1,16 @@ +diff -ru fds-r17534.orig/FDS_Compilation/makefile fds-r17534/FDS_Compilation/makefile +--- fds-r17534.orig/FDS_Compilation/makefile 2013-11-21 17:36:53.000000000 +0100 ++++ fds-r17534/FDS_Compilation/makefile 2015-05-19 13:01:04.892548269 +0200 +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb new file mode 100644 index 0000000000..0b9177003e --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r22681' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-r18915_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' -- GitLab From 65f9f761750f7e2fd484d4da6704cb5aba44af38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:25:23 +0200 Subject: [PATCH 821/911] {vis}[intel/2015a] matplotlib 1.4.3 (w/ Python 3.4.3) --- ...tplotlib-1.4.3-intel-2015a-Python-3.4.3.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb new file mode 100644 index 0000000000..147a7f4db6 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb @@ -0,0 +1,38 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '3.4.3' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From acdd3c93de06322ccdce81b8fb9926564d4e9063 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:38:09 +0200 Subject: [PATCH 822/911] remove useless comment --- .../m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb | 1 - .../m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb | 1 - .../m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb index d97e421867..6a25c33b0c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.6'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb index 0e33120d40..0397044fea 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.9'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb index da06531921..8072aaea0f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -25,7 +25,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 3a24c2da81..25762ccdf7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -27,7 +27,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb index 147a7f4db6..5849d559f7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb @@ -27,7 +27,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { -- GitLab From 9880d63fb8810ac68b62411fcfd610b43b6e7830 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 11:49:17 +0200 Subject: [PATCH 823/911] rename to R-bundle, depend on -extra bundle --- ...undle-20150520-intel-2015a-R-3.1.3-devtools.eb} | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/r/{R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb => R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb} (77%) diff --git a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb similarity index 77% rename from easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index 8cb259acf8..d4a983401d 100644 --- a/easybuild/easyconfigs/r/R-bundles/R-bundles-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -1,10 +1,9 @@ easyblock = 'Bundle' -name = 'R-bundles' +name = 'R-bundle' version = '20150520' -bundlename = 'devtools' rver = '3.1.3' -versionsuffix = '-R-%s-%s' % (rver, bundlename) +versionsuffix = '-R-%s-devtools' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,30 +16,25 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('cURL', '7.40.0'), - ('libxml2', '2.9.2'), + ('R-bundle', '20150323-R-%s-extra' % rver), ] -name_tmpl = '%(name)s_%(version)s.tar.gz' ext_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s_%(version)s.tar.gz' } # !! order of packages is important !! exts_list = [ - ('XML', '3.98-1.1', ext_options), ('memoise', '0.2.1', ext_options), ('whisker', '0.3-2', ext_options), ('rstudioapi', '0.3.1', ext_options), ('roxygen2', '4.1.1', ext_options), ('git2r', '0.10.1', ext_options), - ('RCurl', '1.95-4.6', ext_options), - ('httr', '0.6.1', ext_options), ('rversions', '1.0.0', ext_options), ('devtools', '1.8.0', ext_options), ] -- GitLab From ed31db7d4b72bef55e57e552e3daa64ead13efac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 12:20:31 +0200 Subject: [PATCH 824/911] rename to R-bundle, move vegan/widgetTools extensions to R easyconfig --- ...dle-20150323-intel-2015a-R-3.1.3-extra.eb} | 10 ++-- .../R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb | 47 ------------------- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 + 3 files changed, 5 insertions(+), 54 deletions(-) rename easybuild/easyconfigs/r/{R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb => R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb} (91%) delete mode 100644 easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb similarity index 91% rename from easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb rename to easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6cd16e2bf9..108db2e37d 100644 --- a/easybuild/easyconfigs/r/R-extra/R-extra-20150323-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -1,9 +1,9 @@ easyblock = 'Bundle' -name = 'R-extra' +name = 'R-bundle' version = '20150323' rver = '3.1.3' -versionsuffix = '-R-%s' % rver +versionsuffix = '-R-%s-extra' % rver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -16,8 +16,6 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('Tcl', '8.6.4'), - ('Tk', '8.6.4', '-no-X11'), ('cURL', '7.41.0'), ('libxml2', '2.9.2'), ] @@ -43,11 +41,9 @@ bioconductor_options = { # !! order of packages is important !! exts_list = [ - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk - ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ('RCurl', '1.95-4.5', ext_options), # requires cURL ('XML', '3.98-1.1', ext_options), # requires libxml2 - # extensions below requires one or more extensions that have an external dependency listed above + # extensions below require one or more extensions that have an external dependency listed above ('picante', '1.6-2', ext_options), ('spacodiR', '0.13.0115', ext_options), ('picante', '1.6-2', ext_options), diff --git a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb b/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb deleted file mode 100644 index e71e3abf1d..0000000000 --- a/easybuild/easyconfigs/r/R-extra/R-extra-3.1.2-1.0.0-foss-2015a.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'Bundle' - -name = 'R-extra' -rver = '3.1.2' -version = '%s-1.0.0' % rver - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'foss', 'version': '2015a'} - -# these are extensions for R -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -dependencies = [ - ('R', rver), - ('GMP', '6.0.0a'), # for gmp -] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], - 'source_tmpl': name_tmpl, -} -# Bioconductor packages have a different download url -bioconductor_options = { - 'source_urls': [ - 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', - 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -exts_list = [ - ('gmp', '0.5-12', ext_options), -] - -modextrapaths = {'R_LIBS': ''} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index fefd97519c..b39267177d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From e6b4b18c41bf0c69fc9c28be5d0df1c98807a8aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 13:06:12 +0200 Subject: [PATCH 825/911] fix remark --- easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb index 7c9526c34b..4e2d371a71 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -16,10 +16,9 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] -# dependencies = [('OpenSSL', '1.0.1m')] - osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# dependencies = [('OpenSSL', '1.0.1m')] # configopts = "--with-ssl=$EBROOTOPENSSL" sanity_check_paths = { -- GitLab From f3ffb1ab5ae2797d56b71885ff0dc5992d6bcb27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:01:00 +0200 Subject: [PATCH 826/911] {*}[foss/2015.05] Python 2.7.9 + Boost 1.58.0 + deps --- .../Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 26 ++++ .../b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 16 +++ .../libreadline-6.3-foss-2015.05.eb | 28 +++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 16 +++ .../p/Python/Python-2.7.9-foss-2015.05.eb | 116 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 39 ++++++ .../t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 26 ++++ .../z/zlib/zlib-1.2.8-foss-2015.05.eb | 23 ++++ 8 files changed, 290 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb new file mode 100644 index 0000000000..99e816f731 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb new file mode 100644 index 0000000000..94eb15f42f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000..09db15bea5 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,28 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..46d3cd55d8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,16 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb new file mode 100644 index 0000000000..2e2b6decfa --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -0,0 +1,116 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), +# ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb new file mode 100644 index 0000000000..a84b2916e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -0,0 +1,39 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015.05'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb new file mode 100644 index 0000000000..c4895ce18b --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb new file mode 100644 index 0000000000..6cb32ff060 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -0,0 +1,23 @@ +# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 5981713451bb61aea69314dfd0e2dd5c45ddea0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:31:09 +0200 Subject: [PATCH 827/911] SPIDER: update patch, use _mp Makefile for -mp/-mpi variants --- .../s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 2 +- .../s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb | 2 +- .../SPIDER-22.10_fix-syntax-ifort.patch | 116 +++++++++++++++++- 3 files changed, 112 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 051f460b6a..1a775fa535 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb index 3638191610..a747562bcb 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -27,7 +27,7 @@ parallel = 1 skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " -buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' modextrapaths = {'PATH': ['spider/bin']} diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch index 57bb1f1a3d..957ed589cf 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -1,5 +1,7 @@ +fix syntax issues that trip Intel Fortran compiler (ifort) +author: Kenneth Hoste (HPC-UGent) --- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 -+++ spider/src/copyfromtif.f 2015-05-20 20:18:45.688100002 +0200 ++++ spider/src/copyfromtif.f 2015-05-21 12:04:17.049891641 +0200 @@ -88,7 +88,7 @@ INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) @@ -18,15 +20,18 @@ IF (IRTFLG .NE. 0) THEN CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) -@@ -432,7 +432,7 @@ +@@ -432,9 +432,9 @@ GOTRESU = .TRUE. ELSEIF (ITAG == 306) THEN - CDATE = CVAL(1)(1:22) + CDATE = CVAL(1:22) c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', - c & CVAL(1)(1:ICOUNT) +-c & CVAL(1)(1:ICOUNT) ++c & CVAL(1:ICOUNT) GOTDATE = .TRUE. + + ELSE --- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 +++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 @@ -269,7 +269,7 @@ @@ -85,14 +90,113 @@ ELSEIF (IOPT == 13) THEN ---- spider/src/lundoc.f.orig 2015-05-21 10:39:00.645329000 +0200 -+++ spider/src/lundoc.f 2015-05-21 10:38:42.870873287 +0200 +--- spider/src/spider.f.orig 2015-04-21 15:30:40.000000000 +0200 ++++ spider/src/spider.f 2015-05-21 15:03:36.159704166 +0200 +@@ -195,9 +195,15 @@ + + #ifndef USE_MPI + #ifndef __APPLE__ ++#ifdef SP_IFC ++ isiz1 = kmp_get_stacksize() ++ CALL kmp_set_stacksize(65536) ++ isiz2 = kmp_get_stacksize() ++#else + isiz1 = omp_get_stack_size() + CALL omp_set_stack_size(65536) + isiz2 = omp_get_stack_size() ++#endif + !write(6,*) ' OMP Stack size: ',isiz1,' -->',isiz2 + + #endif +--- spider/src/lundoc.f.orig 2015-03-27 14:08:10.000000000 +0100 ++++ spider/src/lundoc.f 2015-05-21 15:26:30.008871936 +0200 @@ -1252,7 +1252,7 @@ INCLUDE 'CMBLOCK.INC' INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG - LOGICAL :: SAYIT -+ LOGICAL :: SAYIT, ENDFILE ++ LOGICAL :: SAYIT, EOF REAL, POINTER :: IPQ(:) CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START +@@ -1319,15 +1319,15 @@ + BACKSPACE(NDOC) ! REREAD LINE + READ(NDOC,*,END=100,IOSTAT=IER) RECLIN + +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ(NDOC,*,END=100,IOSTAT=IER) NKEY,NREGPLINE +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + +- 100 CALL BCAST_MPI('LUNDOCINFO','ENDFILE',ENDFILE,1,'L',ICOMM) ++ 100 CALL BCAST_MPI('LUNDOCINFO','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','IER',IER,1,'I',ICOMM) +- IF (ENDFILE) GOTO 799 ++ IF (EOF) GOTO 799 + + CALL BCAST_MPI('LUNDOCINFO','NKEY',NKEY,1,'I',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','NREGPLINE',NREGPLINE,1, +@@ -1434,7 +1434,7 @@ + + REAL :: PLIST(*) + CHARACTER(LEN=180) :: RECLIN +- LOGICAL :: TILLEND ++ LOGICAL :: TILLEND, EOF, ERRFILE + + CALL SET_MPI(ICOMM,MYPID,MPIERR) ! SETS ICOMM AND MYPID + +@@ -1464,18 +1464,18 @@ + 10 CONTINUE + IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=200) RECLIN + 81 FORMAT(A120) + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + 100 CALL BCAST_MPI('LUNDOCGETCOM','ERRFILE',ERRFILE,1,'L',ICOMM) + IF (ERRFILE) GOTO 998 + +-200 CALL BCAST_MPI('LUNDOCGETCOM','ENDFILE',ENDFILE,1,'L',ICOMM) +- IF (ENDFILE) GOTO 997 ++200 CALL BCAST_MPI('LUNDOCGETCOM','EOF',EOF,1,'L',ICOMM) ++ IF (EOF) GOTO 997 + + CALL BCAST_MPI('LUNDOCGETCOM','RECLIN',RECLIN,180,'C',ICOMM) + +@@ -1580,7 +1580,7 @@ + CHARACTER *120 RECLIN + #ifdef USE_MPI + include 'mpif.h' +- LOGICAL ENDFILE, ERRFILE ++ LOGICAL EOF, ERRFILE + ICOMM = MPI_COMM_WORLD + CALL MPI_COMM_RANK(ICOMM, MYPID, MPIERR) + #else +@@ -1595,15 +1595,15 @@ + #ifdef USE_MPI + 10 IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=100) RECLIN + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + +-100 CALL BCAST_MPI('LUNDOCSAYHDR','ENDFILE',ENDFILE,1,'L',ICOMM) ++100 CALL BCAST_MPI('LUNDOCSAYHDR','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCSAYHDR','ERRFILE',ERRFILE,1,'L',ICOMM) +- IF (ENDFILE .OR. ERRFILE) GOTO 999 ++ IF (EOF .OR. ERRFILE) GOTO 999 + + CALL BCAST_MPI('LUNDOCSAYHDR','RECLIN',RECLIN,120,'C',ICOMM) + #else -- GitLab From 7962d2cba1c7cd60964509de65f0b96a257106ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:35:47 +0200 Subject: [PATCH 828/911] add patch for installing paycheck as Py3 extension --- .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ ...aycheck-1.0.2_setup-open-README-utf8.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c5e5b4ddcb..d79f2b54ad 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -55,6 +55,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], diff --git a/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..193336def4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,22 @@ +open README file with utf-8 encoding, to avoid error like: +UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 577: ordinal not in range(128) +author: Kenneth Hoste (HPC-UGent) +--- paycheck-1.0.2/setup.py.orig 2015-05-21 16:09:24.300074046 +0200 ++++ paycheck-1.0.2/setup.py 2015-05-21 16:11:43.503945542 +0200 +@@ -1,6 +1,7 @@ + from distutils.cmd import Command + from distutils.core import setup + ++import codecs + import sys + if sys.version_info >= (3, 0): + try: +@@ -24,7 +25,7 @@ + name = 'paycheck', + version ='1.0.2', + description ='A Python QuickCheck implementation', +- long_description = open("README.txt").read(), ++ long_description = codecs.open("README.txt", encoding='utf-8').read(), + author ='Mark Chadwick', + author_email ='mark.chadwick@gmail.com', + maintainer ='Gregory Crosswhite', -- GitLab From 2294aff5b5e3a456e7598f75d227a55b0454b5c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 16:38:30 +0200 Subject: [PATCH 829/911] fix remark --- .../b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb | 1 - easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb | 1 - 8 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb index 99e816f731..24316a807f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_23-09-52 name = 'Boost' version = '1.58.0' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb index 94eb15f42f..1c3c8d1851 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-07 name = 'bzip2' version = '1.0.6' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 09db15bea5..c23d9ba711 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-10-20 easyblock = 'ConfigureMake' name = 'libreadline' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 46d3cd55d8..63b54fa7c4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-09-34 name = 'ncurses' version = '5.9' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 2e2b6decfa..ce15e506fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-50-18 name = 'Python' version = '2.7.9' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb index a84b2916e1..5e77859d07 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-17-48 ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb index c4895ce18b..bd202e0e1b 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-16-41 easyblock = 'ConfigureMake' name = 'Tcl' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb index 6cb32ff060..7668682872 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.2.0dev on 2015-05-20_22-07-46 easyblock = 'ConfigureMake' name = 'zlib' -- GitLab From 9884eda25ed3c0acd92494e121676cf6519bffae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 17:14:31 +0200 Subject: [PATCH 830/911] fix mpi variant of SPIDER --- .../easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb index 1a775fa535..cdcacc4631 100644 --- a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -9,7 +9,7 @@ description = """SPIDER (System for Processing Image Data from Electron microsco an image processing system for electron microscopy.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'static': True, 'usempi': True} +toolchainopts = {'usempi': True} source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] sources = ['spiderweb.%(version)s.tar.gz'] @@ -28,7 +28,7 @@ skipsteps = ['configure', 'install'] prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' -buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS"' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS -ldl -lpthread"' modextrapaths = {'PATH': ['spider/bin']} -- GitLab From e3f796267c030c4988e24274c0074483a8681d04 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 21 May 2015 18:23:16 +0200 Subject: [PATCH 831/911] CHARMM for intel/2015a --- .../c/CHARMM/CHARMM-37b2-intel-2015a.eb | 28 ++++++++++ ...CHARMM-37b2_fix-qgas-double-declared.patch | 53 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb new file mode 100644 index 0000000000..155eb5a8ae --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = "CHARMM" +version = "37b2" + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch new file mode 100644 index 0000000000..2c8d36a45f --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch @@ -0,0 +1,53 @@ +reproduction of CHARMM SVN revision 272 (Check-in: http:/charmm.hanyang.ac.kr/6187) +renamed qgas variable in pbeq to qgas1 and updated references in energy +diff -ru c37b2.orig/source/energy/energy.src c37b2/source/energy/energy.src +--- c37b2.orig/source/energy/energy.src 2012-09-29 08:01:42.000000000 +0200 ++++ c37b2/source/energy/energy.src 2015-05-21 16:57:43.951197202 +0200 +@@ -266,7 +266,7 @@ + use param + use pathm + use mpathint, only: qpint, epint !##PATHINT +- use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas,qsmbp,smbp0 !##PBEQ ++ use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas1,qsmbp,smbp0 !##PBEQ + use pbound + use pert + use polarm, only: qpolar, polar1 !##POLAR +@@ -3203,7 +3203,7 @@ + + CALL PBFORCE(NATOM,X,Y,Z,CG,ETERM(PBELEC),ETERM(PBNP), & + DX,DY,DZ,NPBEQ,ecalls,.false. & +- ,QETERM(QMEL),ETERM(QMEL),QGAS & !##SCCDFTB ++ ,QETERM(QMEL),ETERM(QMEL),QGAS1 & !##SCCDFTB + ) + IF (TIMER.GT.1) & + CALL WRTTIM('Poisson Boltzmann Solvation energy times:') +diff -ru c37b2.orig/source/misc/pbeq.src c37b2/source/misc/pbeq.src +--- c37b2.orig/source/misc/pbeq.src 2012-08-08 20:08:30.000000000 +0200 ++++ c37b2/source/misc/pbeq.src 2015-05-21 16:55:47.871787533 +0200 +@@ -19,7 +19,7 @@ + !public :: pbeq0,pbforce,gsbp0,srdist + !QC: export more + public :: pbeq0,pbforce,gsbp0,srdist,m3,dm3,rpowerl2,cosmphi2,sinmphi2,& +- alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas, & ++ alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas1, & + pbeq_iniall,smbp0 + + !variables +@@ -115,7 +115,7 @@ + + ! The following is related to QM/MM implementation of gsbp and pb + ! Xiao_QC_UW0609 +- LOGICAL QPSC,QGAS ++ LOGICAL QPSC,QGAS1 + ##IF SCCDFTB + ! + ! COEFX -----> heap index for COEFX(NTPOL) +@@ -2734,7 +2734,7 @@ + ! XIAO_QC_UW0609 keyword for SCC/PB + MXTPSC = GTRMI(COMLYN,COMLEN,'MXPS',5000) + PSCTOL = GTRMF(COMLYN,COMLEN,'PSTL',1.0D-2) +- QGAS = INDXA(COMLYN,COMLEN,'IGAS').GT.0 ++ QGAS1 = INDXA(COMLYN,COMLEN,'IGAS').GT.0 + ! XIAO_QC_UW0609 add charge dependant radii + QCHDRAD = INDXA(COMLYN,COMLEN,'CHDR').GT.0 + IF (QCHDRAD) THEN -- GitLab From 2642b0323b03578be61758ff225fb8effb98dac6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:09:11 +0200 Subject: [PATCH 832/911] add patch for installing deap as Py3 extension --- .../p/Python/Python-3.4.1-intel-2014b.eb | 6 ++++++ .../p/Python/Python-3.4.1-intel-2015a.eb | 6 ++++++ .../p/Python/Python-3.4.3-intel-2015a.eb | 3 +++ .../deap-1.0.2_setup-open-README-utf8.patch | 17 +++++++++++++++++ 4 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 07f5694321..49334fee76 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index ba75d726f9..8ddd32db67 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -56,6 +56,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { 'source_urls': ['http://argparse.googlecode.com/files/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index d79f2b54ad..a71f6ecf62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -81,6 +81,9 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000..6dece6f5d8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.2.orig/setup.py 2015-05-12 04:06:49.000000000 +0200 ++++ deap-1.0.2/setup.py 2015-05-21 19:06:03.792820042 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -10,7 +11,7 @@ + from pypandoc import convert + except ImportError: + print("warning: pypandoc module not found, could not convert Markdown to RST") +- read_md = lambda f: open(f, 'r').read() ++ read_md = lambda f: codecs.open(f, encoding='utf-8').read() + else: + read_md = lambda f: convert(f, 'rst') + -- GitLab From 4e5c4223b6c9fe5010909f037306404fef1a24ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:25:22 +0200 Subject: [PATCH 833/911] bump rtracklayer version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 108db2e37d..42f13415a0 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -51,7 +51,7 @@ exts_list = [ ('tkWidgets', '1.44.0', bioconductor_options), ('Mfuzz', '2.26.0', bioconductor_options), ('maSigPro', '1.38.0', bioconductor_options), - ('rtracklayer', '1.26.2', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), ('BSgenome', '1.34.1', bioconductor_options), ('GEOquery', '2.32.0', bioconductor_options), ('biomaRt', '2.22.0', bioconductor_options), -- GitLab From 929ead97b4a3abcee028477e385cb3c4fe6ab2e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:34:47 +0200 Subject: [PATCH 834/911] bump GenomicFeatures version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 42f13415a0..6fa810b17b 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -62,7 +62,7 @@ exts_list = [ ('GOstats', '2.32.0', bioconductor_options), ('geneplotter', '1.44.0', bioconductor_options), ('DESeq2', '1.6.3', bioconductor_options), - ('GenomicFeatures', '1.18.4', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), ('VariantAnnotation', '1.12.9', bioconductor_options), ('biovizBase', '1.14.1', bioconductor_options), ('OrganismDbi', '1.8.1', bioconductor_options), -- GitLab From 50b099be684215bc154f134486e6a16d856bed98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:47:36 +0200 Subject: [PATCH 835/911] bump KEGGprofile version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 6fa810b17b..732d498ea8 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -78,7 +78,7 @@ exts_list = [ ('Homo.sapiens', '1.1.2', bioconductor_options), ('KEGGgraph', '1.24.0', bioconductor_options), ('KEGGREST', '1.6.4', bioconductor_options), - ('KEGGprofile', '1.8.0', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), -- GitLab From bed4ccdb0fe734f652941f2bf890ae4792000c92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 19:59:16 +0200 Subject: [PATCH 836/911] bump GViz version --- .../r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb index 732d498ea8..a6d53af385 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150323-intel-2015a-R-3.1.3-extra.eb @@ -82,7 +82,7 @@ exts_list = [ ('minfi', '1.12.0', bioconductor_options), ('methylumi', '2.12.0', bioconductor_options), ('lumi', '2.18.0', bioconductor_options), - ('Gviz', '1.10.10', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), ('methyAnalysis', '1.8.0', bioconductor_options), ('pathview', '1.6.0', bioconductor_options), ('SPIA', '2.18.0', bioconductor_options), -- GitLab From 1c264c26a5d5c529eb5cc583f7fb2a4458a7b0dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 21:09:56 +0200 Subject: [PATCH 837/911] move vegan/widgetTools extensions to R foss/2015a easyconfig --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 5d7d661a1f..26e352af95 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -380,6 +380,8 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk ] moduleclass = 'lang' -- GitLab From 9cdee34afd8e5216d72b171cb7b50f3879f4e3fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 May 2015 22:29:45 +0200 Subject: [PATCH 838/911] include deap v1.0.1 specific patch --- .../p/Python/Python-3.4.1-intel-2014b.eb | 2 +- .../p/Python/Python-3.4.1-intel-2015a.eb | 2 +- .../deap-1.0.1_setup-open-README-utf8.patch | 17 +++++++++++++++++ 3 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 49334fee76..d3f83f3c59 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index 8ddd32db67..9f71e6e86f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -81,7 +81,7 @@ exts_list = [ ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 'patches': [ - 'deap-1.0.2_setup-open-README-utf8.patch', + 'deap-1.0.1_setup-open-README-utf8.patch', ], }), ('decorator', '3.4.0', { diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch new file mode 100644 index 0000000000..b7c896999f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.1.orig/setup.py 2014-04-08 15:49:52.000000000 +0200 ++++ deap-1.0.1/setup.py 2015-05-21 22:25:37.345008000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -11,7 +12,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=open('README.txt').read(), ++ long_description=codecs.open('README.txt', encoding='utf-8').read(), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='http://deap.googlecode.com', -- GitLab From 54ddbfbfdc33fa68c1ff125bca4e3783e3088d4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 May 2015 10:18:44 +0200 Subject: [PATCH 839/911] fix versionsuffix for extra R-bundle dep --- .../R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb index d4a983401d..5a2b464944 100644 --- a/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb +++ b/easybuild/easyconfigs/r/R-bundle/R-bundle-20150520-intel-2015a-R-3.1.3-devtools.eb @@ -16,7 +16,7 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") dependencies = [ ('R', rver), - ('R-bundle', '20150323-R-%s-extra' % rver), + ('R-bundle', '20150323', '-R-%s-extra' % rver), ] ext_options = { -- GitLab From d3d92f131d3efdaabfe60b03eb261de2f1730ebf Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 11:24:24 +0200 Subject: [PATCH 840/911] OpenFOAM foss 2015.05 flavour: needed for Centos6 on Haswell --- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb new file mode 100644 index 0000000000..14bd0cffc2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -0,0 +1,58 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432217883, + "build_time": 2389.2, + "install_size": 1888270856, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From 757910d0c00fcd3f85f4367e5fb29e55b92f4081 Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 12:15:43 +0200 Subject: [PATCH 841/911] adding missing libreadline,SCOTCH,ncurses,flex --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 40 ++++++++++++++ .../libreadline-6.3-foss-2015.05.eb | 53 +++++++++++++++++++ .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 48 +++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 40 ++++++++++++++ 4 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb new file mode 100644 index 0000000000..4e10bab03a --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 +name = 'flex' +version = '2.5.39' + +homepage = 'http://flex.sourceforge.net/' +description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215494, + "build_time": 21.24, + "install_size": 2865429, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000..1ad6cea720 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,53 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '6.3' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' +description = """The GNU Readline library provides a set of functions for use by applications that + allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. + The Readline library includes additional functions to maintain a list of previously-entered command lines, + to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215473, + "build_time": 17.27, + "install_size": 2395805, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000..5ba0974ce8 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,48 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build, no custom configure options + '', + # the UTF-8 enabled version (ncursesw) + '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +moduleclass = 'devel' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215455, + "build_time": 80.56, + "install_size": 24625439, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb new file mode 100644 index 0000000000..e388e08516 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -0,0 +1,40 @@ +# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' + +# Build statistics +buildstats = [{ + "easybuild-framework_version": "2.1.0", + "easybuild-easyblocks_version": "2.1.0", + "timestamp": 1432215375, + "build_time": 70.85, + "install_size": 6501533, + "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], + "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), + "core_count": 12, + "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", + "cpu_speed": 1600.0, + "cpu_vendor": "Intel", + "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", + "glibc_version": "2.12", + "hostname": "boot-tenova", + "os_name": "centos", + "os_type": "Linux", + "os_version": "6.6", + "platform_name": "x86_64-unknown-linux", + "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", + "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", + "system_python_path": "/usr/bin/python", +}] -- GitLab From a70c7d4b41166f23af8d4a68311170c86dd1594f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 14:28:00 +0200 Subject: [PATCH 842/911] cleaned comments in flex-2.5.39-foss-2015.05.eb libreadline-6.3-foss-2015.05.eb ncurses-5.9-foss-2015.05.eb OpenFOAM-2.3.1-foss-2015.05.eb SCOTCH-6.0.4-foss-2015.05.eb --- .../f/flex/flex-2.5.39-foss-2015.05.eb | 25 ------------------- .../libreadline-6.3-foss-2015.05.eb | 25 ------------------- .../n/ncurses/ncurses-5.9-foss-2015.05.eb | 25 ------------------- .../o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 25 ------------------- .../s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 25 ------------------- 5 files changed, 125 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 4e10bab03a..5f048f3577 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-38-14 name = 'flex' version = '2.5.39' @@ -14,27 +13,3 @@ source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215494, - "build_time": 21.24, - "install_size": 2865429, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 1ad6cea720..93acd649a7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-53 easyblock = 'ConfigureMake' name = 'libreadline' @@ -27,27 +26,3 @@ sanity_check_paths = { moduleclass = 'lib' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215473, - "build_time": 17.27, - "install_size": 2395805, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index 5ba0974ce8..e8393ca7cf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-37-36 name = 'ncurses' version = '5.9' @@ -22,27 +21,3 @@ configopts = [ moduleclass = 'devel' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215455, - "build_time": 80.56, - "install_size": 24625439, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 14bd0cffc2..6f0594b990 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_16-18-05 name = 'OpenFOAM' version = '2.3.1' @@ -32,27 +31,3 @@ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432217883, - "build_time": 2389.2, - "install_size": 1888270856, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index e388e08516..25db821e80 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -1,4 +1,3 @@ -# Built with EasyBuild version 2.1.0 on 2015-05-21_15-36-15 name = 'SCOTCH' version = '6.0.4' @@ -14,27 +13,3 @@ sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' -# Build statistics -buildstats = [{ - "easybuild-framework_version": "2.1.0", - "easybuild-easyblocks_version": "2.1.0", - "timestamp": 1432215375, - "build_time": 70.85, - "install_size": 6501533, - "command_line": ['--buildpath=/sw/eb/build', '--debug', '--installpath=/sw/eb', '--prefix=/sw/eb', '--repositorypath=/sw/eb/ebfiles_repo', '--robot=/sw/eb/software/EasyBuild/2.1.0/lib/python2.6/site-packages/easybuild_easyconfigs-2.1.0-py2.6.egg/easybuild/easyconfigs', '--sourcepath=/sw/eb/sources', '--try-toolchain="[\'foss\', \'2015.05\']"', 'OpenFOAM-2.3.1-intel-2015a.eb'], - "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'), - "core_count": 12, - "cpu_model": "Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz", - "cpu_speed": 1600.0, - "cpu_vendor": "Intel", - "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/sw/eb/software/GCC/4.9.2-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --enable-bootstrap --prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25 --with-local-prefix=/sw/eb/software/GCC/4.9.2-binutils-2.25; Thread model: posix; gcc version 4.9.2 (GCC) ; ", - "glibc_version": "2.12", - "hostname": "boot-tenova", - "os_name": "centos", - "os_type": "Linux", - "os_version": "6.6", - "platform_name": "x86_64-unknown-linux", - "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]", - "system_gcc_path": "/sw/eb/software/GCC/4.9.2-binutils-2.25/bin/gcc", - "system_python_path": "/usr/bin/python", -}] -- GitLab From ec29cc694ff50160a089ce904e308b967912d93f Mon Sep 17 00:00:00 2001 From: Stefano Bridi Date: Fri, 22 May 2015 15:11:53 +0200 Subject: [PATCH 843/911] a byte cleaner ;) --- easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb | 1 - .../easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb | 1 - easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb | 1 - easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb | 1 - easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb index 5f048f3577..208a02e540 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb @@ -12,4 +12,3 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb index 93acd649a7..c23d9ba711 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -25,4 +25,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb index e8393ca7cf..3ab27d3a62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -20,4 +20,3 @@ configopts = [ ] moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb index 6f0594b990..9e1b2ca02b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -30,4 +30,3 @@ dependencies = [ builddependencies = [('flex', '2.5.39')] moduleclass = 'cae' - diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb index 25db821e80..f5bdd9828b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -12,4 +12,3 @@ source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] sources = ['%(namelower)s_%(version)s.tar.gz'] moduleclass = 'math' - -- GitLab From ae63f1c4b91fbb4ed2ba8a4966887b4f4185c404 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 09:41:18 +0200 Subject: [PATCH 844/911] Update to Clang 3.6.1 --- .../c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb new file mode 100644 index 0000000000..15c22eef9c --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '4.9.2'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.0.0'), + ('ISL', '0.14'), +] + +builddependencies = [ + ('CMake', '3.2.1'), + ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' -- GitLab From 84c98379f747142ef37eaa45900c867af0f792cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:04:16 +0200 Subject: [PATCH 845/911] fix GMP 6.0.0a with GCC/4.9.2 --- .../c/Clang/Clang-3.6.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb | 2 +- .../easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb | 2 +- 4 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 445ace0985..40f0a86d6f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb index 08df157950..df7b8848c5 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0-GCC-4.9.2.eb @@ -9,7 +9,7 @@ operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = ["%(namelower)s-%(version)sa.tar.bz2"] +sources = ["%(namelower)s-%(version)s.tar.bz2"] source_urls = [GNU_SOURCE] # enable C++ interface diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb new file mode 100644 index 0000000000..a9855e2029 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.0.0a-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.0.0a' + +homepage = 'http://gmplib.org/' +description = """GMP is a free library for arbitrary precision arithmetic, +operating on signed integers, rational numbers, and floating point numbers. """ + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ["%(namelower)s-%(version)s.tar.bz2"] +source_urls = [GNU_SOURCE] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 3ba25676db..f6423e5d6e 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -dependencies = [('GMP', '6.0.0')] +dependencies = [('GMP', '6.0.0a')] sanity_check_paths = { 'files': ['lib/libisl.so', 'lib/libisl.a'], -- GitLab From 6f3f4dcf481be0bd3542527498c81f8346bf0a11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 11:30:48 +0200 Subject: [PATCH 846/911] {bio}[dummy] fastqc 0.11.2 + 0.11.3 --- .../easyconfigs/f/fastqc/fastqc-0.11.2.eb | 27 +++++++++++++++++++ .../easyconfigs/f/fastqc/fastqc-0.11.3.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb create mode 100644 easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb new file mode 100644 index 0000000000..9ff730ebed --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_60')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb new file mode 100644 index 0000000000..c5f20b9165 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.3' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' -- GitLab From 0af5491f63d43f506f1382e7c4b8b03394f31089 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 27 May 2015 11:59:09 +0200 Subject: [PATCH 847/911] Change name of gmp version --- easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb index 15c22eef9c..966759d71c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] -- GitLab From ac56b0de721ee0821608eb2d6a84be210e2c4ac1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 May 2015 14:42:17 +0200 Subject: [PATCH 848/911] add fpp + deps as R extensions --- easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 4 ++++ easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 26e352af95..dee61f1e01 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index b39267177d..d50dfde38a 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,6 +382,10 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' -- GitLab From e1c84d962128346b1073db16e6f069a8d4acbec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 11:13:08 +0200 Subject: [PATCH 849/911] include patch to build forecast with Intel compilers --- easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index d50dfde38a..56604be04c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -382,7 +382,7 @@ exts_list = [ ('Rsubread', '1.16.1', bioconductor_options), ('vegan', '2.2-1', ext_options), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), ('fma', '2.01', ext_options), ('expsmooth', '2.3', ext_options), ('fpp', '0.5', ext_options), diff --git a/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch new file mode 100644 index 0000000000..8582ea93ae --- /dev/null +++ b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch @@ -0,0 +1,9 @@ +ignore warning/error when building with Intel C++ compiler by including -wd308 flag in $CXXFLAGS +author: Kenneth Hoste (HPC-UGent) +--- forecast/src/Makevars.orig 2015-05-12 11:56:10.000000000 +0200 ++++ forecast/src/Makevars 2015-05-28 10:53:13.878100139 +0200 +@@ -1,2 +1,4 @@ + ## Use the R_HOME indirection to support installations of multiple R version + PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 -- GitLab From ac6d71a57e7784a9017eb7d5416c05efb0088eca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:47:03 +0200 Subject: [PATCH 850/911] {lang}[intel/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-intel-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb new file mode 100644 index 0000000000..e42c4eb9ce --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb new file mode 100644 index 0000000000..7f1dc7e31f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 9a43d2783570dc62fe774b79cd59b0143b8c8e04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 12:49:18 +0200 Subject: [PATCH 851/911] {lang}[foss/2015a] Python 2.7.10 --- .../p/Python/Python-2.7.10-foss-2015a.eb | 120 ++++++++++++++++++ .../s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 40 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb new file mode 100644 index 0000000000..16e9072248 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -0,0 +1,120 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['http://argparse.googlecode.com/files/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb new file mode 100644 index 0000000000..d5bf2693bd --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From bcdea025bfc604af17e7d4e6b7d2b60796af2937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:33:19 +0200 Subject: [PATCH 852/911] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb index 7f1dc7e31f..03c9b50fba 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 8ab6b2e829ee34003022ad74349f38f9ffb9ce50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:34:51 +0200 Subject: [PATCH 853/911] extend sanity check for SQLite --- easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb index d5bf2693bd..fbe46bacc9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -33,8 +33,8 @@ dependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['bin/sqlite3'], - 'dirs': [], + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], } moduleclass = 'devel' -- GitLab From 7d572304650bd03f278d32035f5665c3a7577f22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:36:46 +0200 Subject: [PATCH 854/911] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb index 16e9072248..08ae2a5f52 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 8ec777916625061646218da5cccda84090b7e1ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 14:37:01 +0200 Subject: [PATCH 855/911] fix remark --- easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb index e42c4eb9ce..5691adf05e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -2,7 +2,8 @@ name = 'Python' version = '2.7.10' homepage = 'http://python.org/' -description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -- GitLab From 3882c4aaaed7c4227813b84110b97205f92eb9e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:07:40 +0200 Subject: [PATCH 856/911] {phys}[intel/2015a] Geant4 10.01.p01 --- .../c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 19 +++++++++++++++ .../g/Geant4/Geant4-10.01.p01-intel-2015a.eb | 24 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb new file mode 100644 index 0000000000..c165bda92e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.5' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb new file mode 100644 index 0000000000..412c19225c --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '10.01.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.2.0.5'), +] + +builddependencies = [('CMake', '3.2.2')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' -- GitLab From 9ec1a46de2390d2d455c64ffc2f10606f4d73db5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 May 2015 15:45:52 +0200 Subject: [PATCH 857/911] add missing CMake build dep --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb index c165bda92e..9408c50361 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -14,6 +14,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +builddependencies = [('CMake', '3.2.2')] + separate_build_dir = True moduleclass = 'numlib' -- GitLab From 84c0c0920951a011d2b4514910b746da00c5ebc2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 10:55:58 +0200 Subject: [PATCH 858/911] added gcc 4.5.2 --- easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb | 37 ++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb new file mode 100644 index 0000000000..719bc6f315 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.5.2' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, + Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.2.tar.gz', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.8.2.tar.gz', +] + +checksums = [ + 'e31fe695d7235f11fb5a63eafdfbfe88', # gcc-4.5.2.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' -- GitLab From 43055375813abdc4dff967afd008353b5646839e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 29 May 2015 11:03:50 +0200 Subject: [PATCH 859/911] Added GCC 4.6.0 --- easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb | 35 ++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb new file mode 100644 index 0000000000..f310421ff2 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.6.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, + Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.9.tar.gz', +] + +checksums = [ + '009f59ee0f9c8100c12939140698cf33', # gcc-4.6.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From a396d464cc65eba9b7d35613d13be752d63a1e43 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Fri, 29 May 2015 11:48:02 +0200 Subject: [PATCH 860/911] Add hanythingondemand eb files. These could otherwise have been installed w/ --try-software-version --- ...ondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ ...ondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 34 +++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb create mode 100644 easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..f6063d9ec3 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.2' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..9182229d2c --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.3' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000..73433b3081 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.4' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' -- GitLab From 87a8597e5c07722acbe0a06dd001bcf9b04e368d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 May 2015 14:07:44 +0200 Subject: [PATCH 861/911] style fixes in pBWA easyconfig --- .../p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb index 754be559e1..fa5b729bcb 100644 --- a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -13,7 +13,7 @@ name = 'pBWA' version = '0.5.9_1.21009' homepage = 'http://pbwa.sourceforge.net/' -description = """pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.""" +description = "pBWA is a parallel implementation of the popular software BWA." toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} @@ -21,18 +21,13 @@ toolchainopts = {'optarch': True, 'pic': True} sources = ['%(name)s_%(version)s.zip'] source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] - - -dependencies = [ - ('BWA', '0.7.4'), -] +dependencies = [('BWA', '0.7.4')] files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] sanity_check_paths = { - 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], - 'dirs': ['.'], - + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], } moduleclass = 'bio' -- GitLab From 3b0eec5db69770911d52947e78b1f89df48c5824 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:00:43 +0200 Subject: [PATCH 862/911] Adding ABySS-1.5.2-goolf-1.4.10 --- .../a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..678a7abd6f --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.5.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] + +dependencies = [('Boost', '1.53.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c5a863a5e45f620767357721fc87bc880f47759b Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:14:18 +0200 Subject: [PATCH 863/911] Adding BEDTools-2.23.0-goolf-1.4.10 --- .../BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..6dd7cdc664 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] +sources = ['v%(version)s/bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' -- GitLab From df353b92cb8dc3d0023eb54ee401cc53622365a5 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:21:00 +0200 Subject: [PATCH 864/911] Comments modifications --- easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb index 678a7abd6f..c055778c8e 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -2,12 +2,10 @@ # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos +# Authors:: Maxime Schmitt , Fotis Georgatos # License:: MIT/GPL # $Id$ # -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## easyblock = 'ConfigureMake' @@ -21,9 +19,8 @@ description = """Assembly By Short Sequences - a de novo, parallel, paired-end s toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} -# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://github.com/bcgsc/abyss/releases/download/1.5.2/'] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] dependencies = [('Boost', '1.53.0')] -- GitLab From 440afe75a71962fb1c166bc2918f0735000d14de Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:23:50 +0200 Subject: [PATCH 865/911] Modifying comments --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 6dd7cdc664..61147b9331 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -1,4 +1,6 @@ -# Author: Pablo Escobar Lopez +# Author: Maxime Schmitt, University of Luxembourg +# +# Based on the work of: Pablo Escobar Lopez # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel -- GitLab From ec543429de043b66a96a3c9df79887ea6bcd0886 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:34:14 +0200 Subject: [PATCH 866/911] Adding Cufflinks-2.2.1-goolf-1.4.10 --- .../Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..9897454369 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['cufflinks-2.2.1.tar.gz'] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c2c18d4e50385d295f2bddd919b09410c0a7887a Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:35:34 +0200 Subject: [PATCH 867/911] Fixing hardcoded version --- .../easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb index 9897454369..3fdf2a0923 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """Transcript assembly, differential expression, and differential toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['cufflinks-2.2.1.tar.gz'] +sources = ['cufflinks-%(version)s.tar.gz'] source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] dependencies = [ -- GitLab From d09ca49609ada079f83cd2fe185768a3fab2eb23 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:39:37 +0200 Subject: [PATCH 868/911] Fixing source url --- .../easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb index 61147b9331..0c511d17e0 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -17,8 +17,8 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'goolf', 'version': '1.4.10'} # https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz -source_urls = ['https://github.com/arq5x/bedtools2/releases/download/'] -sources = ['v%(version)s/bedtools-%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] buildopts = 'CXX="$CXX"' -- GitLab From ea33e462b738dabf5a7599968dbaef758b8a0b2c Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 15:51:37 +0200 Subject: [PATCH 869/911] Adding Cython-0.22-goolf-1.4.10-Python-2.7.3.eb --- .../Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..d2b4a22df9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.22' + +homepage = 'http://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) +cythonlibdir = '/'.join([pylibdir, cythonsubdir]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], +} + +moduleclass = 'lang' -- GitLab From b2e3c06deb1e415505a3d7d1423a7fc39ca30902 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:28:06 +0200 Subject: [PATCH 870/911] Better use of variables --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index d2b4a22df9..55a97c1d73 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -14,11 +14,9 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -pylibdir = 'lib/python%s/site-packages' % pythonshortver -cythonsubdir = '-'.join(['Cython', version, 'py'+pythonshortver, 'linux-x86_64.egg']) -cythonlibdir = '/'.join([pylibdir, cythonsubdir]) versionsuffix = '-%s-%s' % (python, pythonver) +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From 10be91757f584afc2df8650f144182daa8338505 Mon Sep 17 00:00:00 2001 From: Maxime Schmitt Date: Fri, 29 May 2015 16:42:55 +0200 Subject: [PATCH 871/911] Fixing name resolutions --- .../c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb index 55a97c1d73..08f3c850f6 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -15,8 +15,8 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -cythonlibdir = 'lib/python%(pythonshortver)s/site-packages/Cython-%(version)s-py%(pythonshortver)s-linux-x86_64.egg' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py' + pyshortver + '-linux-x86_64.egg' dependencies = [(python, pythonver)] -- GitLab From 7739627e35c49cff90c67712ea8af592f3b73509 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 13:44:11 +0200 Subject: [PATCH 872/911] fix typo, remove unneeded configopts --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index e5ab48448f..25c6d013bc 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -17,8 +17,7 @@ checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' -configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-netcdf-libs="-L$EBROOTLIBXC/lib -lxc" ' -configopts += "fcflags_opt_43_ptgroups='-O0 -g -extend-source'" +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' dependencies = [ ('libxc', '2.2.2'), -- GitLab From 553df5b666baa5856f9ccac51602e323a27b9d78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 14:48:19 +0200 Subject: [PATCH 873/911] {chem}[intel/2015a] ABINIT 7.10.4 --- .../a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb new file mode 100644 index 0000000000..955b1cd4f1 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +moduleclass = 'chem' -- GitLab From c67a9ec7774a9c9f488781a504cf51ab135cf180 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:06 +0200 Subject: [PATCH 874/911] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 955b1cd4f1..24a268901b 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 050fa061b42d083907090abebe3df8017142b871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 15:05:23 +0200 Subject: [PATCH 875/911] add custom sanity check paths for ABINIT --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 25c6d013bc..51c5aef3d9 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -25,4 +25,9 @@ dependencies = [ ('netCDF-Fortran', '4.4.0'), ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'chem' -- GitLab From 57168333ad91183825fc00bbb34cc0322bcbdccd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:13 +0200 Subject: [PATCH 876/911] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb index 51c5aef3d9..97bc886c26 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 0f48dfa2c9bc9443825325f101a985d9e306ae5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 May 2015 20:31:35 +0200 Subject: [PATCH 877/911] fix typo --- easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb index 24a268901b..7561f6f45c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -26,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optics']], + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], } -- GitLab From 6857cd98a5c3de64c6a53265cd490c4da464b4a9 Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 10:37:53 +0200 Subject: [PATCH 878/911] Gromacs 5.0.5-intel2015a easycofig --- .../GROMACS-5.0.5-intel-2015a-hybrid.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb new file mode 100644 index 0000000000..09ed0e7dc1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University +# Authors:: Wiktor Jurkowski , Fotis Georgatos , \ +# George Tsouloupas , Kenneth Hoste +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html +## +name = 'GROMACS' +version = '5.0.5' +versionsuffix = '-hybrid' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.1.0'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] + +moduleclass = 'bio' -- GitLab From 73db870ee8050759cb01d991f35404ca5d37887f Mon Sep 17 00:00:00 2001 From: Ingrid Barcena Roig Date: Mon, 1 Jun 2015 17:35:50 +0200 Subject: [PATCH 879/911] Gromacs 5.0.5-intel2015a easycofig --- .../easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb index 09ed0e7dc1..c7e0273a3e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb @@ -25,10 +25,10 @@ source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('CMake', '3.1.0'), + ('CMake', '3.2.2'), ('libxml2', '2.9.2') ] -dependencies = [('Boost', '1.57.0', '-Python-2.7.9')] +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] moduleclass = 'bio' -- GitLab From bd81df67d7ee4ce73bb19e2869d24077f280b9fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Jun 2015 18:59:22 +0200 Subject: [PATCH 880/911] fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 3 +-- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 3 +-- .../QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 3 +-- 10 files changed, 10 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 9409f95fc2..89cf3c3778 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index 4a03ccc94b..ec449db284 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index d97dae5c5d..476628bcd5 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index d7fb61f42c..e0dbe69249 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 04f547b28a..0b54c5912d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index 479e526fb3..c6b5e835da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index 1b9a405ed8..a5a5338771 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 5740815aa1..9007ee9bb7 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index bf87cf39af..f4b21d4cab 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index a341ebad38..aa0ea72322 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz 'http://files.qe-forge.org/index.php?file=', # others + 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] patches = [ -- GitLab From be2f94d281c7560934c72b997676ac1b65dceac7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 09:42:46 +0200 Subject: [PATCH 881/911] fix remark --- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 2 +- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 89cf3c3778..d000d6ec7f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index ec449db284..a34afc570a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index 476628bcd5..5ef2e6d1b1 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index e0dbe69249..1e036026da 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 0b54c5912d..464f263647 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index c6b5e835da..cd0fac60cb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index a5a5338771..9533b73dfd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 9007ee9bb7..b3212736f0 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index f4b21d4cab..ae347ad0bd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,7 +30,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index aa0ea72322..2a054ef2d3 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,7 +29,7 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ - 'http://files.qe-forge.org/index.php?file=', # others + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz ] -- GitLab From f0b78c2b17b0111a3369d9987b94c32d70b0156f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:29:40 +0200 Subject: [PATCH 882/911] {vis}[intel/2015a] libXScrnSaver 1.2.2 + libXft 2.3.2 --- .../fontconfig-2.11.93-intel-2015a.eb | 22 ++++++++++++ .../k/kbproto/kbproto-1.0.7-intel-2015a.eb | 19 +++++++++++ .../libXScrnSaver-1.2.2-intel-2015a.eb | 24 +++++++++++++ .../libXft-2.3.2-intel-2015a-libX11-1.6.3.eb | 34 +++++++++++++++++++ .../libXrender-0.9.9-intel-2015a.eb | 28 +++++++++++++++ .../renderproto-0.11-intel-2015a.eb | 20 +++++++++++ 6 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb create mode 100644 easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb create mode 100644 easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb new file mode 100644 index 0000000000..77235f32a1 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +homepage = 'http://www.freedesktop.org/software/fontconfig' +description = """Fontconfig is a library designed to provide system-wide font configuration, customization and +application access.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb new file mode 100644 index 0000000000..62923f260f --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000..0889930509 --- /dev/null +++ b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXScrnSaver' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Screen Saver extension client library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3') +] + +sanity_check_paths = { + 'files': ['lib/libXss.a', 'lib/libXss.so', 'include/X11/extensions/scrnsaver.h'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000..65123b2fae --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb new file mode 100644 index 0000000000..393ccdfa93 --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('renderproto', '0.11'), +] + +dependencies = [ + ('kbproto', '1.0.7'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb new file mode 100644 index 0000000000..b1d4936121 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' -- GitLab From b559f80695feb569bbee527ed6d64fae204ced1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 10:48:47 +0200 Subject: [PATCH 883/911] include Tk as dependency in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015.05.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-foss-2015a.eb | 1 + .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 1 + .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 1 + .../p/Python/Python-2.7.9-intel-2015a.eb | 1 + .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 +++++++++++++++++++ .../t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb | 24 ++++++++++++++++++ .../t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb | 24 ++++++++++++++++++ 16 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 3974b6e842..e9840cb7eb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index ce15e506fc..0fa5529cb0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 669c54c38d..5eed3b0154 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 3273aa0399..1ff5189a78 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e206b78e22..2f9941dfab 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,6 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 9a1f9af5fc..536743d8c5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2c02867a9..499a28228b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 95f4d38205..71a627c500 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.4', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb new file mode 100644 index 0000000000..fcf9fcc830 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb new file mode 100644 index 0000000000..a933eab557 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb new file mode 100644 index 0000000000..099c4a95f4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb new file mode 100644 index 0000000000..150f56cf00 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb new file mode 100644 index 0000000000..3530d74282 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb new file mode 100644 index 0000000000..337e722e7b --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb new file mode 100644 index 0000000000..58076d4e59 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb new file mode 100644 index 0000000000..6b858f2d9d --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 04bfc4827d82c852f29b1360dc93240de08a80e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:19:37 +0200 Subject: [PATCH 884/911] include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works --- .../p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.1.29.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.25.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb | 10 +++++++++- .../p/Python/Python-2.7.9-CrayGNU-5.2.40.eb | 10 +++++++++- 6 files changed, 54 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb index 2ec3cb1dc8..5c84059a20 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index fdb44db0d0..39d6b11c34 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb index 09917d5025..1e9572eb83 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index bb0be0ac85..466ad2cc0c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb index 10c6659238..3fafaaa920 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 3950c920d4..5a66cda69a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' -- GitLab From 7e6618a5642325d9039922026ba539a5ff50fce7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:27:09 +0200 Subject: [PATCH 885/911] use Tk 8.6.3 rather than Tk 8.6.4 as dep in Python 2.7.9 easyconfigs --- .../p/Python/Python-2.7.9-GCC-4.9.2-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015.05.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-foss-2015a.eb | 2 +- .../Python/Python-2.7.9-gompi-1.5.16-bare.eb | 2 +- .../p/Python/Python-2.7.9-goolf-1.5.14.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a-bare.eb | 2 +- .../p/Python/Python-2.7.9-intel-2015a.eb | 2 +- .../easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-foss-2015.05.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb | 25 ------------------- .../t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb | 25 ------------------- ...no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} | 2 +- .../t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb | 24 ++++++++++++++++++ ...X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} | 2 +- ...X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} | 2 +- 17 files changed, 36 insertions(+), 112 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-GCC-4.9.2-no-X11.eb => Tk-8.6.3-GCC-4.9.2-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-foss-2015.05-no-X11.eb => Tk-8.6.3-foss-2015.05-no-X11.eb} (97%) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-gompi-1.5.16-no-X11.eb => Tk-8.6.3-gompi-1.5.16-no-X11.eb} (97%) rename easybuild/easyconfigs/t/Tk/{Tk-8.6.4-goolf-1.5.14-no-X11.eb => Tk-8.6.3-goolf-1.5.14-no-X11.eb} (97%) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index e9840cb7eb..7f438347a5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb index 0fa5529cb0..d0661c356d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 5eed3b0154..dc26dc666b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 1ff5189a78..cc0e90d0e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index 2f9941dfab..ad2c37f79a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,7 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 536743d8c5..bb0fac1650 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index 499a28228b..d6a4eb1b3c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 71a627c500..ed4d77fc45 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), - ('Tk', '8.6.4', '-no-X11'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's # nice to have an up to date openssl for security reasons ] diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb deleted file mode 100644 index fcf9fcc830..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GCC-4.9.2.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'GCC', 'version': '4.9.2'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb deleted file mode 100644 index a933eab557..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015.05.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'foss', 'version': '2015.05'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb deleted file mode 100644 index 099c4a95f4..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-gompi-1.5.16.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'gompi', 'version': '1.5.16'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb deleted file mode 100644 index 150f56cf00..0000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.5.14.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.4' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" - -toolchain = {'name': 'goolf', 'version': '1.5.14'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -dependencies = [ - ('zlib', '1.2.8'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb index 3530d74282..602101704a 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GCC-4.9.2-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb index 337e722e7b..8ff29d34a2 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015.05-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb new file mode 100644 index 0000000000..c34f24fd99 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb index 58076d4e59..a292e06eb8 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-gompi-1.5.16-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb similarity index 97% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb index 6b858f2d9d..cd4da6afb6 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.5.14-no-X11.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.4' +version = '8.6.3' versionsuffix = '-no-X11' homepage = 'http://www.tcl.tk/' -- GitLab From 37f24102612713bb52c192907e11889040d172e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:34:16 +0200 Subject: [PATCH 886/911] kbproto is just a build dep --- .../easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb index 778cd1670c..cea866f2b7 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb index fe8ecdca33..80e0f6ea24 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb index 393ccdfa93..52e06388f3 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.7'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.7'), ('libX11', '1.6.3', '-Python-2.7.9'), ] -- GitLab From 6dbc6268d466d2a34aaad21e94b9b5168f25406c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 11:43:49 +0200 Subject: [PATCH 887/911] add missing Tk 8.6.3 intel/2015a easyconfig --- .../t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb new file mode 100644 index 0000000000..d841e7bd84 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From a8b8cd6eeb84d5902bdc13b762b65f95a992f383 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:10:50 +0200 Subject: [PATCH 888/911] {data}[intel/2015a] HDF5 1.8.15 --- .../h/HDF5/HDF5-1.8.15-intel-2015a.eb | 27 ++++++ .../h/HDF5/HDF5-1.8.15_configure_intel.patch | 95 +++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb new file mode 100644 index 0000000000..e820f700da --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.15' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-%(version)s_configure_intel.patch', + 'configure_libtool.patch', +] + +configopts = "--enable-gpfs" +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch new file mode 100644 index 0000000000..b74e70593e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch @@ -0,0 +1,95 @@ +--- hdf5-1.8.15/configure.orig 2015-05-01 20:56:59.000000000 +0200 ++++ hdf5-1.8.15/configure 2015-06-02 15:04:26.757168623 +0200 +@@ -5190,7 +5190,7 @@ + ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_fc_compiler_gnu + if test -n "$ac_tool_prefix"; then +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5234,7 +5234,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -11993,7 +11993,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc*| ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -12629,11 +12629,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13115,7 +13115,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -16113,7 +16113,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -19024,7 +19024,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc* | ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -19645,11 +19645,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20103,7 +20103,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then -- GitLab From d52f65e1ad073313821ba555c1cfa7d83f6e580c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:42:09 +0200 Subject: [PATCH 889/911] drop gpfs versionsuffix and use no longer existing --enable-gpfs configopt for recent HDF5 versions --- ...1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} | 2 -- easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb | 1 - ...-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} | 5 ++--- easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb | 2 +- easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.8.14-intel-2015a-gpfs.eb => HDF5-1.8.14-intel-2015a.eb} (92%) rename easybuild/easyconfigs/h/h5py/{h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb => h5py-2.5.0-intel-2015a-Python-2.7.9.eb} (88%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 081c94297d..2b7af38374 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.14' -versionsuffix = '-gpfs' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of @@ -17,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb index e820f700da..9b028b25b8 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -16,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 88% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index d6f4de7c55..665337345c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,12 +17,11 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) +versionsuffix = '-%s-%s%s' % (python, pyver) dependencies = [ (python, pyver), - ('HDF5', '1.8.14', hdf5suff), + ('HDF5', '1.8.14'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 822615186c..baee3155cf 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -20,7 +20,7 @@ patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libctl', '3.2.2'), ('GSL', '1.16'), ('FFTW', '3.3.4') diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb index bd7faf3909..0f9bc0fa5f 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.9'), # should have a working sqlite, and provide numpy ('freetype', '2.5.5'), ('LibTIFF', '4.0.4beta'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python -- GitLab From d7c8a53fc9087c0fdaf8c5abffe9330540ad3a50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jun 2015 16:55:12 +0200 Subject: [PATCH 890/911] fix typo --- .../easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index 665337345c..44ec9edf7c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -versionsuffix = '-%s-%s%s' % (python, pyver) +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ (python, pyver), -- GitLab From 06f663105c14f3491674941f2cc4101acf93f6c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 16:57:17 +0200 Subject: [PATCH 891/911] cURL added as dependency --- easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index cdf98f1940..1931792850 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -21,6 +21,7 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), ('netCDF', '4.3.2') + ('cURL', '7.37.1') ] moduleclass = 'math' -- GitLab From b1d2fff1ebdf73d28a511d6c7d29417d4349507c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:12:20 +0200 Subject: [PATCH 892/911] Added external matplotlib dependency and source changed to PYPI --- .../HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 7 +++- ...tplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 37 +++++++++++++++++++ 2 files changed, 42 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index 1f11e79748..b9dd51cded 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' @@ -17,7 +17,10 @@ pyshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver -dependencies = [(python, pythonver)] +dependencies = [ + (python, pythonver), + ('matplotlib', '1.3.1'), +] sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000..91d3707f42 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.3'), + ('libpng', '1.6.12'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' -- GitLab From a8a944bb018cc966c76271071b87249621bba31b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:19:13 +0200 Subject: [PATCH 893/911] toolchain corrected in matplotlib --- .../m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb index 91d3707f42..765f86a131 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -8,7 +8,7 @@ description = """matplotlib is a python 2D plotting library which produces publi hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" -toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 6bfc7b9b575209908f2ae661dc2180271d60c315 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:25:50 +0200 Subject: [PATCH 894/911] using GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb index 77009b52a1..aef6e26abf 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From 4e6379444e094b0540033f5c84af4a56c197d32b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 2 Jun 2015 17:43:43 +0200 Subject: [PATCH 895/911] versionsuffix added for matplotlib dependency --- .../h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb index b9dd51cded..0118dd4b32 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -19,7 +19,7 @@ eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver dependencies = [ (python, pythonver), - ('matplotlib', '1.3.1'), + ('matplotlib', '1.3.1', versionsuffix), ] sanity_check_paths = { -- GitLab From a81ac042848534cce51d17a81c942d378ca67459 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:26:53 +0200 Subject: [PATCH 896/911] include checksum + switch to manual download in JUBE easyconfig --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 0044a1ec87..e0a6db9551 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -1,7 +1,7 @@ -easyblock = "VersionIndependentPythonPackage" +easyblock = 'VersionIndependentPythonPackage' -name = "JUBE" -version = "2.0.3" +name = 'JUBE' +version = '2.0.3' homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, @@ -9,8 +9,9 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ["http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s"] +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s sources = [SOURCELOWER_TAR_GZ] +checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} -- GitLab From b2b544310020b5da5d34d5b5baf35ba59b686d5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:27:08 +0200 Subject: [PATCH 897/911] add easyconfigs for JUBE 2.0.4 an 2.0.5 --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 23 ++++++++++++++++++++++ easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 23 ++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb new file mode 100644 index 0000000000..dc76af6562 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.4' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96a7946d38d678b25ba4bbd539482a14'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb new file mode 100644 index 0000000000..ea72eb6be6 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.5' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f506e9f39898af3d7456890ba219ab90'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 662aeb0bdca15c55e38160a0249872c94e802cf9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 08:34:47 +0200 Subject: [PATCH 898/911] commas corrected --- .../easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb index 1931792850..47cf63ba0e 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -20,8 +20,8 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ('netCDF', '4.3.2') - ('cURL', '7.37.1') + ('netCDF', '4.3.2'), + ('cURL', '7.37.1'), ] moduleclass = 'math' -- GitLab From cf66efb4e2461ba170c389924bbb7928fcabadb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 08:37:53 +0200 Subject: [PATCH 899/911] SOURCELOWER -> SOURCE --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index e0a6db9551..ffff4a9c2e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index dc76af6562..373d162154 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] options = {'modulename': 'jube2'} diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ea72eb6be6..ebf3c0a914 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -10,7 +10,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} # requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] options = {'modulename': 'jube2'} -- GitLab From 4454fbfccee430c04edbba49254539a3b724388a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:01:02 +0200 Subject: [PATCH 900/911] Both packages use dependency GMP-GCC-4.9.2 --- easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb index 00491cc9ba..270390d86d 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.55-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s/'] -dependencies = [('GMP', '6.0.0a')] +dependencies = [('GMP', '6.0.0a', '', ('GCC', '4.9.2'))] configopts = "--with-gmp" -- GitLab From d3824d539f8d45ed0b2537a3631a4e75dceac622 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 3 Jun 2015 09:11:24 +0200 Subject: [PATCH 901/911] md5schecksum added --- easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb index 2698ca5e91..920ee4c4fa 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -25,5 +25,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = [('md5', '90b1b8f77313600cc294d9271741f4da')] moduleclass = 'system' -- GitLab From 0c716a66441012c284d71f3bc0a81b70147ac387 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:26:11 +0300 Subject: [PATCH 902/911] Fixed config --- .../easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb index 99d44c6862..79d3f53e5a 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -1,11 +1,12 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Copyright:: Copyright 2014-2015 The Cyprus Institute # Authors:: Thekla Loizou # License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'MATIO' version = '1.5.2' @@ -16,10 +17,8 @@ description = """matio is an C library for reading and writing Matlab MAT files. toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] - -dependencies = [('zlib','1.2.7'), -] +dependencies = [('zlib','1.2.7')] moduleclass = 'lib' -- GitLab From a5f4228dc8bc378fe248f5d9b86c1dd5a6c64750 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 10:43:11 +0300 Subject: [PATCH 903/911] Fixes in easyconfig --- .../DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb index d3ec591256..2734b69ecf 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -7,19 +7,20 @@ # $Id$ # ## - easyblock = "PythonPackage" name = 'DendroPy' version = '3.12.0' homepage = 'https://pypi.python.org/pypi/DendroPy/' -description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. -""" +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] -sources = ['%s-%s.tar.gz' % (name, version)] +sources = [SOURCE_TAR_GZ] python = "Python" pythonversion = '2.7.3' @@ -30,7 +31,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py','bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', + 'bin/sumtrees.py','bin/strict_consensus_merge.py'], 'dirs': [], } -- GitLab From 3027f180c35a32b5289a5ed0b669c5d95e5a9915 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 09:58:57 +0200 Subject: [PATCH 904/911] add source_urls using download.php?file= --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index ffff4a9c2e..2803f111f1 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 373d162154..31b888866e 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index ebf3c0a914..4313248d99 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -# requires manual download via http://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=%(version)s +source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 283908c4c27cc74b3b44d5d4499ee76aaffd8826 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2015 10:02:36 +0200 Subject: [PATCH 905/911] fix typo --- easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb | 2 +- easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 2803f111f1..903be570eb 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 31b888866e..545b5785ea 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['96a7946d38d678b25ba4bbd539482a14'] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index 4313248d99..b270f53d57 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -9,7 +9,7 @@ description = """The JUBE benchmarking environment provides a script based frame toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] checksums = ['f506e9f39898af3d7456890ba219ab90'] -- GitLab From 884bc004100e2103387e49640296ab011510c3e4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:12:07 +0200 Subject: [PATCH 906/911] use autotools --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index c3b27fffcb..43293cbe1d 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autoconf', '2.69')] +builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 1df688fd2a9832a2b272060ed4e14c35680005ae Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Jun 2015 10:18:49 +0200 Subject: [PATCH 907/911] correct version --- easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb index 43293cbe1d..c4afd6154b 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [('Autotools', '20150205', '', ('GCC', '4.9.2'))] +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] patches = ['cairo-1.12.18-pthread-check.patch'] -- GitLab From 03a20f0bcdfefa678a34e5a201eda032b944b7b4 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:33:48 +0300 Subject: [PATCH 908/911] Changes in config file --- .../b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index d749578a18..beb147df02 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -6,30 +6,26 @@ # License:: MIT/GPL # ## - easyblock = "Tarball" name = 'Bismark' version = '0.10.1' homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' -description = """A tool to map bisulfite converted sequence reads and determine cytosine methylation states""" +description = """A tool to map bisulfite converted sequence reads and +determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] - -dependencies = [ - ('Bowtie2', '2.0.2'), -] +dependencies = [('Bowtie2', '2.0.2')] sanity_check_paths = { - 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], 'dirs': [], } -modextrapaths = {'PATH': ''} - moduleclass = 'bio' -- GitLab From 91aa792c2defe803b961a11f29f81ca5540bf6a8 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 11:45:23 +0300 Subject: [PATCH 909/911] removing ABINIT files; bismark branch --- .../a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb | 38 ------------------- .../ABINIT-7.4.3-x86_64_linux_gnu4.5.eb | 32 ---------------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 29 -------------- 3 files changed, 99 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb delete mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb delete mode 100644 easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb deleted file mode 100644 index a3fe29c410..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ABINIT' -version = '7.4.3' - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing - condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = ['%s-%s.tar.gz' % (name.lower(), version)] -source_urls = ['http://ftp.abinit.org/'] - -configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' -configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' -configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' - -dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), -] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb deleted file mode 100644 index fb4d81965f..0000000000 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-x86_64_linux_gnu4.5.eb +++ /dev/null @@ -1,32 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -easyblock = "Tarball" - -name = 'ABINIT' -version = '7.4.3' -versionsuffix = '-x86_64_linux_gnu4.5' - -altversions = ['7.0.3', '7.0.4', '7.0.5'] - -homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# eg. http://ftp.abinit.org/abinit-7.0.5_x86_64_linux_gnu4.5.bz2 -sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')] -source_urls = ['http://ftp.abinit.org/'] - -sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb deleted file mode 100644 index 350da2d908..0000000000 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ /dev/null @@ -1,29 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -## - -name = 'ETSF_IO' -version = '1.0.4' - -homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] - -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" - -dependencies = [ ('netCDF', '4.1.3') ] - -sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } - -moduleclass = 'chem' -- GitLab From 8550a555814b6331d8193536a75e6ac41672181c Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:05:35 +0300 Subject: [PATCH 910/911] Fixing source_url --- easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb index beb147df02..337980614f 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ determine cytosine methylation states""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["www.bioinformatics.babraham.ac.uk/projects/bismark/"] +source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] dependencies = [('Bowtie2', '2.0.2')] -- GitLab From 3a8ac4416f6863c307ee4d585d749cc355853ab0 Mon Sep 17 00:00:00 2001 From: Thekla Loizou Date: Wed, 3 Jun 2015 12:18:14 +0300 Subject: [PATCH 911/911] Fixed configs according to comments --- ...BINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} | 23 +++++++++++-------- .../e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb | 21 +++++++++++------ 2 files changed, 28 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-7.4.3-goolf-1.4.10.eb => ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb} (59%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb similarity index 59% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb index c1d2b559d8..4d319523ac 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -1,35 +1,40 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = "ConfigureMake" name = 'ABINIT' version = '7.4.3' +versionsuffix = '-ETSF_IO-1.0.4' homepage = 'http://www.abinit.org/' -description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' -configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" --with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' dependencies = [ - ('netCDF', '4.1.3'), - ('ETSF_IO', '1.0.4'), + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), ] sanity_check_paths = { - 'files': ["bin/abinit"], - 'dirs': [] - } + 'files': ["bin/abinit"], + 'dirs': [] +} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb index 7e1b945d47..f270612d5f 100644 --- a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -1,27 +1,34 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: Copyright 2014 The Cyprus Institute +# Copyright:: Copyright 2013-2014 The Cyprus Institute # Authors:: Thekla Loizou +# License:: MIT/GPL # ## +easyblock = 'ConfigureMake' name = 'ETSF_IO' version = '1.0.4' homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' -description = """A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. """ +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['http://www.etsf.eu/system/files/etsf_io-1.0.4.tar.gz'] +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] -configopts = "--with-netcdf-prefix=$EBROOTNETCDF --with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' --with-netcdf-incs='-I$EBROOTNETCDF/include'" +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" dependencies = [ ('netCDF', '4.1.3') ] sanity_check_paths = { - 'files': ["bin/etsf_io"], - 'dirs': [] - } + 'files': ["bin/etsf_io"], + 'dirs': [] +} +moduleclass = 'lib' -- GitLab