From 15e0894257fb722f79e70de8f16787f0b2f9aff7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 26 Apr 2013 13:15:00 +0200 Subject: [PATCH 001/566] add QE-ictce-5.3.0 easyconfigs Signed-off-by: Fotis Georgatos --- .../QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb | 42 +++++++++++++++ .../QuantumESPRESSO-4.2-ictce-5.3.0.eb | 38 +++++++++++++ ...uantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 54 +++++++++++++++++++ .../QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 50 +++++++++++++++++ 4 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb new file mode 100644 index 0000000000..9252372604 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb @@ -0,0 +1,42 @@ +name = 'QuantumESPRESSO' +version = '4.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%s.tar.gz' % version, + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', + ] +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz + ] + +patches = [ + 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', + ] + +makeopts = 'all gipaw vdw w90 want gww xspectra yambo' + +# parallel build tends to fail +parallel = 1 + +# hybrid build (enable OpenMP) +hybrid = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..2c9da47c8d --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb @@ -0,0 +1,38 @@ +name = 'QuantumESPRESSO' +version = '4.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%s.tar.gz' % version, + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', + ] +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz + ] + +patches = [ + 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', + ] + +makeopts = 'all gipaw vdw w90 want gww xspectra yambo' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000..2acbc21f76 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -0,0 +1,54 @@ +name = 'QuantumESPRESSO' +version = '5.0.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso-5.0.2/install/plugins_list +sources = [ + 'espresso-%s.tar.gz' % version, + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', + ] +missing_sources = [ + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + ] + +patches = [ + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', + ] + +# parallel build tends to fail +parallel = 1 + +# gipaw excluded, because v5.0 isn't stable +# xspectra v5.0.2 is nowhere to be found +makeopts = 'all w90 want yambo plumed' + +# hybrid build (enable OpenMP) +hybrid = True + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000..854d3543cf --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -0,0 +1,50 @@ +name = 'QuantumESPRESSO' +version = '5.0.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso-5.0.2/install/plugins_list +sources = [ + 'espresso-%s.tar.gz' % version, + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', + ] +missing_sources = [ + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + ] + +patches = [ + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', + ] + +# gipaw excluded, because v5.0 isn't stable +# xspectra v5.0.2 is nowhere to be found +makeopts = 'all w90 want yambo plumed' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From e547920285e1ee47142e74962fc73e3ca96074ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Aug 2013 14:48:42 +0200 Subject: [PATCH 002/566] add easyconfigs for Parallel Python (PP) --- .../PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb | 30 +++++++++++++++++++ .../PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..53d4aebdfe --- /dev/null +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'PP' +version = '1.6.4' + +homepage = 'http://www.parallelpython.com/' +description = """PP is a python module which provides mechanism for parallel execution of python code on SMP +(systems with multiple processors or cores) and clusters (computers connected via network).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.parallelpython.com/downloads/pp/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb new file mode 100644 index 0000000000..7cae0123b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'PP' +version = '1.6.4' + +homepage = 'http://www.parallelpython.com/' +description = """PP is a python module which provides mechanism for parallel execution of python code on SMP +(systems with multiple processors or cores) and clusters (computers connected via network).""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://www.parallelpython.com/downloads/pp/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion] +} + +moduleclass = 'lang' -- GitLab From 8366331f7f9ba29b43fc2f940c14a7ea392e2878 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2013 17:08:26 +0200 Subject: [PATCH 003/566] add imkl easyconfig for 11.1.0.080 + style fixes --- .../i/imkl/imkl-10.2.6.038-32bit.eb | 5 ++-- .../easyconfigs/i/imkl/imkl-10.2.6.038.eb | 5 ++-- .../easyconfigs/i/imkl/imkl-10.3.10.319.eb | 5 ++-- .../easyconfigs/i/imkl/imkl-11.1.0.080.eb | 30 +++++++++++++++++++ 4 files changed, 39 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 17496e5915..6ff37fb0a5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -15,9 +15,10 @@ sources = ['l_mkl_p_%(version)s.tar.gz'] dontcreateinstalldir = 'True' # deps for interface build +compver = '11.1.073-32bit' dependencies = [ - ('icc', '11.1.073-32bit'), - ('ifort', '11.1.073-32bit'), + ('icc', compver), + ('ifort', compver), ('impi', '4.0.0.028-32bit'), ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index f8105ef53d..a693a15b86 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -14,9 +14,10 @@ sources = ['l_mkl_p_%(version)s.tar.gz'] dontcreateinstalldir = 'True' # deps for interface build +compver = '11.1.073' dependencies = [ - ('icc', '11.1.073'), - ('ifort', '11.1.073'), + ('icc', compver), + ('ifort', compver), ('impi', '4.0.0.028'), ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index 608d782783..b3d47b810d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -12,9 +12,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mkl_%(version)s_intel64.tgz'] # deps for interface build +compver = '2011.10.319' dependencies = [ - ('icc', '2011.10.319'), - ('ifort', '2011.10.319'), + ('icc', compver), + ('ifort', compver), ('impi', '4.0.2.003'), ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb new file mode 100644 index 0000000000..a835fca22a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -0,0 +1,30 @@ +name = 'imkl' +version = '11.1.0.080' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mkl_%(version)s.tgz'] + +# deps for interface build +compver = '2013.sp1.080' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.1.036') +] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' -- GitLab From 93e95e4aa24336310de83319e5569f31740f8c7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Sep 2013 17:17:40 +0200 Subject: [PATCH 004/566] add icc and ifort easyconfigs for 2013_sp1.0.080 + style fixes --- .../easyconfigs/i/icc/icc-11.1.073-32bit.eb | 6 +++--- easybuild/easyconfigs/i/icc/icc-11.1.073.eb | 6 +++--- easybuild/easyconfigs/i/icc/icc-11.1.075.eb | 6 +++--- easybuild/easyconfigs/i/icc/icc-2011.10.319.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2011.13.367.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2011.3.174.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2011.6.233.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2013.1.117.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2013.2.146.eb | 4 ++-- easybuild/easyconfigs/i/icc/icc-2013.3.163.eb | 5 ++--- easybuild/easyconfigs/i/icc/icc-2013.4.183.eb | 5 ++--- easybuild/easyconfigs/i/icc/icc-2013.5.192.eb | 5 ++--- .../easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 17 +++++++++++++++++ .../easyconfigs/i/ifort/ifort-11.1.073-32bit.eb | 6 +++--- easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb | 6 +++--- easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb | 6 +++--- .../easyconfigs/i/ifort/ifort-2011.10.319.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2011.13.367.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2011.3.174.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2011.6.233.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2013.1.117.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2013.2.146.eb | 4 ++-- .../easyconfigs/i/ifort/ifort-2013.3.163.eb | 5 ++--- .../easyconfigs/i/ifort/ifort-2013.4.183.eb | 5 ++--- .../easyconfigs/i/ifort/ifort-2013.5.192.eb | 5 ++--- .../easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb | 17 +++++++++++++++++ 26 files changed, 88 insertions(+), 60 deletions(-) create mode 100644 easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index d99b8550b8..25d906e87f 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -9,11 +9,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cproc_p_%s.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - dontcreateinstalldir = 'True' # license file @@ -21,3 +19,5 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") m32 = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index cca27f98ee..270e177a0c 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -8,13 +8,13 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cproc_p_%s.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - 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/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index ead27506ae..005adc34f3 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -8,13 +8,13 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cproc_p_%s_intel64.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - 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/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index 7da3e690e4..e8019bf5f8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index 7ae1a1aafb..17d0cd2bbe 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index 359651488a..cf51e4e41b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 686e02c34f..4079daa6ca 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index dd5ed9dc3d..818ade63f2 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index e037b77a5d..086b7132e2 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index 6cf0697eeb..08d3496656 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%s.tgz' % version] -# compiler class -moduleclass = 'compiler' - 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/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index b4b9b50107..8c5cfaeab5 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%(version)s.tgz'] -# compiler class -moduleclass = 'compiler' - 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/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index 326e4303ab..3be64f6a79 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_ccompxe_%(version)s.tgz'] -# compiler class -moduleclass = 'compiler' - 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/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb new file mode 100644 index 0000000000..af863bb54e --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2013_sp1.0.080' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_2013_%(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/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index f82df2060c..c4b7144887 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -9,11 +9,9 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cprof_p_%s.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - dontcreateinstalldir = 'True' # license file @@ -21,3 +19,5 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") m32 = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index 3f25c39122..da0e19e8a7 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -8,13 +8,13 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cprof_p_%s.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - 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/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index a47f1292cd..f8534d1717 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -8,13 +8,13 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_cprof_p_%s_intel64.tgz' % version] -## small patch for the installer +# small patch for the installer patches = ['specified-paths.patch'] -moduleclass = 'compiler' - 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/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index 2f99029196..c0ab005da2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index 90b6da56be..8d6eeaafb4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 82182ae836..65ff75aa5c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index 1347acd620..0749ed0e0c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_intel64_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 49f0ac1b18..99bf3863c6 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index bfc7da7af9..54b49ddcaf 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%s.tgz' % version] -moduleclass = 'compiler' - 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/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index aa3ec53ee3..4efd890d23 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%s.tgz' % version] -# compiler class -moduleclass = 'compiler' - 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/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index 375028b1ab..05c638d451 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%(version)s.tgz'] -# compiler class -moduleclass = 'compiler' - 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/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 158defc0fc..32705da10f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -8,11 +8,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_fcompxe_%(version)s.tgz'] -# compiler class -moduleclass = 'compiler' - 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/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb new file mode 100644 index 0000000000..dc69a4da5e --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2013_sp1.0.080' + +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' -- GitLab From 6126e6ec5d087f741773581aa1c9746694da7d0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Sep 2013 18:32:26 +0200 Subject: [PATCH 005/566] add easyconfigs for numpy, Python 3.3.2, python-dateutil --- .../numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb | 26 +++ ...py-1.7.1_distutils_multiple-lib-dirs.patch | 202 ++++++++++++++++++ .../p/Python/Python-3.3.2-goolf-1.4.10.eb | 44 ++++ .../p/Python/Python-3.3.2-ictce-4.1.13.eb | 44 ++++ .../p/Python/Python-3.3.2-ictce-5.3.0.eb | 44 ++++ ...-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb | 31 +++ ...-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb | 31 +++ 7 files changed, 422 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch create mode 100644 easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb new file mode 100644 index 0000000000..df7582a273 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.7.1' + +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': 'ictce', 'version': '4.1.13'} + +source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.7.1_distutils_multiple-lib-dirs.patch'] + +python = 'Python' +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch b/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch new file mode 100644 index 0000000000..12501c6754 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch @@ -0,0 +1,202 @@ +diff -ru numpy-1.7.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.7.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.7.0.orig/numpy/distutils/fcompiler/__init__.py 2013-02-09 22:04:55.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/fcompiler/__init__.py 2013-05-13 10:40:59.806346107 +0200 +@@ -626,7 +626,11 @@ + 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 -ru numpy-1.7.0.orig/numpy/distutils/system_info.py numpy-1.7.0/numpy/distutils/system_info.py +--- numpy-1.7.0.orig/numpy/distutils/system_info.py 2013-02-09 22:04:56.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/system_info.py 2013-05-13 10:48:49.063599772 +0200 +@@ -588,7 +588,7 @@ + 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, '') +@@ -630,6 +630,23 @@ + 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. +@@ -643,6 +660,18 @@ + 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 = [] +@@ -653,6 +682,9 @@ + 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) +@@ -668,6 +700,19 @@ + 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. + +@@ -709,6 +754,22 @@ + 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. +@@ -944,7 +1005,7 @@ + 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) ++ info = self.check_libs2_all(lib_dirs, mkl_libs) + if info is None: + return + dict_append(info, +@@ -1008,16 +1069,13 @@ + 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 +@@ -1096,7 +1154,7 @@ + info = {} + atlas_libs = self.get_libs('atlas_libs', + self._lib_names + self._lib_atlas) +- atlas = self.check_libs2(lib_dirs, atlas_libs, []) ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs, []) + if atlas is None: + return + include_dirs = self.get_include_dirs() +@@ -1144,7 +1202,7 @@ + lib_dirs = self.get_lib_dirs() + + lapack_libs = self.get_libs('lapack_libs', self._lib_names) +- info = self.check_libs(lib_dirs, lapack_libs, []) ++ info = self.check_libs_all(lib_dirs, lapack_libs, []) + if info is None: + return + info['language'] = 'f77' +@@ -1521,7 +1579,7 @@ + lib_dirs = self.get_lib_dirs() + + blas_libs = self.get_libs('blas_libs', self._lib_names) +- info = self.check_libs(lib_dirs, blas_libs, []) ++ info = self.check_libs_all(lib_dirs, blas_libs, []) + if info is None: + return + info['language'] = 'f77' # XXX: is it generally true? +Only in numpy-1.7.0/numpy/distutils: system_info.py.orig +Only in numpy-1.7.0/numpy/distutils: system_info.py.rej +diff -ru numpy-1.7.0.orig/numpy/distutils/unixccompiler.py numpy-1.7.0/numpy/distutils/unixccompiler.py +--- numpy-1.7.0.orig/numpy/distutils/unixccompiler.py 2013-02-09 22:04:55.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/unixccompiler.py 2013-05-13 10:40:59.833592000 +0200 +@@ -109,3 +109,12 @@ + + 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/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 new file mode 100644 index 0000000000..0a4ab2b959 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -0,0 +1,44 @@ +name = 'Python' +version = '3.3.2' + +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': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.1' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.1.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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-1.7.1_distutils_multiple-lib-dirs.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..38956ed8cb --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -0,0 +1,44 @@ +name = 'Python' +version = '3.3.2' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.1' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.1.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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-1.7.1_distutils_multiple-lib-dirs.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..c1fb8acaac --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -0,0 +1,44 @@ +name = 'Python' +version = '3.3.2' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.1' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.1.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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-1.7.1_distutils_multiple-lib-dirs.patch'], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..6f00563718 --- /dev/null +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "python-dateutil" +version = "2.1" + +homepage = "https://pypi.python.org/pypi/python-dateutil" +description = """The dateutil module provides powerful extensions to the datetime module available in the Python standard library.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.3" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%%(name)s" % py_short_ver + +sanity_check_paths = { + 'files': ["%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver)], + 'dirs': [] +} + +options = {'modulename': 'dateutil'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb new file mode 100644 index 0000000000..fae72a3762 --- /dev/null +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "python-dateutil" +version = "2.1" + +homepage = "https://pypi.python.org/pypi/python-dateutil" +description = """The dateutil module provides powerful extensions to the datetime module available in the Python standard library.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.3" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%%(name)s" % py_short_ver + +sanity_check_paths = { + 'files': ["%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver)], + 'dirs': [] +} + +options = {'modulename': 'dateutil'} + +moduleclass = 'lib' -- GitLab From ba6c5a511ed0440790ea97703e82993b00733ce6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Oct 2013 14:20:19 +0200 Subject: [PATCH 006/566] add easyconfigs for NCL with ictce + deps --- .../c/cURL/cURL-7.28.1-ictce-4.1.13.eb | 22 ++++++++++ .../e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb | 26 ++++++++++++ .../f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb | 17 ++++++++ .../g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb | 22 ++++++++++ .../g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb | 20 +++++++++ .../h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 21 ++++++++++ .../h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb | 25 +++++++++++ .../n/NCL/NCL-6.1.2-ictce-4.1.13.eb | 37 +++++++++++++++++ .../netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb | 22 ++++++++++ .../u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb | 41 +++++++++++++++++++ 10 files changed, 253 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-4.1.13.eb b/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..0b0ea92016 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-4.1.13.eb @@ -0,0 +1,22 @@ +name = 'cURL' +version = '7.28.1' + +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': 'ictce', 'version': '4.1.13'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..f76aa98e59 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb @@ -0,0 +1,26 @@ +name = 'ESMF' +version = '6.1.1' + +homepage = 'http://sourceforge.net/projects/esmf' +description = """The Earth System Modeling Framework (ESMF) is software for building and coupling weather, + climate, and related models.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s_%s_src.tar.gz' % (name.lower(), '_'.join(version.split('.')))] + +dependencies = [ + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('netCDF-C++', '4.2'), +] + +# LDFLAGS has to be unset to avoid linking issues +preinstallopts = "unset LDFLAGS && " + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..e473bccccb --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb new file mode 100644 index 0000000000..8f1faabe98 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-4.1.13.eb @@ -0,0 +1,22 @@ +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': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..73e2caf3fb --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb @@ -0,0 +1,20 @@ +name = 'g2lib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True} + +dependencies = [('JasPer', '1.900.1')] + +sources = ['%s-%s.tar' % (name, version)] +source_urls = [homepage] + +patches = ['fix_makefile.patch'] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb new file mode 100644 index 0000000000..29e1c9b8d8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -0,0 +1,21 @@ +name = 'HDF' +version = '4.2.8' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True, 'pic': True} + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), + ] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] + +configopts = "--with-szip=$EBROOTSZIP" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb new file mode 100644 index 0000000000..8fec53bc83 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = '-no-mpi' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'configure_libtool.patch', +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb new file mode 100644 index 0000000000..6006d25573 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb @@ -0,0 +1,37 @@ +name = 'NCL' +version = '6.1.2' + +homepage = 'http://www.ncl.ucar.edu' +description = """NCL is an interpreted language designed specifically for scientific data analysis and + visualization.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] + +patches = [ + 'NCL-6.1_fix-HDF-includes.patch', +] + +dependencies = [ + ('cURL', '7.28.1'), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('JasPer', '1.900.1'), + ('g2lib', '1.4.0'), + ('g2clib', '1.4.0'), + ('HDF', '4.2.8'), + ('Szip', '2.1'), + ('freetype', '2.4.11'), + ('zlib', '1.2.7'), + ('GDAL', '1.9.2'), + ('UDUNITS', '2.1.24'), + ('ESMF', '6.1.1'), + ('bzip2', '1.0.6'), +] +builddependencies = [('makedepend', '1.0.4')] + +osdependencies = ['cairo-devel'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb new file mode 100644 index 0000000000..7c205aa876 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb @@ -0,0 +1,22 @@ +name = 'netCDF-C++' +version = '4.2' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} + +sources = ['netcdf-cxx-%(version)s.tar.gz'] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +sanity_check_paths = { + 'files': ['include/ncvalues.h', 'include/netcdfcpp.h', 'include/netcdf.hh', 'lib/libnetcdf_c++.a', 'lib/libnetcdf_c++.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.eb new file mode 100644 index 0000000000..de58c80ab6 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-4.1.13.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, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# 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 +## + +name = 'UDUNITS' +version = '2.1.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True, 'pic': True} + +# eg. ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +sanity_check_paths = { + 'files': [ + 'bin/udunits2', + 'include/converter.h', + 'include/udunits2.h', + 'include/udunits.h', + 'lib/libudunits2.a', + 'lib/libudunits2.so', + ], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' -- GitLab From 2ec9f558d6e55e0dd25892971351cc2c07d58010 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Oct 2013 14:37:32 +0200 Subject: [PATCH 007/566] add missing g2clib dep for NCL --- .../g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..42f32bafc7 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb @@ -0,0 +1,18 @@ +name = 'g2clib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ("C" version).""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True} + +dependencies = [('JasPer', '1.900.1')] + +sources = ['%s-%s.tar' % (name, version)] +source_urls = [homepage] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' -- GitLab From 3a041bcf665b59ba67e0914b08ff5667e1380e10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Oct 2013 14:58:23 +0200 Subject: [PATCH 008/566] add missing JasPer dep for HDF --- .../b/Bison/Bison-2.5-iqacml-3.7.3.eb | 20 +++++++++++++++++++ .../f/flex/flex-2.5.35-iqacml-3.7.3.eb | 14 +++++++++++++ .../HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 9 +++++---- .../h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 9 +++++---- .../h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 9 +++++---- .../h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 9 +++++---- .../h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 9 +++++---- .../h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 9 +++++---- 8 files changed, 64 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.5-iqacml-3.7.3.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.35-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-iqacml-3.7.3.eb new file mode 100644 index 0000000000..1b1d714087 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-iqacml-3.7.3.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '2.5' + +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': 'iqacml', 'version': '3.7.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +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/f/flex/flex-2.5.35-iqacml-3.7.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.35-iqacml-3.7.3.eb new file mode 100644 index 0000000000..e1c44104d5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.35-iqacml-3.7.3.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.35' + +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': 'iqacml', 'version': '3.7.3'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 77aaf88b28..6c4821a391 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -8,10 +8,11 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index beeac81a9f..1ca5d08181 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -7,10 +7,11 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 4cfefc2018..d71e54280e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -8,10 +8,11 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 0bbde1cc9d..df3727db52 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -9,10 +9,11 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index 29e1c9b8d8..12c89a77b4 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -8,10 +8,11 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), - ('Szip', '2.1'), - ] + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 652ae87480..a3407d071e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -8,10 +8,11 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -- GitLab From 774e8f3b382787805992580dd8e5ea0f7253e5c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Oct 2013 14:58:05 +0200 Subject: [PATCH 009/566] add easyconfigs for new versions of FSL and fmri + dependencies --- .../f/FSL/FSL-5.0.4-ictce-5.3.0.eb | 26 +++++++++++++++++ .../f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb | 29 +++++++++++++++++++ .../f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb | 17 +++++++++++ .../t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb | 19 ++++++++++++ .../easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb | 19 ++++++++++++ 5 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-5.0.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..295efc5d97 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4-ictce-5.3.0.eb @@ -0,0 +1,26 @@ +name = 'FSL' +version = '5.0.4' + +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': 'ictce', 'version': '5.3.0'} + +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-devel is required for X11/Xlib.h, required by tk build +osdependencies = ['libX11-devel'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000..f685ae9e45 --- /dev/null +++ b/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'fmri' +version = '1.5-0' + +homepage = 'http://cran.r-project.org/web/packages/fmri' +description = """The package contains R-functions to perform an fmri analysis as described in K. Tabelow, + J. Polzehl, H.U. Voss, and V. Spokoiny, Analysing fMRI experiments with structure adaptive smoothing procedures, + NeuroImage, 33:55-62 (2006) and J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive segmentation for statistical + parametric mapping, NeuroImage, 52:515-523 (2010).""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://cran.r-project.org/src/contrib/'] +sources = ['%s_%s.tar.gz' % (name, version)] + +r = 'R' +rver = '2.15.3' +versionsuffix = '-%s-%s' % (r, rver) + +tcltkver = '8.5.15' + +dependencies = [ + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..e473bccccb --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000..808b442937 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.5.15' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%s%s-src.tar.gz' % (name.lower(), version)] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..fb3f5af8c8 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'Tk' +version = '8.5.15' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%s%s-src.tar.gz' % (name.lower(), version)] + +dependencies = [('Tcl', version)] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' -- GitLab From 16c92bda0b5ebf28846d05f16a555d480ce7472b Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 29 Oct 2013 19:47:27 +0100 Subject: [PATCH 010/566] add TDK from Nvidia Signed-off-by: Fotis Georgatos --- .../Tesla-Deployment-Kit-5.319.43.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb new file mode 100644 index 0000000000..4db2aee3fd --- /dev/null +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: University of Luxembourg / LCSB +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = "Tarball" + +name = "Tesla-Deployment-Kit" +version = "5.319.43" + +homepage = 'https://developer.nvidia.com/tesla-deployment-kit' +description = """The Tesla Deployment Kit is a set of tools provided primarily for the NVIDIA Tesla + range of GPUs. They aim to empower users to better manage their NVIDIA GPUs by providing a broad + range of functionalities. The kit contains: + * NVIDIA Management Library (NVML), + * Tesla Deployment Kit - Linux Edition (Aug 1st, 2013)""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['tdk_%(version)s.tar.gz'] +source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/nvml'] + +sanity_check_paths = { + 'files': ["nvidia-healthmon/nvidia-healthmon", "nvidia-healthmon/nvidia-healthmon_x86"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': 'nvidia-healthmon', + 'CPATH': 'nvml/include', +} + +moduleclass = 'system' -- GitLab From 6a66bed38deb905df0bdeef69b7a3c49ff8183a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2013 21:56:08 +0100 Subject: [PATCH 011/566] provide alternative download URL for Mesa --- .../m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 ++++- .../m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb | 5 ++++- .../m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb | 5 ++++- .../m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb | 5 ++++- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 0dbc448069..d3ced86b9d 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True} sources = ['%sLib-%s.tar.gz' % (name, version)] -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/%s' % version] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb index b038930e50..aa7d43dd2e 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-goolf-1.4.10-Python-2.7.3.eb @@ -8,7 +8,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = ['%sLib-%s.tar.gz' % (name, version)] -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/%s' % version] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb index d3a225896d..2b0c88be6d 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True} sources = ['%sLib-%s.tar.gz' % (name, version)] -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/%s' % version] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb index bc2ba6b2f5..c2adb7e2f2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-7.11.2-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = ['%sLib-%s.tar.gz' % (name, version)] -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/%s' % version] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) -- GitLab From 00af0ebdb652df8b103857cdf637f2f04009ed06 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 14 Nov 2013 12:06:47 +0100 Subject: [PATCH 012/566] added gbm package to R --- easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb | 2 ++ easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb | 1 + easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb | 1 + easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 1 + 10 files changed, 11 insertions(+) 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 a2e641a449..8468c6029d 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 @@ -135,6 +135,8 @@ exts_list = [ ('R.oo', '1.13.0', ext_options), ('R.matlab', '1.7.0', ext_options), ('Rniftilib', '0.0-32', ext_options), + ('gbm', '2.1', ext_options), + ] moduleclass = 'lang' 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 cdf742e159..84d3f3e99e 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 @@ -135,6 +135,7 @@ exts_list = [ ('R.oo', '1.13.0', ext_options), ('R.matlab', '1.7.0', ext_options), ('Rniftilib', '0.0-32', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 71f7f43050..70126d1ce6 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 @@ -135,6 +135,7 @@ exts_list = [ ('R.oo', '1.13.0', ext_options), ('R.matlab', '1.7.0', ext_options), ('Rniftilib', '0.0-32', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 f9ee59bde0..3a90cc17eb 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 @@ -135,6 +135,7 @@ exts_list = [ ('R.oo', '1.13.0', ext_options), ('R.matlab', '1.7.0', ext_options), ('Rniftilib', '0.0-32', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 6eb235ac8f..201aa6b636 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 @@ -135,6 +135,7 @@ exts_list = [ ('R.oo', '1.13.0', ext_options), ('R.matlab', '1.7.0', ext_options), ('Rniftilib', '0.0-32', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 9ea41bf416..65f22fa5a8 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 @@ -140,6 +140,7 @@ exts_list = [ ('ShortRead', '1.18.0', bioconductor_options), ('graph', '1.38.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 9cf2522c37..2672165c50 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 @@ -140,6 +140,7 @@ exts_list = [ ('ShortRead', '1.18.0', bioconductor_options), ('graph', '1.38.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 54e7b1e0bc..2f2b2a553e 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 @@ -140,6 +140,7 @@ exts_list = [ ('ShortRead', '1.18.0', bioconductor_options), ('graph', '1.38.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 521894ec3c..2d510cfe36 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 @@ -140,6 +140,7 @@ exts_list = [ ('ShortRead', '1.18.0', bioconductor_options), ('graph', '1.38.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' 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 1f762f49eb..e9312bcac5 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 @@ -138,6 +138,7 @@ exts_list = [ ('ShortRead', '1.20.0', bioconductor_options), ('graph', '1.40.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('gbm', '2.1', ext_options), ] moduleclass = 'lang' -- GitLab From 42ca6fd848fcf781ce2ab891ea1289a40e7e2815 Mon Sep 17 00:00:00 2001 From: Andreas Panteli Date: Fri, 15 Nov 2013 10:46:56 +0200 Subject: [PATCH 013/566] Contribute new easyconfig for Libint with ictce-4.1.13 needed for CP2K --- .../l/Libint/Libint-1.1.4-ictce-4.1.13.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb new file mode 100644 index 0000000000..6f64e7b117 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--with-pic --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 f97ae80cc98fd99e4fcf5d9ccbf647d0725343ec Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 15 Nov 2013 17:41:17 +0100 Subject: [PATCH 014/566] add OCaml & Erlang Signed-off-by: Fotis Georgatos --- .../e/Erlang/Erlang-R16B02-goolf-1.4.10.eb | 32 +++++++++++++++++ .../o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 35 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb new file mode 100644 index 0000000000..903021b2af --- /dev/null +++ b/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.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:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +name = "Erlang" +version = "R16B02" + +homepage = 'http://www.example.com' +description = """Erlang is a programming language used to build massively scalable + soft real-time systems with requirements on high availability. Some of its uses are + in telecoms, banking, e-commerce, computer telephony and instant messaging. Erlang's + runtime system has built-in support for concurrency, distribution and fault tolerance.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = ['otp_src_%(version)s.tar.gz'] +source_urls = ['http://www.erlang.org/download/'] + +builddependencies = [('Autoconf', '2.69')] +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/erl", "bin/erlc"], + 'dirs': [] +} + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..1274793c40 --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +name = "OCaml" +version = "4.01.0" + +homepage = 'http://www.example.com' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = ['ocaml-%(version)s.tar.gz'] +source_urls = ['http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s'] + +builddependencies = [('Autoconf', '2.69')] +dependencies = [('ncurses', '5.9')] + +prefix_opt = "-prefix " +makeopts = "world" + +sanity_check_paths = { + 'files': ["bin/ocaml", "bin/ocamlc"], + 'dirs': [] +} + +moduleclass = 'lang' -- GitLab From 682275e6918aa827d2c062492dc998572e1961e0 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 15 Nov 2013 17:51:02 +0100 Subject: [PATCH 015/566] add homepages for OCaml/Erlang & optimize better OCaml build Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb index 903021b2af..f16d2df15b 100644 --- a/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb @@ -10,7 +10,7 @@ name = "Erlang" version = "R16B02" -homepage = 'http://www.example.com' +homepage = 'http://www.erlang.org/' description = """Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability. Some of its uses are in telecoms, banking, e-commerce, computer telephony and instant messaging. Erlang's 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 1274793c40..cb3cc4532d 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 @@ -10,7 +10,7 @@ name = "OCaml" version = "4.01.0" -homepage = 'http://www.example.com' +homepage = 'http://ocaml.org/' description = """OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, @@ -25,7 +25,7 @@ builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " -makeopts = "world" +makeopts = "world.opt" sanity_check_paths = { 'files': ["bin/ocaml", "bin/ocamlc"], -- GitLab From 1b65ccf2e765592d0fd0fdb168425c9f2183c704 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 18 Nov 2013 21:45:41 +0100 Subject: [PATCH 016/566] add new elements for goolfc/2.0.10 Signed-off-by: Fotis Georgatos --- .../f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb | 32 ++++++++++++ .../easyconfigs/g/gompic/gompic-1.6.10.eb | 29 +++++++++++ .../easyconfigs/g/goolfc/goolfc-2.0.10.eb | 41 +++++++++++++++ ...enBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb | 51 +++++++++++++++++++ .../OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb | 40 +++++++++++++++ ...mpic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb | 25 +++++++++ 6 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb create mode 100644 easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb new file mode 100644 index 0000000000..7dd42f220e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb @@ -0,0 +1,32 @@ +name = 'FFTW' +version = '3.3.3' + +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': 'gompic', 'version': '1.6.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb b/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb new file mode 100644 index 0000000000..525fd48b04 --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb @@ -0,0 +1,29 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '1.6.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.2' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.7.3' + +cudaname = 'CUDA' +cudaver = '5.5.22' +cudasuffix = '-' + cudaname + '-' + cudaver + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, cudasuffix, comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb new file mode 100644 index 0000000000..549e0bec37 --- /dev/null +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb @@ -0,0 +1,41 @@ +easyblock = "Toolchain" + +name = 'goolfc' +version = '2.0.10' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_version = '4.8.2' +comp = (comp_name, comp_version) + +# toolchain used to build goolfc dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc_ver = '1.6.10' +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +cudaname = 'CUDA' +cudaver = '5.5.22' +cudasuffix = '-' + cudaname + '-' + cudaver + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +blassuff = '-LAPACK-3.4.2' +blas = '-%s-%s%s' % (blaslib, blasver, blassuff) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, # part of gompic + ('OpenMPI', '1.7.3', cudasuffix, comp), # part of gompic, which includes also CUDA + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.3', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..dfef0b31c1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb @@ -0,0 +1,51 @@ +name = 'OpenBLAS' +version = '0.2.8' + +lapackver = '3.4.2' +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': 'gompic', 'version': '1.6.10'} + +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 = [ + # 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +makeopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb new file mode 100644 index 0000000000..64159cacf9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb @@ -0,0 +1,40 @@ +name = 'OpenMPI' +version = "1.7.3" +versionsuffix = '-CUDA-5.5.22' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69') +] + +dependencies = [ + ('hwloc', '1.7.2'), + ('CUDA', '5.5.22', '', True), +] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --disable-dlopen is incompatible + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_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' + +patches = ['openmpi-mca-params.conf-1.4.5-local.patch', 'pax_disable.patch'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..0bc94ce1d6 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.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': 'gompic', 'version': '1.6.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s.tgz'] + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +blassuff = '-LAPACK-3.4.2' + +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 1d85a645e9ba730fdd0ddf5a9a1a52aadc018a78 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 19 Nov 2013 12:39:02 +0100 Subject: [PATCH 017/566] Added ghostscript --- .../ghostscript-9.10-goolf-1.4.10.eb | 24 +++++++++++++++++++ .../ghostscript-9.10-ictce-4.1.13.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb new file mode 100644 index 0000000000..c2f7480573 --- /dev/null +++ b/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +name = 'ghostscript' +version = '9.10' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that. +""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ +# optional, these are actually patched and included in the sources, +# ('expat', '2.1.0'), +# ('freetype', '2.4.10'), +# ('libpng', '1.6.2'), + ('LibTIFF', '4.0.3'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb b/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb new file mode 100644 index 0000000000..d38ce6de2c --- /dev/null +++ b/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb @@ -0,0 +1,24 @@ +name = 'ghostscript' +version = '9.10' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that. +""" +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ +# optional, these are actually patched and included in the sources, +# ('expat', '2.1.0'), +# ('freetype', '2.4.10'), +# ('libpng', '1.6.2'), + ('LibTIFF', '4.0.3'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'lib' -- GitLab From f12f0bf4fdcaf8eb20aec04e3b9e337f859f59ba Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 19 Nov 2013 16:23:53 +0100 Subject: [PATCH 018/566] added CAP3 assembler config files for intel-x86, intel-x86_64 and opteron --- .../easyconfigs/c/CAP3/CAP3-intel-x86.eb | 23 +++++++++++++++++++ .../easyconfigs/c/CAP3/CAP3-intel-x86_64.eb | 23 +++++++++++++++++++ easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb | 23 +++++++++++++++++++ 3 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb create mode 100644 easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb create mode 100644 easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb b/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb new file mode 100644 index 0000000000..e9d20d0c64 --- /dev/null +++ b/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb @@ -0,0 +1,23 @@ + +name = 'CAP3' +version = 'intel-x86_12-21-2007' + +easyblock = 'PackedBinary' + +homepage = 'http://seq.cs.iastate.edu/' +description = """CAP3 assembly program """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [('http://seq.cs.iastate.edu/CAP3/')] +sources = ['cap3.linux.tar'] + +sanity_check_paths = { + 'files': ['cap3','formcon'], + 'dirs': [], +} + + +moduleclass = 'bio' + + diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb b/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb new file mode 100644 index 0000000000..46918913be --- /dev/null +++ b/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb @@ -0,0 +1,23 @@ + +name = 'CAP3' +version = 'intel-x86_64_12-21-2007' + +easyblock = 'PackedBinary' + +homepage = 'http://seq.cs.iastate.edu/' +description = """CAP3 assembly program """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [('http://seq.cs.iastate.edu/CAP3/')] +sources = ['cap3.linux.x86_64.tar'] + +sanity_check_paths = { + 'files': ['cap3','formcon'], + 'dirs': [], +} + + +moduleclass = 'bio' + + diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb b/easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb new file mode 100644 index 0000000000..559fab20ae --- /dev/null +++ b/easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb @@ -0,0 +1,23 @@ + +name = 'CAP3' +version = 'opteron-12-21-2007' + +easyblock = 'PackedBinary' + +homepage = 'http://seq.cs.iastate.edu/' +description = """CAP3 assembly program """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [('http://seq.cs.iastate.edu/CAP3/')] +sources = ['cap3.linux.opteron64.tar'] + +sanity_check_paths = { + 'files': ['cap3','formcon'], + 'dirs': [], +} + + +moduleclass = 'bio' + + -- GitLab From 07104ce9598fd3007c1f21d5a8b2640ac37b342b Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 19 Nov 2013 16:33:55 +0100 Subject: [PATCH 019/566] added R-3.0.2-goolf-1.4.10-bare --- .../r/R/R-3.0.2-goolf-1.4.10-bare.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb new file mode 100644 index 0000000000..d0aa0dd324 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb @@ -0,0 +1,37 @@ +name = 'R' +version = '3.0.2' +versionsuffix = '-bare' # bare, as in no extensions included + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +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', '6.2'), + ('ncurses', '5.9'), + ('libpng', '1.6.2'), # for plotting in R + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] # just to make it explicit this module doesn't include any extensions + +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': [] +} + +moduleclass = 'lang' -- GitLab From 713a352f100870850f2673c9e7c4281d24dffffb Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 02:40:22 +0100 Subject: [PATCH 020/566] template with SOURCE_TGZ Signed-off-by: Fotis Georgatos --- .../easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- .../easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb | 2 +- .../easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/lxml/lxml-3.1.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/l/lxml/lxml-3.1.2-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb | 2 +- .../n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb | 2 +- .../o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-ictce-4.1.13.eb | 2 +- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-iqacml-4.4.13.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 +- .../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-2.7.3-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-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 +- .../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/problog/problog-1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/p/problog/problog-1.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/p/problog/problog-1.1-ictce-5.3.0.eb | 2 +- 54 files changed, 54 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb index 40eaf1a383..5d4df914d3 100644 --- a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ description = """The BAM format is an efficient method for storing and sharing d toolchain = {'name': 'goolf', 'version': '1.4.10'} # eg. http://www.hudsonalpha.org/gsl/static/software/bam2fastq-1.1.0.tgz -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] source_urls = ['http://www.hudsonalpha.org/gsl/static/software/'] files_to_copy = [(["bam2fastq"], 'bin')] diff --git a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb index c22f2d6caf..4243fd37f2 100644 --- a/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bam2fastq/bam2fastq-1.1.0-ictce-5.3.0.eb @@ -23,7 +23,7 @@ description = """The BAM format is an efficient method for storing and sharing d toolchain = {'name': 'ictce', 'version': '5.3.0'} # eg. http://www.hudsonalpha.org/gsl/static/software/bam2fastq-1.1.0.tgz -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] source_urls = ['http://www.hudsonalpha.org/gsl/static/software/'] files_to_copy = [(["bam2fastq"], 'bin')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb index 0f69cf489c..a957f3428f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} # there is no tarball provided, only SVN checkout through: # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index 83a222c545..073b6bae5c 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # there is no tarball provided, only SVN checkout through: # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb index 6b96386814..de5d0fcdf9 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} # there is no tarball provided, only SVN checkout through: # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 20b367819c..e1bcb81951 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # there is no tarball provided, only SVN checkout through: # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] dependencies = [('Java', '1.7.0_15', '', True)] 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 dea6e016af..7ab203990e 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 @@ -9,7 +9,7 @@ description = """The lxml XML toolkit is a Pythonic binding for the C libraries toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://lxml.de/files/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] python = 'Python' pythonversion = '2.7.3' 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 ada05f00c3..7c17d46955 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 @@ -9,7 +9,7 @@ description = """The lxml XML toolkit is a Pythonic binding for the C libraries toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://lxml.de/files/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] python = 'Python' pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 9d8732ce41..3522f8a87b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index 64f64c54eb..f954a9b12a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 97bd2dfeb6..6a10d2ec63 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 00d09276a8..4913ef008f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 7d12bb5e12..8b7d3a2416 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 064d35ca84..1632ef23de 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 8bd4bda916..43375f2a29 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True, 'pic': True} # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb index f4cd636622..47f96c354b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goalf-1.1.0-no-OFED.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb index 17e9162920..fc95905bea 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb index 0e8e0b1c76..9a382ba0a0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-4.0.6.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb index c16690c3c6..846b27e9ad 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.1.1-ictce-5.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-goolf-1.4.10.eb index b192fe9ac2..4f2803ebd1 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-ictce-4.1.13.eb index 6268f6a338..93b4f37bde 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-ictce-4.1.13.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-iqacml-4.4.13.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-iqacml-4.4.13.eb index 73282af7a1..3f2e8fb697 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.0-iqacml-4.4.13.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'iqacml', 'version': '4.4.13'} source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] 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 8831f1a81b..bb57de5afb 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 @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 f626304d89..8ee11e4811 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 @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 7cd7a6cc68..97c0820aec 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 @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 5defdd9ca7..536c688b86 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 @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 350cff539f..45f1f26710 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 78733636f2..78d4528c83 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 965f7680f9..76f06b40da 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 d6df6cdaaa..7aac7b2dfc 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 f097672302..601fa79282 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 d6387e790c..cab3752cb6 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 36c7fd70fe..3e7e8f9aa4 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 cb3e4c646f..6cefbb84da 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 2904d6f980..bc83d85dbe 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 44396979b5..e1104a66dd 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 e69840bf6a..05893e2a35 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 0fcb35553c..289c124daa 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 0ef59f1a6c..bf8beca6cb 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 6d4756c14e..a79b557e86 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 @@ -12,7 +12,7 @@ scipyversion = '0.11.0' pytablesversion = '2.4.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 591a7c22f0..709e1ad8ad 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python_libffi_int128_icc.patch'] 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 61eaa9350c..8aa152a8fd 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 890f3ac899..dc1af16dd5 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 ba61bc3e08..837e9740b5 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 9cd24fe3ae..7700c24281 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 4896534784..e12d4e2536 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.1' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 fbb0800072..2b51a97a46 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-%(version)s_libffi_int128_icc.patch'] 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 087bed47a1..540e0abee8 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 f52c47b304..304dcc8026 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 938b80ce48..0ca1a89dd3 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 @@ -11,7 +11,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 7971193188..17470443c6 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 @@ -12,7 +12,7 @@ numpyversion = '1.6.1' scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/problog/problog-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/problog/problog-1.1-goolf-1.4.10.eb index 98e5e870b9..7d7645d75c 100644 --- a/easybuild/easyconfigs/p/problog/problog-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/problog/problog-1.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ source_urls = [ 'http://www.cs.kuleuven.be/~theo/tools/', # SimpleCUDD ] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'SimpleCUDD.tar.gz', # no version number?! ] diff --git a/easybuild/easyconfigs/p/problog/problog-1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/p/problog/problog-1.1-ictce-4.1.13.eb index 3ad722d21e..ee27ea143c 100644 --- a/easybuild/easyconfigs/p/problog/problog-1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/problog/problog-1.1-ictce-4.1.13.eb @@ -11,7 +11,7 @@ source_urls = [ 'http://www.cs.kuleuven.be/~theo/tools/', # SimpleCUDD ] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'SimpleCUDD.tar.gz', # no version number?! ] diff --git a/easybuild/easyconfigs/p/problog/problog-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/problog/problog-1.1-ictce-5.3.0.eb index 9761353794..bb29badc8b 100644 --- a/easybuild/easyconfigs/p/problog/problog-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/problog/problog-1.1-ictce-5.3.0.eb @@ -11,7 +11,7 @@ source_urls = [ 'http://www.cs.kuleuven.be/~theo/tools/', # SimpleCUDD ] sources = [ - '%(name)s-%(version)s.tgz', + SOURCE_TGZ, 'SimpleCUDD.tar.gz', # no version number?! ] -- GitLab From d199ac1a326376b697d02c76a63caf2953e56db6 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 02:45:37 +0100 Subject: [PATCH 021/566] template with SOURCELOWER_TGZ Signed-off-by: Fotis Georgatos --- .../LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb | 2 +- .../l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb | 2 +- .../easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich2-1.4.8.eb | 2 +- easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb | 2 +- easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.4.10.eb | 2 +- .../easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb | 2 +- .../m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb | 2 +- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb | 2 +- ...APACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb | 2 +- ...LAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb | 2 +- ...ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...CK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...LAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- .../ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...ScaLAPACK-2.0.2-gmpich2-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...LAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...ACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- ...aLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb | 2 +- .../ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- .../ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 2 +- .../ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb | 2 +- ...PACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb | 2 +- .../ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb | 2 +- .../ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb | 2 +- 32 files changed, 32 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb index 8b15048447..c9319bda9f 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] versionsuffix = '-%s-%s' % ('ATLAS', '3.8.4') diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb index 654ef2b7f9..7722ab0a36 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] blaslib = 'ATLAS' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb index 908402fe2b..7a9d14764d 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich2-1.4.8.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich2-1.4.8.eb index c68bfa3e9c..b8517be37b 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich2-1.4.8.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich2-1.4.8.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gmpich2', 'version': '1.4.8'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb index b0cffff94e..6bdb18e61f 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.3.12'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.4.10.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.4.10.eb index 4350fbda75..9be946f5e8 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.4.10.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.4.10.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.4.10'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb index da972092a4..c930b5d2ba 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb index 7292fa7362..5a6e906741 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'gompi', 'version': '1.5.12'} toolchainopts = {'pic': True} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb index 8d81812dc2..cee59253ac 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3-hwloc-chkpt.eb @@ -8,7 +8,7 @@ It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb index 19e6c4de4e..53cdff914e 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.7-GCC-4.6.3.eb @@ -7,7 +7,7 @@ It is based on MPICH2 and MVICH.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] # note: this URL will only work for the most recent version (previous versions no longer available?) source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2'] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb index 2b6e8dfed4..9be4dedbf3 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.8.1-GCC-4.7.2.eb @@ -7,7 +7,7 @@ description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb index 9ff3ca9a33..602d1c4c80 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-GCC-4.7.3.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb index 5b4bd89d04..86fdc73adc 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9a2-GCC-4.7.2.eb @@ -7,7 +7,7 @@ description = "This is an MPI-2 implementation (conforming to MPI 2.1 standard) toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb index 05e1fd9ee5..1c45f04807 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9b-GCC-4.7.2.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'GCC', 'version': '4.7.2'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb index 1eb4d70733..892dac4687 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb index 27a74baecd..9e7d8d7641 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-GCC-4.7.3.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'GCC', 'version': '4.7.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb index d71631e46b..adc0860457 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-iiqmpi-3.3.0-ACML-5.3.0-ifort-64bit-BLACS-1.1.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'iiqmpi', 'version': '3.3.0'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] # BLAS and LAPACK acmln = 'ACML' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb index 168e48a0db..269cb64669 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.1-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'ATLAS' blasver = '3.8.4' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index b943203372..904f9125ac 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmpich-1.1.6-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'cgmpich', 'version': '1.1.6'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 5bea6d5a9b..df6546768d 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.1.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'cgmvapich2', 'version': '1.1.12rc1'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index eee66ed24d..799e3b5272 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgmvapich2-1.2.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'cgmvapich2', 'version': '1.2.7'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index cfe77a497f..d0e2892049 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-cgompi-1.1.7-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'cgompi', 'version': '1.1.7'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich2-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich2-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 5b744a280f..967d7b0bda 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich2-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmpich2-1.4.8-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gmpich2', 'version': '1.4.8'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 5ff70cf998..9f4ac4da77 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gmvapich2', 'version': '1.7.12'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index 060eb83f03..4e2c7a1161 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.12rc1-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gmvapich2', 'version': '1.7.12rc1'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb index f68c5fe5d4..b8ff206dfb 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gmvapich2-1.7.9a2-ACML-5.2.0-gfortran-64bit.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gmvapich2', 'version': '1.7.9a2'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blas_lapack_lib = 'ACML' blas_lapack_ver = '5.2.0' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index ee98eec7c9..04f36f4b91 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.3.12'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb index c1e8c6b2e6..8f7ad295d1 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.4.10'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.6' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb index 8027e58830..7e8bf14eee 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-ATLAS-3.10.1-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.5.12'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'ATLAS' blasver = '3.10.1' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb index 5fd2b5ab55..68e8936860 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.12-no-OFED-ATLAS-3.10.1-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.5.12-no-OFED'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'ATLAS' blasver = '3.10.1' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb index 5baf987e04..b037ae507c 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'gompi', 'version': '1.6.10'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blaslib = 'OpenBLAS' blasver = '0.2.8' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb index 9f74510c4f..325514fe67 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-iiqmpi-4.4.13-ACML-5.3.1-ifort-64bit.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'iiqmpi', 'version': '4.4.13'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] blas_lapack_lib = 'ACML' blas_lapack_ver = '5.3.1' -- GitLab From c770ae372cd3133712152b17dc145cb8c0540226 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 02:53:44 +0100 Subject: [PATCH 022/566] template even more with SOURCELOWER_TGZ Signed-off-by: Fotis Georgatos --- .../b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb | 2 +- .../easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb | 2 +- .../easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb | 2 +- ....0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb index abce8e1ac7..15eee3a6b7 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb @@ -13,7 +13,7 @@ version = '1.03e' homepage = 'http://www.coker.com.au/bonnie++/' description = """Bonnie++-1.03e: Enhanced performance Test of Filesystem I/O""" -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb index cc7ea34456..00dc69f950 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goolf-1.4.10.eb @@ -13,7 +13,7 @@ version = '1.03e' homepage = 'http://www.coker.com.au/bonnie++/' description = """Bonnie++-1.03e: Enhanced performance Test of Filesystem I/O""" -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb index 34d9dfcf6e..b0b5384914 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb @@ -13,7 +13,7 @@ version = '1.03e' homepage = 'http://www.coker.com.au/bonnie++/' description = """Bonnie++-1.03e: Enhanced performance Test of Filesystem I/O""" -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://www.coker.com.au/bonnie++/'] toolchain = {'version': '4.0.6', 'name': 'ictce'} diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb index bc3566fe23..23c215e249 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-5.3.0.eb @@ -13,7 +13,7 @@ version = '1.03e' homepage = 'http://www.coker.com.au/bonnie++/' description = """Bonnie++-1.03e: Enhanced performance Test of Filesystem I/O""" -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://www.coker.com.au/bonnie++/'] diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb index 1c90c20dab..3e399ef780 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb @@ -7,7 +7,7 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb index 1b21e9763c..8b8782fe4b 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-goolf-1.4.10.eb @@ -7,7 +7,7 @@ In contrast to bison, it is written to avoid dependencies upon a particular comp toolchain = {'name': 'goolf', 'version': '1.4.10'} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb index 1c347cdee7..9b30eede50 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb @@ -7,7 +7,7 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc toolchain = {'name': 'ictce', 'version' : '4.0.6'} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb index 523a138e8a..3f0c68f0c2 100644 --- a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc toolchain = {'name': 'ictce', 'version': '5.3.0'} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['ftp://invisible-island.net/byacc'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goalf-1.1.0-no-OFED.eb index ee57773249..8a5facff39 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goolf-1.4.10.eb index f7b209a5b8..f9f4f41e38 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-4.0.6.eb index 322bdf428f..3585a1adbe 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'pic': True} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] # CLHEP compiles with icc instead of icpc diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-5.3.0.eb index 7510428bdd..b61ee5dfbe 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.1.0-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] # CLHEP compiles with icc instead of icpc diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb index ccb736b20c..382a1b327e 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb @@ -8,7 +8,7 @@ description = """The e-Core technology simulates the natural processes of sedime toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb index 611b783f5d..210286f19d 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1.eb @@ -8,7 +8,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of toolchain = {'name': 'gompi', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s-%s.tgz' % (name.lower(), version)] +sources = [SOURCELOWER_TGZ] source_urls = [homepage] blaslib = 'ATLAS' -- GitLab From e85d92e135d31e00666c54e02a97eb6aab24dbe2 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 02:56:03 +0100 Subject: [PATCH 023/566] template with SOURCELOWER_ZIP Signed-off-by: Fotis Georgatos --- .../Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 1dd4e23222..d3d564e940 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,7 +13,7 @@ description = """The greenlet package is a spin-off of Stackless, a version of C toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb index 73c65c5dea..4de1c939b5 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb @@ -13,7 +13,7 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb index bb349c82a4..5384581b45 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -13,7 +13,7 @@ description = """The greenlet package is a spin-off of Stackless, a version of C toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb index d3dfb0cdef..1091c7035e 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb @@ -14,7 +14,7 @@ description = """The greenlet package is a spin-off of Stackless, a version of C toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.3' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb index d84cd89ae9..8936c49f7b 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """The JasPer Project is an open-source initiative to provide a fr toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb index e34b6a8e71..2c331ec80f 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb index f049a7290f..2a9c066f57 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb @@ -7,7 +7,7 @@ description = """The JasPer Project is an open-source initiative to provide a fr toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb index 8d5cc91b46..1c14c19383 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """The JasPer Project is an open-source initiative to provide a fr toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-5.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-5.3.0.eb index 148776315e..2bbc6e083e 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """The JasPer Project is an open-source initiative to provide a fr toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb index db861191fd..778a35918b 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb @@ -7,7 +7,7 @@ description = """The JasPer Project is an open-source initiative to provide a fr toolchain = {'name': 'iqacml', 'version': '3.7.3'} -sources = ['%s-%s.zip' % (name.lower(), version)] +sources = [SOURCELOWER_ZIP] source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] sanity_check_paths = { -- GitLab From bcd5ddeb8625e45eb67ac7765b8197e082df81b1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 03:02:00 +0100 Subject: [PATCH 024/566] template with SOURCE_TAR Signed-off-by: Fotis Georgatos --- .../easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb | 2 +- .../easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb index dbced3e64b..aa40c8e163 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb index 40a9844a04..ad06ddb722 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb index 6626ea0412..52560e746f 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb index 1e29860282..c4f3a2a7e0 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb index 36b9488a21..ef8adc2283 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb index cd9cd1eda9..f194362219 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] patches = ['fix_makefile.patch'] diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb index d471cd44b2..1c99de3550 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] patches = ['fix_makefile.patch'] diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb index 7012aa01db..6a4c924d81 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] patches = ['fix_makefile.patch'] diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb index c7e5c2c63f..9c96a28d96 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] patches = ['fix_makefile.patch'] diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb index 7e04bd54d3..6ebe064edf 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb @@ -9,7 +9,7 @@ toolchainopts = {'opt': True} dependencies = [('JasPer', '1.900.1')] -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] patches = ['fix_makefile.patch'] -- GitLab From bac7ee84af4698c9f4342455c9cf79780c758fc5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 03:11:52 +0100 Subject: [PATCH 025/566] template with SOURCELOWER_TAR_GZ Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb index 9b84ed765c..4fa7753215 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions toolchain = {'name': 'ictce', 'version': '5.3.0'} -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] dependencies = [ diff --git a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb index 1156a3d1e9..f7f33b20cd 100644 --- a/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/h5utils/h5utils-1.12.1-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """h5utils is a set of utilities for visualization and conversion convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).""" source_urls = ['http://ab-initio.mit.edu/h5utils/'] -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] patches = ['libpng1.5_fix.patch'] diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb index 32972e3ae5..74ca15b43e 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] dependencies = [('guile', '1.8.8')] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index c3709d8e78..271da139b9 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -6,7 +6,7 @@ description = """GNU libmatheval is a library (callable from C and Fortran) to p and evaluate symbolic expressions input as text.""" source_urls = ['http://ftp.gnu.org/gnu/libmatheval/'] -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} 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 90651eb628..a5d16e83a0 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 @@ -12,7 +12,7 @@ toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': source_urls = ['http://ab-initio.mit.edu/meep/', 'http://ab-initio.mit.edu/meep/old/'] -sources = ['%s-%s.tar.gz' % (name.lower(), version)] +sources = [SOURCELOWER_TAR_GZ] patches = ['Meep-%s_version-string-without-spaces.patch' % version] -- GitLab From 5c41a2cfb7e5d4ad56107e536e19aa2552c6da9a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 03:16:12 +0100 Subject: [PATCH 026/566] template with SOURCE_TGZ Signed-off-by: Fotis Georgatos --- .../m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb | 2 +- .../easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb | 2 +- .../easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb index 83a3f3611c..3ab6fccc96 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goalf-1.1.0-no-OFED.eb @@ -19,7 +19,7 @@ description = """A short read assember for metagenomics""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s.tgz' % (name, version)] +sources = [SOURCE_TGZ] source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src'] # Actually, just a "soft"-dependency as MetaVelvet includes a velvet-distribution in its own package. diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb index 59ff6b35c3..c9bcb07364 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """A short read assember for metagenomics""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s.tgz' % (name, version)] +sources = [SOURCE_TGZ] source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src'] # Actually, just a "soft"-dependency as MetaVelvet includes a velvet-distribution in its own package. diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb index d264b2ce44..c7d1a1094e 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-4.0.6.eb @@ -19,7 +19,7 @@ description = """A short read assember for metagenomics""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s.tgz' % (name, version)] +sources = [SOURCE_TGZ] source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src'] # Actually, just a "soft"-dependency as MetaVelvet includes a velvet-distribution in its own package. diff --git a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb index 2a88c56f9e..a9129b8002 100644 --- a/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MetaVelvet/MetaVelvet-1.2.01-ictce-5.3.0.eb @@ -20,7 +20,7 @@ description = """A short read assember for metagenomics""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s.tgz' % (name, version)] +sources = [SOURCE_TGZ] source_urls = ['http://metavelvet.dna.bio.keio.ac.jp/src'] # Actually, just a "soft"-dependency as MetaVelvet includes a velvet-distribution in its own package. -- GitLab From 9877e3f6bf689c06ad21b7efe80cdce39cd5bfc2 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 03:18:55 +0100 Subject: [PATCH 027/566] template with SOURCE_TAR_XZ Signed-off-by: Fotis Georgatos --- .../easyconfigs/c/cairo/cairo-1.12.14-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/c/cairo/cairo-1.12.14-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-4.1.13.eb | 2 +- .../easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goalf-1.1.0-no-OFED.eb index acd5a35b61..6264b44320 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['http://cairographics.org/releases/'] -sources = ['%(name)s-%(version)s.tar.xz'] +sources = [SOURCE_TAR_XZ] dependencies = [ ('libpng', '1.5.14'), diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goolf-1.4.10.eb index 6b7a9cdd10..fe30ba2cfb 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-goolf-1.4.10.eb @@ -9,7 +9,7 @@ PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://cairographics.org/releases/'] -sources = ['%(name)s-%(version)s.tar.xz'] +sources = [SOURCE_TAR_XZ] dependencies = [ ('libpng', '1.5.14'), diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-3.2.2.u3.eb index c483aa6c2f..768941a832 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-3.2.2.u3.eb @@ -9,7 +9,7 @@ PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} source_urls = ['http://cairographics.org/releases/'] -sources = ['%(name)s-%(version)s.tar.xz'] +sources = [SOURCE_TAR_XZ] dependencies = [ ('libpng', '1.5.14'), diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-4.1.13.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-4.1.13.eb index 89a55a0ac7..c623937595 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.14-ictce-4.1.13.eb @@ -9,7 +9,7 @@ PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ['http://cairographics.org/releases/'] -sources = ['%(name)s-%(version)s.tar.xz'] +sources = [SOURCE_TAR_XZ] dependencies = [ ('libpng', '1.5.14'), diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb index 3a776649d4..05a624232e 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb @@ -7,7 +7,7 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = ['%s-%s.tar.xz' % (name, version)] +sources = [SOURCE_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb index 1ae868fbce..ccb40b1358 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = ['%s-%s.tar.xz' % (name, version)] +sources = [SOURCE_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), -- GitLab From aadb27c7370041537cd4f3efab72eb1df3f4f69f Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 20 Nov 2013 03:29:20 +0100 Subject: [PATCH 028/566] template with SOURCELOWER_TAR Signed-off-by: Fotis Georgatos --- .../python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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 4a10173f4d..2643e2c09c 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 @@ -8,7 +8,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] -sources = ['%s-%s.tar' % (name.lower(), version)] +sources = [SOURCELOWER_TAR] patches = [ 'MPI_destructor_1.3.patch' 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 e3438c674f..67aaeea480 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 @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] -sources = ['%s-%s.tar' % (name.lower(), version)] +sources = [SOURCELOWER_TAR] patches = [ 'MPI_destructor_1.3.patch' 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 d4a1091638..dccd4207fd 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 @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] -sources = ['%s-%s.tar' % (name.lower(), version)] +sources = [SOURCELOWER_TAR] patches = [ 'MPI_destructor_1.3.patch' -- GitLab From f494bd3ef3fbd37a7d8ba7b5389768ad9c83b51a Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 12:21:42 +0100 Subject: [PATCH 029/566] added HTSeq and new matplotlib goolf versions --- .../h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb | 26 ++++++++++++++ ...plotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb | 34 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb new file mode 100644 index 0000000000..d36513cc06 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' +name = 'HTSeq' +version = '0.5.4p5' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html' +description = """HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing +assays.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + ('matplotlib', '1.2.1', versionsuffix), + (python, pythonver), +] + + +options = {'modulename': name} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..b35452ca6d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.4.11'), + ('libpng', '1.6.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' -- GitLab From 07325159c3f79c816f61c9277df4a5860e8de16f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 13:49:14 +0100 Subject: [PATCH 030/566] bumped matplotib version --- easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb index d36513cc06..a4920b1638 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb @@ -16,7 +16,7 @@ pythonver = '2.7.5' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - ('matplotlib', '1.2.1', versionsuffix), + ('matplotlib', '1.3.1', versionsuffix), (python, pythonver), ] -- GitLab From 1a24e7db3c80c083430978ec0e0f51c3ace29b7f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 13:52:31 +0100 Subject: [PATCH 031/566] added new matplotlib for goolf and ictce + ictce for HTSeq --- .../h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb | 26 ++++++++++++++ .../1.3.1-goolf-1.4.10-Python-2.7.5.eb | 36 +++++++++++++++++++ ...plotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb | 36 +++++++++++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb new file mode 100644 index 0000000000..880a628b44 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' +name = 'HTSeq' +version = '0.5.4p5' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html' +description = """HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing +assays.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + ('matplotlib', '1.3.1', versionsuffix), + (python, pythonver), +] + + +options = {'modulename': name} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..e21841f64e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,36 @@ +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': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.0.1'), + ('libpng', '1.6.6'), +] + +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-1.3.1-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb new file mode 100644 index 0000000000..1a8bdada73 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb @@ -0,0 +1,36 @@ +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': '4.1.13'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.0.1'), + ('libpng', '1.6.6'), +] + +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 14755acf3942fdd149622718759f05e2d8084275 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 13:56:19 +0100 Subject: [PATCH 032/566] added freetype for 4.1.13 + bumped zlib version in libpng for consistency --- .../freetype/freetype-2.5.0.1-ictce-4.1.13.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.6-goolf-1.4.10.eb | 2 +- 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..de48d98038 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-4.1.13.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.0.1' + +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': 'ictce', 'version': '4.1.13'} + +source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.6')] + +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/libpng/libpng-1.6.6-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb index 3e4fd3d652..c31ece3983 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" -- GitLab From d2cef945960fab913bf9e5166911e25b0dc14b62 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 14:06:02 +0100 Subject: [PATCH 033/566] added new freetype for goolf --- .../freetype/freetype-2.5.0.1-goolf-1.4.10.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..c8025842ef --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.0.1' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.6')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' -- GitLab From c83cc8a655c8178ac5ec8ebb31ea38ea1221af89 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 14:13:36 +0100 Subject: [PATCH 034/566] bumped libpng's zlib on 2 more occasions --- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb index 3abbc07090..c7377b1613 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb index 150ca35db4..076608ccb2 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'optarch': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" -- GitLab From 936f1022e6e15ec915bf25c990642ccc4d1008ae Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 14:46:26 +0100 Subject: [PATCH 035/566] undid changes of libpng's zlib bump --- easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb index c31ece3983..3e4fd3d652 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [('zlib', '1.2.7')] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb index c7377b1613..3abbc07090 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [('zlib', '1.2.7')] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb index 076608ccb2..150ca35db4 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'optarch': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [('zlib', '1.2.7')] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb index cc63b4067d..7324290431 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.8')] +dependencies = [('zlib', '1.2.7')] configopts = "--with-pic" -- GitLab From 380982d54abfb7ba069e9b618f62d4842e0a3e36 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 14:53:26 +0100 Subject: [PATCH 036/566] added new python + matplotlibs for this python --- ...plotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb | 34 +++++++++++ ...plotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb | 36 +++++++++++ .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 61 +++++++++++++++++++ .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 61 +++++++++++++++++++ 4 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb new file mode 100644 index 0000000000..2e3028812f --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb @@ -0,0 +1,34 @@ +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.7'), + ('freetype', '2.4.11'), + ('libpng', '1.6.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000..2e66e93a73 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb @@ -0,0 +1,36 @@ +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': '4.1.13'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.7'), + ('freetype', '2.5.0.1'), + ('libpng', '1.6.6'), +] + +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/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 new file mode 100644 index 0000000000..41832c9598 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -0,0 +1,61 @@ +name = 'Python' +version = '2.7.6' + +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': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.0' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +patches = ['python-%(version)s_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'), +] + +# order is important! +exts_list = [ + ('setuptools', '0.6c11', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('nose', '1.3.0', { + '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, + 'numpy-iqacml.patch', + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + 'source_urls': ['http://www.cython.org/release/'], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..5cd8489340 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -0,0 +1,61 @@ +name = 'Python' +version = '2.7.5' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.0' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +patches = ['python-%(version)s_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'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.4', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('nose', '1.3.0', { + '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, + 'numpy-iqacml.patch', + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + 'source_urls': ['http://www.cython.org/release/'], + }), +] + +moduleclass = 'lang' -- GitLab From 4d19f41eef603ab6fa105b357b8b80f24201120b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 14:54:26 +0100 Subject: [PATCH 037/566] fixed wrong patch --- 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 +- 2 files changed, 1 insertion(+), 3 deletions(-) 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 41832c9598..d5f0fba73e 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 @@ -13,8 +13,6 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), 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 5cd8489340..06f0c86066 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 @@ -13,7 +13,7 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +# patches = ['python-%(version)s_libffi_int128_icc.patch'] # python needs bzip2 to build the bz2 package dependencies = [ -- GitLab From f13c5c009e91521357c8b473d23fee7eb9b6e3f8 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:01:06 +0100 Subject: [PATCH 038/566] forgot to change python version --- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 06f0c86066..0b34fdc73a 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 @@ -1,5 +1,5 @@ name = 'Python' -version = '2.7.5' +version = '2.7.6' homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." -- GitLab From d6a037a2c358252c6132aea49cd07b01175def21 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:04:35 +0100 Subject: [PATCH 039/566] removed wrong matpotlib easyconfigs --- .../1.3.1-goolf-1.4.10-Python-2.7.5.eb | 36 ------------------- ...plotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb | 36 ------------------- 2 files changed, 72 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100644 index e21841f64e..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/1.3.1-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,36 +0,0 @@ -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': 'goolf', 'version': '1.4.10'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -python = "Python" -pythonversion = '2.7.5' -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), - ('zlib', '1.2.8'), - ('freetype', '2.5.0.1'), - ('libpng', '1.6.6'), -] - -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-1.3.1-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb deleted file mode 100644 index 1a8bdada73..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.5.eb +++ /dev/null @@ -1,36 +0,0 @@ -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': '4.1.13'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -python = "Python" -pythonversion = '2.7.5' -pyshortver = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), - ('zlib', '1.2.8'), - ('freetype', '2.5.0.1'), - ('libpng', '1.6.6'), -] - -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 0ca0eb9ce41039e4ff4fa19afdbad146724a34a5 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:18:01 +0100 Subject: [PATCH 040/566] added zlib 1.2.7 build for ictce 5.5.0 --- .../z/zlib/zlib-1.2.7-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb new file mode 100644 index 0000000000..c39a877574 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +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': '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')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 5de86918be056eb8555793ea608f979b5b9babbd Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:24:48 +0100 Subject: [PATCH 041/566] removed failing sanity check, if import matplotlib works, we're happy --- .../matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb | 4 ---- .../matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb | 1 + 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb index 2e3028812f..e4c90c4c44 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-goolf-1.4.10-Python-2.7.6.eb @@ -26,9 +26,5 @@ dependencies = [ ('libpng', '1.6.6'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], -} moduleclass = 'vis' 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 2e66e93a73..9bd2215f1c 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 @@ -26,6 +26,7 @@ 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 = { -- GitLab From 13f17b209b55c3e1ff2777c6f602e04165c646d7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:26:38 +0100 Subject: [PATCH 042/566] bumped python version for htseq --- easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb index a4920b1638..a28674575c 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb @@ -12,7 +12,7 @@ source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.5' +pythonver = '2.7.6' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb index 880a628b44..aa8a6d2d2b 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb @@ -12,7 +12,7 @@ source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.5' +pythonver = '2.7.6' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ -- GitLab From 30440f5e924e2096434e6d354294a939a7c62277 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:28:55 +0100 Subject: [PATCH 043/566] forgot to bump version of python in matplotlib: --- .../m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 9bd2215f1c..d97e421867 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 @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = "Python" -pythonversion = '2.7.5' +pythonversion = '2.7.6' pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -- GitLab From 2012748eee7cfbdc4b997aaf1fda4a25791ba4dc Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 15:57:55 +0100 Subject: [PATCH 044/566] changed one version to much, reverting --- easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb index 7324290431..cc63b4067d 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-5.5.0.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('zlib', '1.2.7')] +dependencies = [('zlib', '1.2.8')] configopts = "--with-pic" -- GitLab From 359dde374a123ef3198e186230ae0d03cc1d563e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 16:01:18 +0100 Subject: [PATCH 045/566] removed zlib 1.2.7 for ictce 5.5.0, we will use 1.2.8 for the 5.5.0 toolchain --- .../z/zlib/zlib-1.2.7-ictce-5.5.0.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb deleted file mode 100644 index c39a877574..0000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -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': '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')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], - 'dirs': [], -} - -moduleclass = 'lib' -- GitLab From 68e47b13c35aad0492e4f41f161bf44acc404e75 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 20 Nov 2013 16:14:27 +0100 Subject: [PATCH 046/566] removed unneeded ec --- ...plotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb deleted file mode 100644 index b35452ca6d..0000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-goolf-1.4.10-Python-2.7.5.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = "PythonPackage" - -name = 'matplotlib' -version = '1.2.1' - -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': 'goolf', 'version': '1.4.10'} - -source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] - -python = "Python" -pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) - -versionsuffix = "-%s-%s" % (python, pythonversion) - -dependencies = [ - (python, pythonversion), - ('zlib', '1.2.8'), - ('freetype', '2.4.11'), - ('libpng', '1.6.6'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], -} - -moduleclass = 'vis' -- GitLab From 89ebf5ce72b96f6a2146a6b47c9446f65e89c928 Mon Sep 17 00:00:00 2001 From: Adam DeConinck Date: Wed, 20 Nov 2013 17:35:37 -0800 Subject: [PATCH 047/566] Add Erlang easyconfigs with and without Java dep Also include the most recent Java, because I couldn't find the most recent Java with an easyconfig on Oracle's site. --- .../ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb | 23 ++++++++++++++++ .../e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 26 +++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb | 15 +++++++++++ 3 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb create mode 100644 easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb new file mode 100644 index 0000000000..819ddd9b6b --- /dev/null +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb @@ -0,0 +1,23 @@ +name = 'ErlangOTP' +version = 'R16B02' +versionsuffix = "-no-Java" + +homepage = 'http://www.erlang.org/' +description = """Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system.""" + +toolchain = {'name': 'GCC', 'version': '4.7.2'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +sources = ['otp_src_%(version)s.tar.gz'] +source_urls = ['http://www.erlang.org/download'] + +configopts = '--without-javac ' +patches = [] + +sanity_check_paths = { + 'files': ['bin/erl'], + 'dirs': ['lib/erlang/bin', 'lib/erlang/lib'] + +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb new file mode 100644 index 0000000000..0415fc7a1c --- /dev/null +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -0,0 +1,26 @@ +name = 'ErlangOTP' +version = 'R16B02' + +homepage = 'http://www.erlang.org/' +description = """Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system.""" + + +toolchain = {'name': 'GCC', 'version': '4.7.2'} +toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... + +sources = ['otp_src_%(version)s.tar.gz'] +source_urls = ['http://www.erlang.org/download'] + +builddependencies = [('Java','1.7.0_45','',True)] + +configopts = '--with-javac ' +patches = [] + +sanity_check_paths = { + 'files': ['bin/erl'], + 'dirs': ['lib/erlang/bin', 'lib/erlang/lib', + 'lib/erlang/lib/jinterface-1.5.8'] # Note java dependency + +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb new file mode 100644 index 0000000000..592d650cab --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_45' + +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 405ba6220c04df6f54bf3221af2f966eeb7209c7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Nov 2013 16:17:13 +0100 Subject: [PATCH 048/566] Valgrind: updated to 3.9 with goalf-1.5.12 --- .../Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..0bcf0e9356 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.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, Ghent University +# Authors:: Fotis Georgatos , Ward Poelmans +# 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_07-02.html +## + +name = 'Valgrind' +version = '3.9.0' + +homepage = 'http://valgrind.org/downloads/' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} + +source_urls = ['http://valgrind.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries], + 'dirs': [] +} + +moduleclass = 'debugger' -- GitLab From 944df1554dacd6e82d44bea51c7d97441c54021f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 25 Nov 2013 16:39:35 +0100 Subject: [PATCH 049/566] Valgrind-3.9.0: shorting header a bit --- .../v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb index 0bcf0e9356..8f5bbc5897 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb @@ -1,7 +1,7 @@ ## # 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, Ghent University +# Copyright:: Copyright 2012-2013 LCSB, Ghent University # Authors:: Fotis Georgatos , Ward Poelmans # License:: MIT/GPL # $Id$ -- GitLab From 312e9eb65a23763798b51cfcecebf67b7737f6cb Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 25 Nov 2013 21:31:44 +0100 Subject: [PATCH 050/566] turn modextrapaths into lists & also populate MANPATH Signed-off-by: Fotis Georgatos --- .../t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb index 4db2aee3fd..bb51694ffd 100644 --- a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -30,8 +30,9 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': 'nvidia-healthmon', - 'CPATH': 'nvml/include', + 'PATH': ['nvidia-healthmon'], + 'CPATH': ['nvml/include'], + 'MANPATH': ['nvml/doc/man'], } moduleclass = 'system' -- GitLab From 6259c71785ba428e9e149b14f93053a309544039 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 26 Nov 2013 14:09:33 +0100 Subject: [PATCH 051/566] init contrib_GMT Signed-off-by: Fotis Georgatos --- .../c/CMake/CMake-2.8.11-goolf-1.4.10.eb | 20 ++++++++++ .../g/GDAL/GDAL-1.9.2-goolf-1.4.10.eb | 22 +++++++++++ .../g/GMT/GMT-5.1.0-goolf-1.4.10.eb | 38 +++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.11-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.11-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.11-goolf-1.4.10.eb new file mode 100644 index 0000000000..3b3474d82a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.11-goolf-1.4.10.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = "2.8.11" + +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': 'goolf', 'version': '1.4.10'} + +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/GDAL/GDAL-1.9.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..62e541c4f9 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-goolf-1.4.10.eb @@ -0,0 +1,22 @@ +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': '1.4.10'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..30ef74821b --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +name = "GMT" +version = "5.1.0" + +easyblock = "CMakeMake" + +homepage = 'http://gmt.soest.hawaii.edu/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = ['gmt-%(version)s-src.tar.bz2'] +source_urls = ['http://gmt.soest.hawaii.edu/files/download?name='] + +builddependencies = [('CMake', '2.8.11')] + +dependencies = [ + ('PCRE', '8.12'), + ('GDAL', '1.9.2'), + ('GEOS', '3.3.5'), + ('Sphinx', '1.1.3', '-Python-2.7.3'), + ('netCDF', '4.2.1.1'), + #('Ghostscript', '9.10'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/gmt', 'bin/isogmt'], + 'dirs': [] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' -- GitLab From 87638b6ae39df24b62aed766f5ab85fe3d113d3c Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 27 Nov 2013 14:18:48 +0100 Subject: [PATCH 052/566] added O2scl 0.913 config file --- .../o/O2scl/o2scl-0.913-goolf-1.4.10.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb new file mode 100644 index 0000000000..a703fdda55 --- /dev/null +++ b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +name = 'o2scl' +version = '0.913' + +homepage = 'http://o2scl.sourceforge.net/' + +description = """ An object-oriented library for scientific +computing in C++ useful for solving, minimizing, differentiating, +integrating, interpolating, optimizing, approximating, analyzing, +fitting, and more.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Eigen', '3.1.4'), + ('libreadline', '6.2'), + ('HDF5', '1.8.11'), + ('Boost', '1.53.0'), + ('GSL', '1.15'), +] + + +moduleclass = 'lib' -- GitLab From e7fda0458f6c49e959e624ad0fde58f7d63c8539 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 27 Nov 2013 23:15:39 +0100 Subject: [PATCH 053/566] added missing dependencies HDF5-1.8.11-goolf-1.4.10.eb Eigen-4.1.4-goolf-1.4.10.eb --- .../e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb | 25 +++++++++++++++++++ .../h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb | 22 ++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..d2d1de373c --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +## +# 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 = 'Eigen' +version = '3.1.4' + +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': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%s.tar.bz2' % version] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb new file mode 100644 index 0000000000..13548661bc --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.11' +versionsuffix = '-serial' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +patches = ['configure_libtool.patch'] + +moduleclass = 'data' -- GitLab From 2c041a9a6ffc42c4cc54d9fde8f9f1d63e6d3d82 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 28 Nov 2013 11:30:37 +0100 Subject: [PATCH 054/566] removed version suffix in HDF5 ebconfig --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb index 13548661bc..4406c160f4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-goolf-1.4.10.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.11' -versionsuffix = '-serial' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of -- GitLab From 5234b1035175f3caab70f32aaefbb2290eb46589 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 28 Nov 2013 16:48:50 +0100 Subject: [PATCH 055/566] added more default packages to python + python 2.7.6 --- .../p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 39 +++++++-- .../Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 37 +++++++- .../p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 37 +++++++- .../p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 36 +++++++- .../p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 36 +++++++- .../p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 36 +++++++- .../p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 35 +++++++- .../Python-2.7.3-goalf-1.1.0-no-OFED.eb | 36 +++++++- .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 36 +++++++- .../p/Python/Python-2.7.3-ictce-4.0.6.eb | 37 +++++++- .../p/Python/Python-2.7.3-ictce-4.1.13.eb | 36 +++++++- .../p/Python/Python-2.7.3-ictce-5.2.0.eb | 36 +++++++- .../p/Python/Python-2.7.3-ictce-5.3.0.eb | 36 +++++++- .../p/Python/Python-2.7.3-iomkl-4.6.13.eb | 37 +++++++- .../p/Python/Python-2.7.3-iqacml-3.7.3.eb | 31 ++++++- .../Python-2.7.5-goalf-1.5.12-no-OFED.eb | 28 +++++- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 29 ++++++- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 28 +++++- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 28 +++++- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 28 +++++- .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 28 +++++- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 85 +++++++++++++++++++ .../Python-3.2.3-goalf-1.1.0-no-OFED.eb | 46 +++++++++- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 46 +++++++++- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 46 +++++++++- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 46 +++++++++- 26 files changed, 896 insertions(+), 83 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb 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 350cff539f..bc9555614f 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 @@ -19,23 +19,29 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -] - -# order is important! +]# order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +51,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 78733636f2..33a828a8a3 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 @@ -20,22 +20,30 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +53,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 965f7680f9..0c06d2fa65 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 @@ -23,19 +23,27 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -43,11 +51,32 @@ exts_list = [ 'source_urls': ['http://argparse.googlecode.com/files/'], }), ('lockfile', '0.9.1', { - 'source_urls': ['http://pylockfile.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 d6df6cdaaa..3b8f57925e 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 @@ -23,19 +23,28 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +54,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 f097672302..ced51446f7 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 @@ -20,22 +20,29 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +52,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 d6387e790c..c32d8b7ed6 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 @@ -20,22 +20,29 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +52,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 36c7fd70fe..20ae20457a 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 @@ -23,19 +23,27 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +53,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 cb3e4c646f..d81b8ae31d 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 @@ -20,22 +20,29 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +52,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 2904d6f980..c71cbd0a39 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 @@ -20,22 +20,29 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + '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': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -45,9 +52,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 44396979b5..93bfab822a 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 @@ -22,22 +22,30 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -47,9 +55,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 e69840bf6a..d661950b98 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 @@ -25,19 +25,28 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -47,9 +56,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 0fcb35553c..47c841baf6 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 @@ -25,19 +25,28 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -47,9 +56,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 0ef59f1a6c..9e11017ac9 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 @@ -25,19 +25,28 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -47,9 +56,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 6d4756c14e..8f38de5208 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 @@ -23,22 +23,30 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] - # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -48,9 +56,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 591a7c22f0..ca8be92f02 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 @@ -26,9 +26,12 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { '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/'], }), @@ -42,6 +45,9 @@ exts_list = [ ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + 'source_urls': ['https://mpi4py.googlecode.com/files/'], + }), ('paycheck', '1.0.2', { 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], }), @@ -51,9 +57,30 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.17.2', { + ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 61eaa9350c..b3c8bdbff1 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 @@ -25,10 +25,13 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -56,6 +59,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 890f3ac899..38147fabe1 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 @@ -23,12 +23,16 @@ dependencies = [ ('ncurses', '5.9'), ] + # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -56,6 +60,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 ba61bc3e08..99e757460c 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 @@ -25,10 +25,13 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -56,6 +59,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 9cd24fe3ae..a72f924582 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 @@ -25,10 +25,13 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -56,6 +59,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 4896534784..61b0dfecda 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 @@ -25,10 +25,13 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -56,6 +59,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 fbb0800072..f217c668fd 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 @@ -26,10 +26,13 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '0.6c11', { + ('setuptools', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('nose', '1.3.0', { + ('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, { @@ -57,6 +60,27 @@ exts_list = [ ('Cython', '0.19.1', { '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-arf/'], + }), + ('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/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 new file mode 100644 index 0000000000..3839bf7e8e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -0,0 +1,85 @@ +name = 'Python' +version = '2.7.6' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.7.0' +scipyversion = '0.12.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +patches = ['python-%(version)s_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'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.4.1', { + '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, + 'numpy-iqacml.patch', + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + '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-arf/'], + }), + ('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/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 087bed47a1..262a4466a4 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 @@ -23,9 +23,8 @@ dependencies = [ # order is important! exts_list = [ - ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], - 'modulename': 'setuptools', + ('setuptools', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], @@ -35,11 +34,50 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.6.1_distutils_multiple-lib-dirs.patch'], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + '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-arf/'], + }), + ('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/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 f52c47b304..fbf9131ead 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 @@ -23,9 +23,8 @@ dependencies = [ # order is important! exts_list = [ - ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], - 'modulename': 'setuptools', + ('setuptools', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], @@ -35,11 +34,50 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.6.1_distutils_multiple-lib-dirs.patch'], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + '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-arf/'], + }), + ('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/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 938b80ce48..17a9e0871c 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 @@ -23,9 +23,8 @@ dependencies = [ # order is important! exts_list = [ - ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], - 'modulename': 'setuptools', + ('setuptools', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], @@ -35,11 +34,50 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.6.1_distutils_multiple-lib-dirs.patch'], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + '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-arf/'], + }), + ('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/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 7971193188..8459b7a082 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 @@ -24,9 +24,8 @@ dependencies = [ # order is important! exts_list = [ - ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], - 'modulename': 'setuptools', + ('setuptools', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], @@ -36,11 +35,50 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': ['numpy-1.6.1_distutils_multiple-lib-dirs.patch'], + 'patches': [ + 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, + 'numpy-iqacml.patch', + ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), + ('mpi4py', '1.3', { + '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', '0.19.1', { + '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-arf/'], + }), + ('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' -- GitLab From df7c8590ede15ef12e864298c75093e744af9024 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 28 Nov 2013 16:54:14 +0100 Subject: [PATCH 056/566] libffi patch no longer needed, fixed it upstream --- easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 -- 1 file changed, 2 deletions(-) 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 3839bf7e8e..307c1882b5 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 @@ -13,8 +13,6 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), -- GitLab From 48fe4bb236ddf4bc0066b27b0eeb7b99f503ce00 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 28 Nov 2013 17:04:23 +0100 Subject: [PATCH 057/566] fixed typo --- 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 +- .../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-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 +- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 3 +-- 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-ictce-4.1.13.eb | 3 +-- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 3 +-- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 3 +-- 25 files changed, 25 insertions(+), 32 deletions(-) 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 bc9555614f..4a0b5c7d11 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 @@ -66,7 +66,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 33a828a8a3..a613874ed7 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 @@ -68,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 0c06d2fa65..8474696bf4 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 @@ -68,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 3b8f57925e..63570ad089 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 @@ -69,7 +69,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 ced51446f7..db195c0bbe 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 @@ -67,7 +67,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 c32d8b7ed6..8c99e72128 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 @@ -67,7 +67,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 20ae20457a..e1bf5116c1 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 @@ -68,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 d81b8ae31d..b70cb62012 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 @@ -67,7 +67,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 c71cbd0a39..9337284cb3 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 @@ -67,7 +67,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 93bfab822a..1f9a33d788 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 @@ -70,7 +70,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 d661950b98..c9f07cf92c 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 47c841baf6..1518cbeadc 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 9e11017ac9..fe22e97e4c 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 8f38de5208..00c9c8c84b 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 ca8be92f02..3842277046 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 @@ -72,7 +72,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 38147fabe1..ee3eba59bf 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 @@ -39,7 +39,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -72,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 99e757460c..88226659dc 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 @@ -38,7 +38,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -71,7 +70,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 a72f924582..50e419b7ce 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 61b0dfecda..5b599ff1d0 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 @@ -71,7 +71,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 f217c668fd..00445c611f 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 @@ -72,7 +72,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 307c1882b5..adc6635723 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 @@ -36,7 +36,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -69,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 262a4466a4..fb7852574b 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 @@ -36,7 +36,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -69,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 fbf9131ead..c42562dc72 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 @@ -36,7 +36,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -69,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 17a9e0871c..9422982772 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 @@ -36,7 +36,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -69,7 +68,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', 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 8459b7a082..66d906e00a 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 @@ -37,7 +37,6 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 'patches': [ 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', ], }), ('scipy', scipyversion, { @@ -70,7 +69,7 @@ exts_list = [ }), ('arff', '1.1', { 'source_tmpl': 'liac-%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arf/'], + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], }), ('pycrypto', '2.6.1', { 'modulename': 'Crypto', -- GitLab From 8caf10f18511da9b77f56d39b80efba1c98727de Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Nov 2013 16:57:54 +0100 Subject: [PATCH 058/566] Config files for nano course Several existing configs were copied and modified for the combination ictce-4.1.13 and Python-2.7.3. The OpenBabel package contains a Python extension, so they should get a Python-2.7.X suffix. A Config for molden was added. --- .../c/CMake/CMake-2.8.12-ictce-4.1.13.eb | 20 ++++++++++ .../e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb | 26 +++++++++++++ .../m/molden/molden-5.0-ictce-4.1.13.eb | 31 +++++++++++++++ .../m/molden/molden-5.0-ictce.patch | 15 ++++++++ .../m/molden/molden-5.0-molden-only.patch | 13 +++++++ .../numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb | 26 +++++++++++++ ....3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb} | 8 +++- ...enBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb | 38 +++++++++++++++++++ ...enBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb} | 8 +++- .../scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 19 ++++++++++ 10 files changed, 202 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch create mode 100644 easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb rename easybuild/easyconfigs/o/OpenBabel/{OpenBabel-2.3.2-goalf-1.5.12-no-OFED.eb => OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb} (81%) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb rename easybuild/easyconfigs/o/OpenBabel/{OpenBabel-2.3.2-ictce-5.5.0.eb => OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb} (82%) create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-4.1.13.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-4.1.13.eb new file mode 100644 index 0000000000..126afc1210 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-4.1.13.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'ictce', 'version': '4.1.13'} + +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/Eigen/Eigen-3.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb new file mode 100644 index 0000000000..da3a06f00f --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb @@ -0,0 +1,26 @@ +## +# 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 = 'Eigen' +version = '3.1.4' + +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': 'ictce', 'version': '4.1.13'} +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/m/molden/molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..2a42235dbc --- /dev/null +++ b/easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb @@ -0,0 +1,31 @@ +easyblock = "MakeCp" + +name = 'molden' +version = '5.0' + +homepage = 'http://www.cmbi.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +sources = [ + '%(name)s%(version)s.tar.gz', +] + +source_urls = [ + 'ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/%(name)s%(version)s.tar.gz' +] + +patches = [ + 'molden-%(version)s-ictce.patch', + 'molden-%(version)s-molden-only.patch', +] + +files_to_copy = [(['molden'],'bin'), 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths={ + 'files': ['bin/molden', 'README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch b/easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch new file mode 100644 index 0000000000..2897b802f0 --- /dev/null +++ b/easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch @@ -0,0 +1,15 @@ +# Because there is no configure script, one has to specify the compiler manually. +# By Toon Verstraelen +--- molden5.0-orig/makefile 2013-11-28 16:02:04.563545000 +0100 ++++ molden5.0/makefile 2013-11-28 16:08:13.606238000 +0100 +@@ -13,8 +13,8 @@ + # Disregard compiler warnings on rdmolf.f + # + # +-CC = cc +-FC = gfortran ++CC = icc ++FC = ifort + LIBS = -lX11 -lm + LDR = ${FC} + LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm diff --git a/easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch b/easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch new file mode 100644 index 0000000000..feffc8a8e0 --- /dev/null +++ b/easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch @@ -0,0 +1,13 @@ +# Only compile the molden binary to keep things simple +# By Toon Verstraelen (toon.verstraelen@ugent.be) +--- molden5.0-orig/makefile 2013-11-28 16:02:04.563545000 +0100 ++++ molden5.0/makefile 2013-11-28 16:08:13.606238000 +0100 +@@ -252,7 +252,7 @@ + # + #LIBSG = -L/usr/X11R6/lib -Wl,-framework -Wl,GLUT -Wl,-framework -Wl,OpenGL -Wl,-framework -Wl,Cocoa -lGLU -lGL -lXmu -lX11 -lm + +-all: molden gmolden ambfor/ambfor ambfor/ambmd surf/surf ++all: molden + + + molden: $(OBJS) mpdum.o xwin.o diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb new file mode 100644 index 0000000000..6bd0ab86b5 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.6.2' + +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': 'ictce', 'version': '4.1.13'} + +source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb similarity index 81% rename from easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb index 41317da7be..7b44103d5e 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb @@ -19,11 +19,17 @@ patches = [ builddependencies = [('CMake', '2.8.12')] +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + dependencies = [ + (python, pythonversion), ('zlib', '1.2.8'), ('libxml2', '2.9.1'), ('Eigen', '3.1.4'), - ('Python', '2.7.5'), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb new file mode 100644 index 0000000000..386a5e44fd --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb @@ -0,0 +1,38 @@ +name = 'OpenBabel' +version = '2.3.2' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many languages of chemical +data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data +from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'OpenBabel-%(version)s-use-xHost.patch', + 'OpenBabel-%(version)s-fix-link-path-tests.patch', + 'OpenBabel-%(version)s-ignore-failed-test.patch', +] + +builddependencies = [('CMake', '2.8.12')] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.7'), + ('libxml2', '2.9.1'), + ('Eigen', '3.1.4'), +] + +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb similarity index 82% rename from easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0.eb rename to easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb index 54fdc7e734..39852f3739 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb @@ -20,11 +20,17 @@ patches = [ builddependencies = [('CMake', '2.8.12')] +python = "Python" +pythonversion = '2.7.7' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + dependencies = [ + (python, pythonversion), ('zlib', '1.2.8'), ('libxml2', '2.9.1'), ('Eigen', '3.1.4'), - ('Python', '2.7.5'), ] runtest = 'test' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb new file mode 100644 index 0000000000..e391cf854c --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.11.0' +versionsuffix = '-Python-2.7.3' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.6.2', versionsuffix), + ] + +moduleclass = 'math' -- GitLab From 143aca9bce744a7c856ce5a186396684b091cd09 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 29 Nov 2013 11:48:04 +0100 Subject: [PATCH 059/566] added ABySS 1.3.6 with google-sparsehash dependency to reduce memory consumption --- .../ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb | 38 +++++++++++++++++++ .../Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb | 26 +++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb 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 new file mode 100644 index 0000000000..54ffe4617c --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.6-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 +# +# 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 = 'ABySS' +version = '1.3.6' +versionsuffix = '-Python-2.7.5' + +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 = ['http://www.bcgsc.ca/downloads/abyss/'] + + +dependencies = [ + ('google-sparsehash', '2.0.2'), + ('Boost', '1.49.0',versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] + } + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000..ff19195a78 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.49.0' + +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('.'))] + +pythonversion = '2.7.5' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' -- GitLab From eecb43ef21610afdbf30a99f81fce7d792bca263 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 29 Nov 2013 15:41:21 +0100 Subject: [PATCH 060/566] Molden with capital M --- .../Molden-5.0-ictce-4.1.13.eb} | 10 +++++----- .../Molden-5.0-ictce.patch} | 0 .../Molden-5.0-molden-only.patch} | 0 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/{molden/molden-5.0-ictce-4.1.13.eb => Molden/Molden-5.0-ictce-4.1.13.eb} (71%) rename easybuild/easyconfigs/m/{molden/molden-5.0-ictce.patch => Molden/Molden-5.0-ictce.patch} (100%) rename easybuild/easyconfigs/m/{molden/molden-5.0-molden-only.patch => Molden/Molden-5.0-molden-only.patch} (100%) diff --git a/easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb similarity index 71% rename from easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb index 2a42235dbc..92aa6cbc83 100644 --- a/easybuild/easyconfigs/m/molden/molden-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb @@ -1,6 +1,6 @@ easyblock = "MakeCp" -name = 'molden' +name = 'Molden' version = '5.0' homepage = 'http://www.cmbi.ru.nl/molden/' @@ -9,16 +9,16 @@ description = """Molden is a package for displaying Molecular Density from the A toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [ - '%(name)s%(version)s.tar.gz', + '%(namelower)s%(version)s.tar.gz', ] source_urls = [ - 'ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/%(name)s%(version)s.tar.gz' + 'ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/%(namelower)s%(version)s.tar.gz' ] patches = [ - 'molden-%(version)s-ictce.patch', - 'molden-%(version)s-molden-only.patch', + 'Molden-%(version)s-ictce.patch', + 'Molden-%(version)s-molden-only.patch', ] files_to_copy = [(['molden'],'bin'), 'CopyRight', 'README', 'REGISTER'] diff --git a/easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch similarity index 100% rename from easybuild/easyconfigs/m/molden/molden-5.0-ictce.patch rename to easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch diff --git a/easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch b/easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch similarity index 100% rename from easybuild/easyconfigs/m/molden/molden-5.0-molden-only.patch rename to easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch -- GitLab From be18a6e83db6bd3b1eda766b7380332814248958 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 29 Nov 2013 15:42:22 +0100 Subject: [PATCH 061/566] added samtools-0.1.19 and required patches this depends on modified samtools.py easyblock --- .../SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb | 33 +++++++++++++ .../SAMtools_0.1.19_Makefile-ncurses.patch | 46 +++++++++++++++++ .../s/SAMtools/SAMtools_0.1.19_misc.patch | 49 +++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb new file mode 100644 index 0000000000..06c8c4d00c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-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:: 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 = 'SAMtools' +version = '0.1.19' + +homepage = 'http://samtools.sourceforge.net/' +description = """SAM (Sequence Alignment/Map) format is a generic format +for storing large nucleotide sequence alignments.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%s/%s' % (name.lower(), version), 'download')] + +patches = ['SAMtools_0.1.19_Makefile-ncurses.patch','SAMtools_0.1.19_misc.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch new file mode 100644 index 0000000000..98fd2203b8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch @@ -0,0 +1,46 @@ +--- samtools-0.1.19.orig/Makefile 2013-03-19 08:48:09.000000000 +0100 ++++ samtools-0.1.19/Makefile 2013-11-29 13:17:00.210306930 +0100 +@@ -12,10 +12,10 @@ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + bam_tview_curses.o bam_tview_html.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses + + .SUFFIXES:.c .o + .PHONY: all lib +@@ -44,13 +44,13 @@ + $(AR) -csru $@ $(LOBJS) + + samtools:lib-recur $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -L$(EBROOTZLIB)/lib -lz -lpthread + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz ++ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz -lpthread + + bgzf.o:bgzf.c bgzf.h + $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ +@@ -81,10 +81,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch new file mode 100644 index 0000000000..b3f2a74519 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch @@ -0,0 +1,49 @@ +--- samtools-0.1.19.orig/misc/Makefile 2013-03-19 08:48:09.000000000 +0100 ++++ samtools-0.1.19/misc/Makefile 2013-11-29 13:34:10.250913354 +0100 +@@ -5,7 +5,8 @@ + DFLAGS= -D_FILE_OFFSET_BITS=64 + OBJS= + PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck +-INCLUDES= -I.. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I.. ++LIBPATH= -L$(EBROOTZLIB)/lib + SUBDIRS= . + + .SUFFIXES:.c .o +@@ -28,19 +29,19 @@ + lib: + + bamcheck:bamcheck.o +- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz ++ $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -L$(EBROOTZLIB)/lib -lz + + bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h + $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c + + ace2sam:ace2sam.o +- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz ++ $(CC) $(CFLAGS) -o $@ ace2sam.o -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -49,10 +50,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c -- GitLab From 50ceb603c0c3464cc1532d2de96da415b63ed202 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 30 Nov 2013 06:11:57 +0100 Subject: [PATCH 062/566] Fixed several formatting issues --- .../easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb | 13 +++++-------- ...Babel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb | 7 ++++--- .../OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb | 7 ++++--- .../OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb | 7 ++++--- ...scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 4 +--- .../scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 4 +--- .../scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb | 4 +--- .../scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 4 +--- .../scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb | 4 +--- .../scipy/scipy-0.12.0-goolf-1.4.10-Python-2.7.3.eb | 4 +--- 10 files changed, 23 insertions(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb index 92aa6cbc83..76a1b7f50f 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb @@ -4,17 +4,14 @@ name = 'Molden' version = '5.0' homepage = 'http://www.cmbi.ru.nl/molden/' -description = """Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac""" +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -sources = [ - '%(namelower)s%(version)s.tar.gz', -] - -source_urls = [ - 'ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/%(namelower)s%(version)s.tar.gz' -] +sources = ['%(namelower)s%(version)s.tar.gz'] +source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] patches = [ 'Molden-%(version)s-ictce.patch', diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb index 7b44103d5e..b0dbc264bd 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-goalf-1.5.12-no-OFED-Python-2.7.5.eb @@ -2,9 +2,10 @@ name = 'OpenBabel' version = '2.3.2' homepage = 'http://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many languages of chemical -data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data -from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.""" +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb index 386a5e44fd..534fdf2177 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-4.1.13-Python-2.7.3.eb @@ -2,9 +2,10 @@ name = 'OpenBabel' version = '2.3.2' homepage = 'http://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many languages of chemical -data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data -from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.""" +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb index 39852f3739..b50e725a50 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb @@ -2,9 +2,10 @@ name = 'OpenBabel' version = '2.3.2' homepage = 'http://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many languages of chemical -data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data -from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.""" +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f466b5ee8a..6be5a1f63a 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), - ] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 952fc435a5..1e2a06545e 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), - ] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb index 564b138ba6..ace3c72316 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), - ] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb index e391cf854c..b80ca9d761 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), - ] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb index 7875f20000..aaa6f260b9 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), - ] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.12.0-goolf-1.4.10-Python-2.7.3.eb index d0822a60e9..0451302efb 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.12.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -12,8 +12,6 @@ toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] -dependencies = [ - ('numpy', '1.6.2', versionsuffix), -] +dependencies = [('numpy', '1.6.2', versionsuffix)] moduleclass = 'math' -- GitLab From 217c15c118a1ac4a7ae64d3ab34c894c58584ca7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Nov 2013 13:56:47 +0100 Subject: [PATCH 063/566] fix remarks --- .../easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb | 2 +- .../easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb index 53d4aebdfe..10676832a7 100644 --- a/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb @@ -5,7 +5,7 @@ version = '1.6.4' homepage = 'http://www.parallelpython.com/' description = """PP is a python module which provides mechanism for parallel execution of python code on SMP -(systems with multiple processors or cores) and clusters (computers connected via network).""" + (systems with multiple processors or cores) and clusters (computers connected via network).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb index 7cae0123b6..da9a5dfc46 100644 --- a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb @@ -5,7 +5,7 @@ version = '1.6.4' homepage = 'http://www.parallelpython.com/' description = """PP is a python module which provides mechanism for parallel execution of python code on SMP -(systems with multiple processors or cores) and clusters (computers connected via network).""" + (systems with multiple processors or cores) and clusters (computers connected via network).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -- GitLab From 4797378337306b614fc6a9e6b7ff7f1f9116f6b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Nov 2013 14:02:55 +0100 Subject: [PATCH 064/566] fix sanity check for PP --- .../easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb | 4 ++-- .../easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb index 10676832a7..da24746b62 100644 --- a/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-goolf-1.4.10-Python-2.7.5.eb @@ -23,8 +23,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion] + 'files': ['lib/python%s/site-packages/%%(namelower)s.py' % pythonshortversion], + 'dirs': [], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb index da9a5dfc46..cbf60d507e 100644 --- a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-4.1.13-Python-2.7.5.eb @@ -23,8 +23,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion] + 'files': ['lib/python%s/site-packages/%%(namelower)s.py' % pythonshortversion], + 'dirs': [], } moduleclass = 'lang' -- GitLab From 1aa8a69249774e5b5e3011caa5cf492cc009d953 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Nov 2013 20:12:02 +0100 Subject: [PATCH 065/566] add CP2K easyconfig with ictce/5.5.0 + deps --- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb | 7 +++---- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb | 7 +++---- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb | 7 +++---- .../easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb | 7 +++---- 4 files changed, 12 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb index 62a0302056..4f975041bc 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb @@ -12,9 +12,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -dependencies = [ - ('HDF5', '1.8.10-patch1'), - ('Doxygen', '1.8.3.1') -] +dependencies = [('HDF5', '1.8.10-patch1')] + +builddependencies = [('Doxygen', '1.8.3.1')] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index 7f0aa16d44..a43794119f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -12,9 +12,8 @@ toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -dependencies = [ - ('HDF5', '1.8.10', '-gpfs'), - ('Doxygen', '1.8.2') -] +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb index b3da59719e..b2e2392049 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb @@ -12,9 +12,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -dependencies = [ - ('HDF5', '1.8.10', '-gpfs'), - ('Doxygen', '1.8.2') - ] +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb index e2a1c7f2e6..dd168910be 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb @@ -12,9 +12,8 @@ toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] -dependencies = [ - ('HDF5', '1.8.10-patch1'), - ('Doxygen', '1.8.3.1') -] +dependencies = [('HDF5', '1.8.10-patch1')] + +builddependencies = [('Doxygen', '1.8.3.1')] moduleclass = 'data' -- GitLab From f957d9c5f5c5d1966a35d6510de0375e116c9810 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Nov 2013 20:27:11 +0100 Subject: [PATCH 066/566] style fixes in QuantumESPRESSO ictce easyconfigs, added ictce/5.5.0 easyconfigs --- ...ESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb | 32 +++++------ ...QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED.eb | 32 +++++------ ...QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb | 32 +++++------ .../QuantumESPRESSO-4.2-goolf-1.4.10.eb | 32 +++++------ .../QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb | 28 +++++----- .../QuantumESPRESSO-4.2-ictce-4.0.6.eb | 28 +++++----- .../QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb | 29 +++++----- .../QuantumESPRESSO-4.2-ictce-5.3.0.eb | 27 +++++----- .../QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb | 41 ++++++++++++++ .../QuantumESPRESSO-4.2-ictce-5.5.0.eb | 37 +++++++++++++ ...PRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 38 ++++++------- ...antumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb | 38 ++++++------- ...antumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 38 ++++++------- .../QuantumESPRESSO-5.0.2-goolf-1.4.10.eb | 38 ++++++------- ...uantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 44 +++++++-------- .../QuantumESPRESSO-5.0.2-ictce-4.0.6.eb | 44 +++++++-------- ...uantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 45 ++++++++-------- .../QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 45 ++++++++-------- ...uantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 53 +++++++++++++++++++ .../QuantumESPRESSO-5.0.2-ictce-5.5.0.eb | 49 +++++++++++++++++ 20 files changed, 463 insertions(+), 287 deletions(-) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb index afa5eaf4f0..c9c39b7a97 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -12,25 +12,25 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-errors.patch', - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'want-2.3.0_fix-memstat-issue.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure-LDFLAGS.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-errors.patch', + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'want-2.3.0_fix-memstat-issue.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure-LDFLAGS.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED.eb index e5ec5f6d62..632b84416c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED.eb @@ -11,25 +11,25 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-errors.patch', - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'want-2.3.0_fix-memstat-issue.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure-LDFLAGS.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-errors.patch', + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'want-2.3.0_fix-memstat-issue.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure-LDFLAGS.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb index 4da00620d4..da2796c1f4 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb @@ -12,25 +12,25 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-errors.patch', - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'want-2.3.0_fix-memstat-issue.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure-LDFLAGS.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-errors.patch', + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'want-2.3.0_fix-memstat-issue.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure-LDFLAGS.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10.eb index 48256367ad..fd96509a3d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10.eb @@ -11,25 +11,25 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-errors.patch', - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'want-2.3.0_fix-memstat-issue.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure-LDFLAGS.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-errors.patch', + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'want-2.3.0_fix-memstat-issue.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure-LDFLAGS.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb index d4e4a77148..1e05a6e28d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb @@ -12,23 +12,23 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure_ictce.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6.eb index b91d022bda..d15d97009b 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6.eb @@ -11,23 +11,23 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure_ictce.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb index 9252372604..8e7a8dd992 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb @@ -8,28 +8,27 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure_ictce.patch', - ] + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb index 2c9da47c8d..4ec5d3ed70 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb @@ -7,28 +7,27 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'want-2.3.0.tar.gz', - 'yambo-3.2.1-r.448.tar.gz', + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', ] source_urls = [ - 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz - ] + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] patches = [ - 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', - 'yambo-3.2.1_fix-objects-files.patch', - 'yambo_fix-configure_ictce.patch', - ] + 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] makeopts = 'all gipaw vdw w90 want gww xspectra yambo' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb new file mode 100644 index 0000000000..ce2a27d6d2 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb @@ -0,0 +1,41 @@ +name = 'QuantumESPRESSO' +version = '4.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', +] +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] + +patches = [ + 'QuantumESPRESSO-%(version)s_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] + +makeopts = 'all gipaw vdw w90 want gww xspectra yambo' + +# parallel build tends to fail +parallel = 1 + +# hybrid build (enable OpenMP) +hybrid = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..8e4fd12593 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0.eb @@ -0,0 +1,37 @@ +name = 'QuantumESPRESSO' +version = '4.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'want-2.3.0.tar.gz', + 'yambo-3.2.1-r.448.tar.gz', + ] +source_urls = [ + 'http://www.qe-forge.org/gf/download/frsrelease/64/96/', # espresso-4.2.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=', # want-2.3.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/64/98/', # yambo-3.2.1-r.448.tar.gz +] + +patches = [ + 'QuantumESPRESSO-4.2_fix-makefile-for-plugins.patch', + 'yambo-3.2.1_fix-objects-files.patch', + 'yambo_fix-configure_ictce.patch', +] + +makeopts = 'all gipaw vdw w90 want gww xspectra yambo' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' 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 2de08f4797..25260f443e 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 @@ -13,27 +13,27 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable (and no longer available) - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] 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 4709569909..b8ec946c61 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 @@ -12,27 +12,27 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable (and no longer available) - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] 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 6807d9cc10..0c8b2cd88a 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 @@ -13,27 +13,27 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable (and no longer available) - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] 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 67dfd49bc1..a27849d9f9 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 @@ -12,27 +12,27 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable (and no longer available) - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] 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 47adff3a59..ae7fa28b20 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 @@ -13,32 +13,32 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] patches = [ - 'yambo-3.2.5_fix-objects-files.patch', - 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', - ] + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] # parallel build tends to fail parallel = 1 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 f982d909d3..7e9edfdb1a 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 @@ -12,32 +12,32 @@ toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] patches = [ - 'yambo-3.2.5_fix-objects-files.patch', - 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', - ] + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] # gipaw excluded, because v5.0 isn't stable # xspectra v5.0.2 is nowhere to be found 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 2acbc21f76..a72624e45a 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 @@ -8,38 +8,37 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] patches = [ - 'yambo-3.2.5_fix-objects-files.patch', - 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', - ] + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] # parallel build tends to fail parallel = 1 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 854d3543cf..e410223931 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 @@ -7,38 +7,37 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ - 'espresso-%s.tar.gz' % version, - 'wannier90-1.2.tar.gz', - 'atomic-5.0.2.tar.gz', - 'neb-5.0.2.tar.gz', - 'PHonon-5.0.2.tar.gz', - 'plumed-1.3-qe.tar.gz', - 'pwcond-5.0.2.tar.gz', - 'tddfpt-5.0.2.tar.gz', - 'want-2.4.0-base.tar.gz', - 'yambo-3.2.5-rev.26.tar.gz', - ] + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] missing_sources = [ - 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable - 'sax-2.0.3.tar.gz', # nowhere to be found - 'xspectra-5.0.2.tar.gz', # nowhere to be found - ] + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 + 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz + 'http://files.qe-forge.org/index.php?file=', # others +] patches = [ - 'yambo-3.2.5_fix-objects-files.patch', - 'QuantumESPRESSO-5.0.2_yambo-fftw.patch', - ] + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] # gipaw excluded, because v5.0 isn't stable # xspectra v5.0.2 is nowhere to be found 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 new file mode 100644 index 0000000000..bdd20f0388 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -0,0 +1,53 @@ +name = 'QuantumESPRESSO' +version = '5.0.2' +versionsuffix = '-hybrid' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso-5.0.2/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] +missing_sources = [ + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 +] + +patches = [ + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] + +# parallel build tends to fail +parallel = 1 + +# gipaw excluded, because v5.0 isn't stable +# xspectra v5.0.2 is nowhere to be found +makeopts = 'all w90 want yambo plumed' + +# hybrid build (enable OpenMP) +hybrid = True + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000..85601025bc --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -0,0 +1,49 @@ +name = 'QuantumESPRESSO' +version = '5.0.2' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft).""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso-5.0.2/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-5.0.2.tar.gz', + 'neb-5.0.2.tar.gz', + 'PHonon-5.0.2.tar.gz', + 'plumed-1.3-qe.tar.gz', + 'pwcond-5.0.2.tar.gz', + 'tddfpt-5.0.2.tar.gz', + 'want-2.4.0-base.tar.gz', + 'yambo-3.2.5-rev.26.tar.gz', +] +missing_sources = [ + 'qe-gipaw-5.0.tar.gz', # gipaw excluded, because v5.0 isn't stable + 'sax-2.0.3.tar.gz', # nowhere to be found + '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 +] + +patches = [ + 'yambo-3.2.5_fix-objects-files.patch', + 'QuantumESPRESSO-%(version)s_yambo-fftw.patch', +] + +# gipaw excluded, because v5.0 isn't stable +# xspectra v5.0.2 is nowhere to be found +makeopts = 'all w90 want yambo plumed' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' -- GitLab From acb14a42a753bfd322ac65737188d345b8786de7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 Dec 2013 09:43:37 +0100 Subject: [PATCH 067/566] enable openmp toolchain option for hybrid QuantumESPRESSO builds --- .../QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb | 2 +- .../QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb | 2 +- .../QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 2 +- .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb index c9c39b7a97..c7c70b133c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [ 'espresso-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb index da2796c1f4..106b9ec5dc 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-goolf-1.4.10-hybrid.eb @@ -9,7 +9,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [ 'espresso-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb index 1e05a6e28d..ff1ccd416c 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-4.0.6-hybrid.eb @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [ 'espresso-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb index 8e7a8dd992..cd5c794061 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [ 'espresso-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb index ce2a27d6d2..1dd41c052b 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.5.0-hybrid.eb @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [ 'espresso-%(version)s.tar.gz', 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 25260f443e..4d7911d2df 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 @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ 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 0c8b2cd88a..df07d19513 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 @@ -9,7 +9,7 @@ It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ 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 ae7fa28b20..5376b7ca12 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 @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ 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 a72624e45a..63c5ce63fa 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 @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ 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 bdd20f0388..04ad81b30e 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 @@ -9,7 +9,7 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes (both norm-conserving and ultrasoft).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} # major part of this list was determined from espresso-5.0.2/install/plugins_list sources = [ -- GitLab From 937083aacdf17b525945b56a1d2a7a14b0cc1e12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 Dec 2013 14:21:52 +0100 Subject: [PATCH 068/566] add missing Doxygen easyconfig --- .../d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..f5c2ee7700 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '5.3.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' -- GitLab From f642702aa779d9a7a9ea626b6df80a61495fb227 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 2 Dec 2013 00:15:34 +0100 Subject: [PATCH 069/566] added BWA-0.7.5a-goolf-1.4.10.eb --- .../b/BWA/BWA-0.7.5a-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb new file mode 100644 index 0000000000..f2eec4ae3c --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.5a-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +## +# 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 +# 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 = 'BWA' +version = '0.7.5a' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] + +moduleclass = 'bio' -- GitLab From 28963ed8aa8ec0e239a160226a6aa1ce75da7e90 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 2 Dec 2013 00:22:26 +0100 Subject: [PATCH 070/566] removed R-3.0.2-goolf-1.4.10-bare.eb from this PR --- .../r/R/R-3.0.2-goolf-1.4.10-bare.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb deleted file mode 100644 index d0aa0dd324..0000000000 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10-bare.eb +++ /dev/null @@ -1,37 +0,0 @@ -name = 'R' -version = '3.0.2' -versionsuffix = '-bare' # bare, as in no extensions included - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -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', '6.2'), - ('ncurses', '5.9'), - ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it -] - -exts_list = [] # just to make it explicit this module doesn't include any extensions - -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': [] -} - -moduleclass = 'lang' -- GitLab From febf46f8ca1625de7ae5034c13eff05b782317f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 10:14:07 +0100 Subject: [PATCH 071/566] use -mt version of netCDF libraries for ESMF and NCL, add patch file for ESMF --- .../c/cURL/cURL-7.27.0-ictce-4.1.13.eb | 22 ++++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb | 18 +++++++++++ .../e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb | 12 ++++---- .../e/ESMF/ESMF-6.1.1_libopts.patch | 11 +++++++ .../HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb | 30 +++++++++++++++++++ .../libjpeg-turbo-1.3.0-ictce-4.1.13.eb | 21 +++++++++++++ .../n/NASM/NASM-2.07-ictce-4.1.13.eb | 29 ++++++++++++++++++ .../n/NCL/NCL-6.1.2-ictce-4.1.13.eb | 6 ++-- .../netCDF-C++-4.2-ictce-4.1.13-mt.eb | 26 ++++++++++++++++ .../netCDF-Fortran-4.2-ictce-4.1.13-mt.eb | 18 +++++++++++ .../netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb | 20 +++++++++++++ 11 files changed, 205 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.27.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-6.1.1_libopts.patch create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.27.0-ictce-4.1.13.eb b/easybuild/easyconfigs/c/cURL/cURL-7.27.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..595b5ff8ef --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.27.0-ictce-4.1.13.eb @@ -0,0 +1,22 @@ +name = 'cURL' +version = '7.27.0' + +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': 'ictce', 'version': '4.1.13'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +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-1.8.3.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..1af9922e91 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '4.1.13'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb index f76aa98e59..5d118d3698 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-ictce-4.1.13.eb @@ -9,16 +9,18 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} source_urls = [SOURCEFORGE_SOURCE] -sources = ['%s_%s_src.tar.gz' % (name.lower(), '_'.join(version.split('.')))] +sources = ['%%(namelower)s_%s_src.tar.gz' % '_'.join(version.split('.'))] + +patches = ['ESMF-6.1.1_libopts.patch'] dependencies = [ - ('netCDF', '4.2.1.1'), - ('netCDF-Fortran', '4.2'), - ('netCDF-C++', '4.2'), + ('netCDF', '4.2.1.1', '-mt'), + ('netCDF-Fortran', '4.2', '-mt'), + ('netCDF-C++', '4.2', '-mt'), ] # LDFLAGS has to be unset to avoid linking issues -preinstallopts = "unset LDFLAGS && " +preinstallopts = "unset LDFLAGS &&" # too parallel causes the build to become really slow maxparallel = 8 diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1_libopts.patch b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1_libopts.patch new file mode 100644 index 0000000000..0d03f78059 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1_libopts.patch @@ -0,0 +1,11 @@ +--- esmf/build/common.mk.orig 2013-11-26 16:58:50.958274359 +0100 ++++ esmf/build/common.mk 2013-11-26 16:59:02.339274158 +0100 +@@ -896,7 +896,7 @@ + endif + ESMF_SL_LIBS_TO_MAKE = libesmf + ESMF_SL_LIBLINKER = $(ESMF_CXXCOMPILER) +-ESMF_SL_LIBOPTS += ++ESMF_SL_LIBOPTS += $(ESMF_CXXCOMPILEOPTS) + ESMF_SL_LIBLIBS += + + # - Shared objects diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb new file mode 100644 index 0000000000..b1532bad95 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb @@ -0,0 +1,30 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs-mt" + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True, 'openmp': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip','2.1'), +] + +configopts = "--enable-gpfs --enable-threadsafe --enable-production " + +preconfigopts = 'export FFLAGS="-fopenmp $FFLAGS" && export F90FLAGS="-fopenmp $F90FLAGS" && ' +premakeopts = 'export FFLAGS="-fopenmp $FFLAGS" && export F90FLAGS="-fopenmp $F90FLAGS" && ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..a8b098068f --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb @@ -0,0 +1,21 @@ +name = 'libjpeg-turbo' +version = '1.3.0' + +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': 'ictce', 'version': '4.1.13'} # tweaked by EasyBuild (was: {'name': 'ictce', 'version': '4.0.10'}) +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.07'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb new file mode 100644 index 0000000000..f6a342b73a --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb @@ -0,0 +1,29 @@ +## +# 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_2012-90.html +## + +name = 'NASM' +version = '2.07' + +homepage = 'http://nasm.sourceforge.net/' +description = """NASM-2.07: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://sourceforge.net/projects/nasm/files', 'download'] + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb index 6006d25573..f2f25fd0a4 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb @@ -6,7 +6,7 @@ description = """NCL is an interpreted language designed specifically for scient visualization.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -toolchainopts = {'opt': True, 'pic': True, 'usempi': True} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'openmp': True} sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] @@ -16,8 +16,8 @@ patches = [ dependencies = [ ('cURL', '7.28.1'), - ('netCDF', '4.2.1.1'), - ('netCDF-Fortran', '4.2'), + ('netCDF', '4.2.1.1', '-mt'), + ('netCDF-Fortran', '4.2', '-mt'), ('JasPer', '1.900.1'), ('g2lib', '1.4.0'), ('g2clib', '1.4.0'), diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb new file mode 100644 index 0000000000..df031c2880 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb @@ -0,0 +1,26 @@ +name = 'netCDF-C++' +version = '4.2' +versionsuffix = '-mt' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = ['netcdf-cxx-%(version)s.tar.gz'] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [ + ('netCDF', '4.2.1.1', versionsuffix), + ('cURL', '7.28.1'), +] + +sanity_check_paths = { + 'files': ['include/ncvalues.h', 'include/netcdfcpp.h', 'include/netcdf.hh', 'lib/libnetcdf_c++.a', 'lib/libnetcdf_c++.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb new file mode 100644 index 0000000000..6b36f2c00b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.2' +versionsuffix = '-mt' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1', versionsuffix)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb new file mode 100644 index 0000000000..1d208f1301 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -0,0 +1,20 @@ +name = 'netCDF' +version = '4.2.1.1' +versionsuffix = '-mt' + +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':'ictce','version':'4.1.13'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs-mt')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' -- GitLab From 0a93f7cd4cc6ff4ed4d05f725ab47adc7d377ceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 10:14:24 +0100 Subject: [PATCH 072/566] correct dep versions --- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index a3407d071e..a83caaaf0c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -8,8 +8,8 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), + ('flex', '2.5.37'), + ('Bison', '2.7'), ('Szip', '2.1'), ('JasPer', '1.900.1'), ] -- GitLab From c38e0ebc22110d36d71f7527212cd03f1fb005ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 10:16:02 +0100 Subject: [PATCH 073/566] add missing easyconfigs --- .../b/Bison/Bison-2.5-ictce-5.5.0.eb | 20 +++++++++++ .../c/CP2K/CP2K-20111205-ictce-5.5.0.eb | 33 +++++++++++++++++++ .../f/flex/flex-2.5.35-ictce-5.5.0.eb | 14 ++++++++ .../easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb | 23 +++++++++++++ 4 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..f025220a43 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '2.5' + +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +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/c/CP2K/CP2K-20111205-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.5.0.eb new file mode 100644 index 0000000000..57f859f95c --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.5.0.eb @@ -0,0 +1,33 @@ +name = 'CP2K' +version = '20111205' + +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCE_TAR_GZ] + +patches = [ + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5'), +] + +dependencies = [('Libint', '1.1.4')] + +# 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 (120/2196 tests fail with segfault) +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.5.0.eb new file mode 100644 index 0000000000..4cd202259c --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.35-ictce-5.5.0.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.35' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb new file mode 100644 index 0000000000..07b38b0359 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/m4'] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 7688a8778f587d7f11befeb68687629f2752a0dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 10:45:39 +0100 Subject: [PATCH 074/566] add missing Doxygen easyconfig file --- .../d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb new file mode 100644 index 0000000000..1af9922e91 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '4.1.13'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' -- GitLab From 4218a17cf13f9ef6d689c5457f24cf691ab6c135 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 10:54:47 +0100 Subject: [PATCH 075/566] add missing Bison easyconfig file --- .../b/Bison/Bison-2.7-ictce-5.3.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb new file mode 100644 index 0000000000..996f2950d9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +builddependencies = [('M4', '1.4.16')] + +sanity_check_paths = { + 'files':["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs':[], +} + +moduleclass = 'lang' -- GitLab From 61c748052fed4287bcfeb4ab482cb7a6e2c58680 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:22:26 +0100 Subject: [PATCH 076/566] added new packages to R --- .../easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 143 ++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb 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 new file mode 100644 index 0000000000..bc9a5be12c --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -0,0 +1,143 @@ +name = 'R' +version = '3.0.2' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +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', '6.2'), + ('ncurses', '5.9'), + ('libpng', '1.6.6'), # for plotting in R + ('Java', '1.7.0_21', '', 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': [] +} + +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.freestatistics.org/src/contrib', # alternative for packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_tmpl': name_tmpl, +} +# !! order of packages is important !! +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! + ('irace', '1.04', ext_options), + ('rJava', '0.9-4', ext_options), + ('lattice', '0.20-24', ext_options), + ('RColorBrewer', '1.0-5', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.1-0', ext_options), + ('png', '0.1-6', ext_options), + ('Rcpp', '0.10.6', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2013.4-1', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-29', ext_options), + ('class', '7.3-9', ext_options), + ('e1071', '1.6-1', ext_options), + ('nnet', '7.3-7', ext_options), + ('car', '2.0-19', ext_options), + ('colorspace', '1.2-4', ext_options), + ('robustbase', '0.9-10', ext_options), + ('sp', '1.0-14', ext_options), + ('vcd', '1.3-1', ext_options), + ('snowfall', '1.84-4', ext_options), + ('rpart', '4.1-3', ext_options), + ('mice', '2.18', ext_options), + ('nlme', '3.1-111', ext_options), + ('mgcv', '1.7-27', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-9', ext_options), + ('cluster', '1.14.4', ext_options), + ('coda', '0.16-1', ext_options), + ('codetools', '0.2-8', ext_options), + ('DBI', '0.2-7', ext_options), + ('foreign', '0.8-57', ext_options), + ('survival', '2.37-4', ext_options), + ('gam', '1.09', ext_options), + ('gamlss.data', '4.2-6', ext_options), + ('gamlss.dist', '4.2-0', ext_options), + ('hwriter', '1.3', ext_options), + ('KernSmooth', '2.23-10', ext_options), + ('zoo', '1.7-10', ext_options), + ('lmtest', '0.9-32', ext_options), + ('mnormt', '1.4-5', ext_options), + ('mvtnorm', '0.9-9996', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('pscl', '1.04.4', ext_options), + ('RSQLite', '0.11.4', ext_options), + ('sandwich', '2.3-0', ext_options), + ('sfsmisc', '1.0-24', ext_options), + ('spatial', '7.3-7', ext_options), + ('VGAM', '0.9-3', ext_options), + ('waveslim', '1.7.1', ext_options), + ('xtable', '1.7-1', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.10-8', ext_options), + ('odesolve', '0.9-9', 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', '1.5.2', ext_options), + ('R.oo', '1.15.8', ext_options), + ('R.matlab', '2.0.5', ext_options), + ('Rniftilib', '0.0-32', ext_options), + ('BiocGenerics', '0.8.0', bioconductor_options), + ('Biobase', '2.22.0', bioconductor_options), + ('IRanges', '1.20.5', bioconductor_options), + ('AnnotationDbi', '1.24.0', bioconductor_options), + ('XVector', '0.2.0', bioconductor_options), + ('Biostrings', '2.30.0', bioconductor_options), + ('GenomicRanges', '1.14.3', bioconductor_options), + ('BSgenome', '1.30.0', bioconductor_options), + ('zlibbioc', '1.8.0', bioconductor_options), + ('Rsamtools', '1.14.1', bioconductor_options), + ('ShortRead', '1.20.0', bioconductor_options), + ('graph', '1.40.0', bioconductor_options), + ('igraph0', '0.5.7', ext_options), +] + +moduleclass = 'lang' -- GitLab From 609d165edebb843df70ded77de548d4e9505d4fa Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:23:24 +0100 Subject: [PATCH 077/566] added bedtools --- .../BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb | 20 +++++++++++++++++++ .../BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb | 15 ++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..41345eb68e --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb @@ -0,0 +1,20 @@ +easyblock = 'MakeCp' +name = 'BEDTools' +version = 'v2.17.0' + +homepage = 'http://code.google.com/p/bedtools/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://bedtools.googlecode.com/files/"] +sources = ['%(name)s.%(version)s.tar.gz'] + +dirs = ["bin", "data", "docs", "genomes", 'scripts'] +# copy all directories to the installation directory +files_to_copy = dirs + +sanity_check_paths = {'files': [], 'dirs': dirs} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb new file mode 100644 index 0000000000..57c9ecc225 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb @@ -0,0 +1,15 @@ +name = 'BEDTools' +version = 'v2.17.0' + +homepage = 'http://code.google.com/p/bedtools/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ["http://bedtools.googlecode.com/files/"] +sources = ['%(name)s.%(version)s.tar.gz'] + +skipsteps = ['configure'] + +moduleclass = 'bio' -- GitLab From d222b60e44a360880ced9a75ea0b3603e5e90e6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 18:25:27 +0100 Subject: [PATCH 078/566] bump extension versions to latest in Python 2.7.6 easyconfig --- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) 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 adc6635723..9d19f216fe 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 @@ -7,8 +7,8 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.7.0' -scipyversion = '0.12.0' +numpyversion = '1.8.0' +scipyversion = '0.13.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] @@ -23,25 +23,25 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '1.4.2', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), - ('pip', '1.1', { + ('pip', '1.4.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), - ('nose', '1.1.2', { + ('nose', '1.3.0', { '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, + 'numpy-%s-mkl.patch' % numpyversion, ], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), - ('mpi4py', '1.3', { + ('mpi4py', '1.3.1', { 'source_urls': ['https://mpi4py.googlecode.com/files/'], }), ('paycheck', '1.0.2', { @@ -53,10 +53,10 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.19.2', { 'source_urls': ['http://www.cython.org/release/'], }), - ('dateutil', '2.1', { + ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], }), -- GitLab From 4a578d690711c117c5c9f1ef7ad3365d6d47efbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 18:26:49 +0100 Subject: [PATCH 079/566] restory faulty version bumps for setuptools and Cython, remove numpy-iqacml.patch where it's not required --- .../easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 4 ++-- .../p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 4 ++-- .../p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 4 ++-- .../p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 4 ++-- .../p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 9 +++------ .../easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb | 4 ++-- 21 files changed, 52 insertions(+), 82 deletions(-) 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 4a0b5c7d11..40021bd464 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 @@ -21,7 +21,7 @@ dependencies = [ ('ncurses', '5.9-20130406'), ]# order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -51,7 +51,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 a613874ed7..84f064c627 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -33,10 +33,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -53,7 +50,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 8474696bf4..e855f7175e 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 @@ -23,7 +23,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -53,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 63570ad089..1876113358 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 @@ -23,7 +23,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -34,10 +34,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -54,7 +51,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 db195c0bbe..a38b2c3f31 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -52,7 +52,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 8c99e72128..c89425f2de 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -52,7 +52,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 e1bf5116c1..137c961318 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 @@ -23,7 +23,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -53,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 b70cb62012..1155745345 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -52,7 +52,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 9337284cb3..1f0a6d0a81 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -52,7 +52,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 1f9a33d788..3b07a66bff 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 = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -35,10 +35,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -55,7 +52,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 c9f07cf92c..dde1df538f 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 @@ -25,7 +25,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 1518cbeadc..9250403c43 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 @@ -25,7 +25,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 fe22e97e4c..17649568df 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 @@ -25,7 +25,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 00c9c8c84b..95ba9a38e7 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 @@ -25,7 +25,7 @@ dependencies = [ ] # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 3842277046..f7db99ce7f 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 @@ -26,7 +26,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -57,7 +57,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 b3c8bdbff1..2447f7bc5d 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 @@ -25,7 +25,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 ee3eba59bf..7c65b339df 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 @@ -26,7 +26,7 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -56,7 +56,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 88226659dc..7031a25f57 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 = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -55,7 +55,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 50e419b7ce..3f66b26c69 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 = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 5b599ff1d0..a7284262e3 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 = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -36,10 +36,7 @@ exts_list = [ }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], - 'patches': [ - 'numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion, - 'numpy-iqacml.patch', - ], + 'patches': ['numpy-%s_distutils_multiple-lib-dirs.patch' % numpyversion], }), ('scipy', scipyversion, { 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], @@ -56,7 +53,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { 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 00445c611f..a510ac66d6 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 = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { + ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { @@ -57,7 +57,7 @@ exts_list = [ ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], }), - ('Cython', '0.19.1', { + ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), ('dateutil', '2.1', { -- GitLab From 312fa97b489d76c31d4238038366a7c7caf3083d Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:30:39 +0100 Subject: [PATCH 080/566] now really added new packages, previous commit was just goolf version of the latest ictce R ec --- .../easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb | 14 ++++++++++++++ easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb | 16 +++++++++++++++- 2 files changed, 29 insertions(+), 1 deletion(-) 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 bc9a5be12c..ad736c3c91 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 @@ -138,6 +138,20 @@ exts_list = [ ('ShortRead', '1.20.0', bioconductor_options), ('graph', '1.40.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('plyr', '1.8', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.1-1', ext_options), + ('Hmisc', '3.13-0', ext_options), + ('stringr', '0.6.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.2', ext_options), + ('scales', '0.2.3', ext_options), + ('fastcluster', '1.1.11', ext_options), + ('reshape2', '1.2.2', ext_options), + ('digest', '0.6.3', ext_options), + ('gtable', '0.1.2', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '0.9.3.1', ext_options), ] moduleclass = 'lang' 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 1f762f49eb..0daaec2313 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 @@ -18,7 +18,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] sanity_check_paths = { @@ -138,6 +138,20 @@ exts_list = [ ('ShortRead', '1.20.0', bioconductor_options), ('graph', '1.40.0', bioconductor_options), ('igraph0', '0.5.7', ext_options), + ('plyr', '1.8', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.1-1', ext_options), + ('Hmisc', '3.13-0', ext_options), + ('stringr', '0.6.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.2', ext_options), + ('scales', '0.2.3', ext_options), + ('fastcluster', '1.1.11', ext_options), + ('reshape2', '1.2.2', ext_options), + ('digest', '0.6.3', ext_options), + ('gtable', '0.1.2', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '0.9.3.1', ext_options), ] moduleclass = 'lang' -- GitLab From e9ca73e70aeeae0ae6422d0ed1cffd1e1b9076bb Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:32:09 +0100 Subject: [PATCH 081/566] fixed ictce bedtools config --- .../easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb index 57c9ecc225..cd12416d3a 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ["http://bedtools.googlecode.com/files/"] sources = ['%(name)s.%(version)s.tar.gz'] -skipsteps = ['configure'] +dirs = ["bin", "data", "docs", "genomes", 'scripts'] +# copy all directories to the installation directory +files_to_copy = dirs + +sanity_check_paths = {'files': [], 'dirs': dirs} moduleclass = 'bio' -- GitLab From d18b7c3f0592aa1a88151b4aa0ac760f557c132e Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:36:26 +0100 Subject: [PATCH 082/566] fixed description --- .../b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb | 7 +++++-- .../b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb | 8 ++++++-- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb index 41345eb68e..8186926dfe 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb @@ -3,8 +3,11 @@ name = 'BEDTools' version = 'v2.17.0' homepage = 'http://code.google.com/p/bedtools/' -description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module - allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" +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. +Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" +several BEDTools together. The following are examples of common questions that one can address with BEDTools. +""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb index cd12416d3a..1de87ad34b 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb @@ -2,8 +2,12 @@ name = 'BEDTools' version = 'v2.17.0' homepage = 'http://code.google.com/p/bedtools/' -description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module - allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" +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. +Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" +several BEDTools together. The following are examples of common questions that one can address with BEDTools. +""" + toolchain = {'name': 'ictce', 'version': '4.1.13'} -- GitLab From 78110085329026895dbe6be65f56e475962fee71 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 2 Dec 2013 18:39:51 +0100 Subject: [PATCH 083/566] fixed ictce for real now --- .../easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb index 1de87ad34b..adcf9bdf19 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb @@ -1,3 +1,4 @@ +easyblock = 'MakeCp' name = 'BEDTools' version = 'v2.17.0' -- GitLab From 4c194732eccc37ef9670904c03b276df15555563 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Dec 2013 18:56:44 +0100 Subject: [PATCH 084/566] add required patch file for numpy v1.8.0 extension --- .../p/Python/numpy-1.8.0-mkl.patch | 213 ++++++++++++++++++ 1 file changed, 213 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/numpy-1.8.0-mkl.patch diff --git a/easybuild/easyconfigs/p/Python/numpy-1.8.0-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.8.0-mkl.patch new file mode 100644 index 0000000000..f2ffc7677b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/numpy-1.8.0-mkl.patch @@ -0,0 +1,213 @@ +diff -ur numpy-1.8.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.0-2/numpy/distutils/fcompiler/__init__.py +--- numpy-1.8.0.orig/numpy/distutils/fcompiler/__init__.py 2013-10-30 19:31:40.000000000 +0100 ++++ numpy-1.8.0-2/numpy/distutils/fcompiler/__init__.py 2013-11-06 15:40:52.146711618 +0100 +@@ -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-1.8.0.orig/numpy/distutils/system_info.py numpy-1.8.0-2/numpy/distutils/system_info.py +--- numpy-1.8.0.orig/numpy/distutils/system_info.py 2013-10-30 19:31:40.000000000 +0100 ++++ numpy-1.8.0-2/numpy/distutils/system_info.py 2013-11-06 15:42:32.397199094 +0100 +@@ -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. +@@ -956,9 +1017,11 @@ + 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) +@@ -1020,16 +1083,13 @@ + 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 +@@ -1108,7 +1168,8 @@ + 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() +@@ -1156,8 +1217,10 @@ + 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) +@@ -1549,8 +1612,10 @@ + 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-1.8.0.orig/numpy/distutils/unixccompiler.py numpy-1.8.0-2/numpy/distutils/unixccompiler.py +--- numpy-1.8.0.orig/numpy/distutils/unixccompiler.py 2013-10-30 19:31:40.000000000 +0100 ++++ numpy-1.8.0-2/numpy/distutils/unixccompiler.py 2013-11-06 15:38:08.942524314 +0100 +@@ -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) -- GitLab From 17471e7f81aaf90c0f94fc10caf45aa1eedc6a6a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 3 Dec 2013 23:50:10 +0100 Subject: [PATCH 085/566] init Coreutils Signed-off-by: Fotis Georgatos --- .../Coreutils/Coreutils-8.21-goolf-1.4.10.eb | 19 +++++++++++++++++++ .../c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb new file mode 100644 index 0000000000..73aff4d255 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +name = "Coreutils" +version = "8.21" + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnu.org/gnu/coreutils'] +sources = [SOURCELOWER_TAR_XZ] + +sanity_check_paths = { + 'files': ["bin/date", "bin/true"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb new file mode 100644 index 0000000000..c61eaf7004 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = "Coreutils" +version = "8.21" + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnu.org/gnu/coreutils'] +sources = [SOURCELOWER_TAR_XZ] + +sanity_check_paths = { + 'files': ["bin/date", "bin/true"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 44d325e7ca224e48689fb89131e542e84f843e91 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 4 Dec 2013 00:21:48 +0100 Subject: [PATCH 086/566] init grep Signed-off-by: Fotis Georgatos --- .../g/grep/grep-2.15-goolf-1.4.10.eb | 19 +++++++++++++++++++ .../g/grep/grep-2.15-ictce-5.3.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb new file mode 100644 index 0000000000..c933f8d1ea --- /dev/null +++ b/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +name = 'grep' +version = '2.15' + +description = "grep: GNU grep" +homepage = 'http://www.gnu.org/software/grep/grep.html' + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://ftp.gnu.org/gnu/grep'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +configopts = ' --disable-perl-regexp ' + +sanity_check_paths = { + 'files': ["bin/grep"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb new file mode 100644 index 0000000000..c1f2292316 --- /dev/null +++ b/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'grep' +version = '2.15' + +description = "grep: GNU grep" +homepage = 'http://www.gnu.org/software/grep/grep.html' + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://ftp.gnu.org/gnu/grep'] + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +configopts = ' --disable-perl-regexp ' + +sanity_check_paths = { + 'files': ["bin/grep"], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From be9cce08b362a0fecfff0589a5bb4fe5ae94b588 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 4 Dec 2013 00:30:05 +0100 Subject: [PATCH 087/566] init XZ Signed-off-by: Fotis Georgatos --- .../easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb | 19 +++++++++++++++++++ .../easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..2393846fce --- /dev/null +++ b/easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +name = 'XZ' +version = '5.0.5' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# configopts = ' --disable-assembler ' # may become useful in non-x86 archs + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb new file mode 100644 index 0000000000..9c4849b2f4 --- /dev/null +++ b/easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'XZ' +version = '5.0.5' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# configopts = ' --disable-assembler ' # may become useful in non-x86 archs + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 18eaf515a1730a432190f2bae23cc44f9a803deb Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 4 Dec 2013 00:45:55 +0100 Subject: [PATCH 088/566] init sed Signed-off-by: Fotis Georgatos --- .../easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb | 17 +++++++++++++++++ .../easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..1aa226aec4 --- /dev/null +++ b/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb @@ -0,0 +1,17 @@ +name = 'sed' +version = '4.2.2' + +homepage = 'http://www.gnu.org/software/sed/sed.html' +description = "sed: GNU implementation of sed, the POSIX stream editor" + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/sed'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sanity_check_paths = { + 'files': ["bin/sed"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..cc1b5fc249 --- /dev/null +++ b/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'sed' +version = '4.2.2' + +homepage = 'http://www.gnu.org/software/sed/sed.html' +description = "sed: GNU implementation of sed, the POSIX stream editor" + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/sed'] + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sanity_check_paths = { + 'files': ["bin/sed"], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 65207f50ba28bfe380847e89d82307c7091aa6bb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 4 Dec 2013 17:08:55 +0100 Subject: [PATCH 089/566] Add support for CHARMM CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. This is a non free program. You need to buy a license to obtain the source code. --- .../CHARMM-37b2-goalf-1.5.12-no-OFED.eb | 31 +++++++++++++++++++ .../c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb | 29 +++++++++++++++++ .../c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 31 +++++++++++++++++++ .../c/CHARMM/main-case-fix-37b2.patch | 13 ++++++++ .../easyconfigs/c/CHARMM/qmmm-pme-37b2.patch | 22 +++++++++++++ .../easyconfigs/c/CHARMM/use-xhost-37b2.patch | 15 +++++++++ 6 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch create mode 100644 easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch create mode 100644 easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..75a0e78635 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb @@ -0,0 +1,31 @@ +# Author 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': 'goalf', 'version': '1.5.12-no-OFED'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "main-case-fix-%(version)s.patch", +] + +# if you specify Gaussian, it will be used for the QM part. +dependencies = [ +# ('Gaussian', 'g09_D.01', '-amd64-gpfs'), +] + +# FFTW will automatically be used because of the toolchain +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-ictce-5.5.0-nompi.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb new file mode 100644 index 0000000000..81985c2134 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb @@ -0,0 +1,29 @@ +# Authors:: Ward Poelmans + +name = "CHARMM" +version = "37b2" +versionsuffix = "nompi" + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'usempi': False} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", +] + +#dependencies = [('Gaussian', 'g09_D.01-ictce-5.5.0-amd64-gpfs')] + +# MKL activated automatically when the MKL is found, same for g09 +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-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb new file mode 100644 index 0000000000..14e379742a --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -0,0 +1,31 @@ +# 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': 'ictce', 'version': '5.5.0'} +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", +] + +# if you specify Gaussian, it will be used for the QM part. +# if you specify FFTW, it will be used instead of the MKL +dependencies = [('Gaussian', 'g09_D.01', '-amd64-gpfs')] + +# 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/main-case-fix-37b2.patch b/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch new file mode 100644 index 0000000000..3ec2563cdb --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch @@ -0,0 +1,13 @@ +# fix a error in the main +diff -ur c37b2.orig/source/charmm/charmm_main.src c37b2/source/charmm/charmm_main.src +--- c37b2.orig/source/charmm/charmm_main.src 2013-02-11 06:27:24.000000000 +0100 ++++ c37b2/source/charmm/charmm_main.src 2013-12-03 16:30:45.539579132 +0100 +@@ -1267,7 +1267,7 @@ + + case('PIPF','PFBA') cmds + ##IF PIPF +- if (wrd == 'PIPF') cmds ++ if (wrd == 'PIPF') then + call pfprep(comlyn,comlen) + else if (wrd == 'PFBA') then + call nosepf(comlyn,comlen) diff --git a/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch b/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch new file mode 100644 index 0000000000..2365077555 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch @@ -0,0 +1,22 @@ +# fixes compile error. Always display the warning +diff -ur c37b2.orig/source/squantm/sqnt_qm2_ewald.src c37b2/source/squantm/sqnt_qm2_ewald.src +--- c37b2.orig/source/squantm/sqnt_qm2_ewald.src 2012-07-17 01:08:32.000000000 +0200 ++++ c37b2/source/squantm/sqnt_qm2_ewald.src 2013-12-03 14:11:46.945196858 +0100 +@@ -1876,7 +1878,7 @@ + ##IF COLFFT (colfft) + !==================COLUMN FFT METHOD ============================== + ##IF QUANTUM MNDO97 SQUANTM GAMESS GAMESSUK QCHEM QTURBO G09 +- if(LQMEWD) call wrndie(-5,'','QM/MM-PME do not support COLFFT.') ++ call wrndie(1,'','QM/MM-PME do not support COLFFT.') + ##ENDIF + ##ELSE (colfft) + !.ab.Fix: xnsymm should be set (not 0 !). +@@ -2146,7 +2148,7 @@ + ##IF COLFFT (colfft) + !==================COLUMN FFT METHOD ============================== + ##IF QUANTUM MNDO97 SQUANTM GAMESS GAMESSUK QCHEM QTURBO G09 +- if(LQMEWD) call wrndie(-5,'','QM/MM-PME do not support COLFFT.') ++ call wrndie(1,'','QM/MM-PME do not support COLFFT.') + ##ENDIF + ##ELSE (colfft) + diff --git a/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch b/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch new file mode 100644 index 0000000000..deb270dfb2 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch @@ -0,0 +1,15 @@ +# lets use the flags the EB sets for us +diff -ur c37b2.orig/build/UNX/Makefile_em64t c37b2/build/UNX/Makefile_em64t +--- c37b2.orig/build/UNX/Makefile_em64t 2012-07-10 14:06:18.000000000 +0200 ++++ c37b2/build/UNX/Makefile_em64t 2013-12-03 15:35:18.997245768 +0100 +@@ -39,8 +39,8 @@ + + FC0 = $(FC) -c -O0 -free + FC1 = $(FC) -c -O1 -free +- FC2 = $(FC) -c -O3 -mp1 -axSSE4.1 -free +- FC3 = $(FC) -c -O3 -mp1 -axSSE4.1 -free ++ FC2 = $(FC) -c -O3 -mp1 -free $(F90FLAGS) ++ FC3 = $(FC) -c -O3 -mp1 -free $(F90FLAGS) + FCR = $(FC) -c -u -V -free + FCD = $(FC) -c -g -O0 -u -traceback -free + ifdef DEBUG -- GitLab From c6b15d3c1cd3dc6b191224857dd591fc2ac7205a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 11:59:28 +0100 Subject: [PATCH 090/566] add missing easyconfigs for ictce/5.3.0, series a-e --- .../a/Automake/Automake-1.14-ictce-5.3.0.eb | 31 +++++++++++++++++++ .../arpack-ng-3.1.3-ictce-5.3.0-mt.eb | 27 ++++++++++++++++ .../b/Bison/Bison-2.7-ictce-5.3.0.eb | 20 ++++++++++++ .../Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb | 28 +++++++++++++++++ .../Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb | 26 ++++++++++++++++ .../b/Boost/Boost-1.53.0-ictce-5.3.0.eb | 22 +++++++++++++ .../c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb | 22 +++++++++++++ .../c/CCfits/CCfits-2.4-ictce-5.3.0.eb | 21 +++++++++++++ .../c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb | 20 ++++++++++++ .../c/CMake/CMake-2.8.10.2-ictce-5.3.0.eb | 18 +++++++++++ .../c/CMake/CMake-2.8.11-ictce-5.3.0.eb | 20 ++++++++++++ .../c/CMake/CMake-2.8.12-ictce-5.3.0.eb | 20 ++++++++++++ .../c/CRF++/CRF++-0.57-ictce-5.3.0.eb | 24 ++++++++++++++ .../Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 28 +++++++++++++++++ .../c/cURL/cURL-7.28.1-ictce-5.3.0.eb | 22 +++++++++++++ .../c/cURL/cURL-7.33.0-ictce-5.3.0.eb | 22 +++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb | 18 +++++++++++ .../e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb | 26 ++++++++++++++++ .../easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb | 17 ++++++++++ 19 files changed, 432 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.11-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/CRF++/CRF++-0.57-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.33.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.eb new file mode 100644 index 0000000000..8b02799901 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-ictce-5.3.0.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:: 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/ +## + +name = 'Automake' +version = "1.14" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +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/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb new file mode 100644 index 0000000000..4abff36b04 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb @@ -0,0 +1,27 @@ +name = 'arpack-ng' +version = '3.1.3' +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': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/'] +sources = [SOURCELOWER_TAR_GZ] + +# do not change the order of the patches or things will break +patches = [ + 'arpack-ng-3.1.3-update-to-head.patch', + 'arpack-ng-3.1.3-pkgconfig.patch', +] + +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/b/Bison/Bison-2.7-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb new file mode 100644 index 0000000000..c8a635c39e --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +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/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..5bff64b1fe --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch'] + +pythonversion = '2.7.3' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..ef9aaeecb5 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.5' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..eedc4e5954 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb new file mode 100644 index 0000000000..41a61d1d6f --- /dev/null +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'CBLAS' +version = '20110120' + +homepage = 'http://www.netlib.org/blas/' +description = "C interface to the BLAS" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/blas/blast-forum/'] +sources = ['cblas.tgz'] + +patches = ['CBLAS_shared-lib.patch'] + +makeopts = 'all shared' + +# parallel build fails occasionally +parallel = 1 + +runtest = 'runtst' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..51afa00583 --- /dev/null +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.4-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'CCfits' +version = '2.4' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/CCfits/' +description = """CCfits is an object oriented interface to the cfitsio library. It is designed to make +the capabilities of cfitsio available to programmers working in C++.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/CCfits/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('CFITSIO','3.34')] + +sanity_check_paths = { + 'files': ['bin/cookbook', 'lib/libCCfits.%s' % SHLIB_EXT, 'lib/pkgconfig/CCfits.pc'], + 'dirs': ['include/CCfits'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb new file mode 100644 index 0000000000..28289da109 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.34-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'CFITSIO' +version = '3.34' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % version.replace('.', '') +source_urls = ['ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/'] +sources = ['%%(namelower)s%s.tar.gz' % srcversion] + +sanity_check_paths = { + 'files':["lib/libcfitsio.a"], + 'dirs':["include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..46545e5ed3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.10.2-ictce-5.3.0.eb @@ -0,0 +1,18 @@ +name = 'CMake' +version = "2.8.10.2" + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.11-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.11-ictce-5.3.0.eb new file mode 100644 index 0000000000..44aa40baa3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.11-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.11' + +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': 'ictce', 'version': '5.3.0'} + +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/CMake/CMake-2.8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-5.3.0.eb new file mode 100644 index 0000000000..99d7f8a098 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'ictce', 'version': '5.3.0'} + +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/CRF++/CRF++-0.57-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CRF++/CRF++-0.57-ictce-5.3.0.eb new file mode 100644 index 0000000000..2f6cf7bcd7 --- /dev/null +++ b/easybuild/easyconfigs/c/CRF++/CRF++-0.57-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'CRF++' +version = '0.57' + +homepage = 'https://code.google.com/p/crfpp/' +description = """CRF++ is a simple, customizable, and open source implementation of + Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is + designed for generic purpose and will be applied to a variety of NLP tasks, such as + Named Entity Recognition, Information Extraction and Text Chunking. """ + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True, 'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://crfpp.googlecode.com/files/'] + +configopts = '--with-pic' +makeopts = 'CXXFLAGS="$CXXFLAGS -Wall -finline"' + +sanity_check_paths = { + 'files': ["bin/crf_learn", "bin/crf_test"], + 'dirs': [] +} + +moduleclass = 'data' 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 new file mode 100644 index 0000000000..3e23a5c022 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.19.1' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..fa10cf6767 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.28.1-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'cURL' +version = '7.28.1' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.33.0-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.33.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..65dd20560e --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.33.0-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'cURL' +version = '7.33.0' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +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-1.8.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..f5c2ee7700 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '5.3.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..0d4662d693 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-5.3.0.eb @@ -0,0 +1,26 @@ +## +# 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 = 'Eigen' +version = '3.1.4' + +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': 'ictce', 'version': '5.3.0'} +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/e/ed/ed-1.9-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb new file mode 100644 index 0000000000..e2bb71d26b --- /dev/null +++ b/easybuild/easyconfigs/e/ed/ed-1.9-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'ed' +version = '1.9' + +homepage = 'http://www.gnu.org/software/ed/ed.html' +description = """GNU ed is a line-oriented text editor.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/%(name)s/'] + +sanity_check_paths = { + 'files' : ['bin/ed'], + 'dirs' : [], +} + +moduleclass = 'tools' -- GitLab From 3359dd976f62e862bd06d06e862d4a8209a806b8 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 12:00:35 +0100 Subject: [PATCH 091/566] add missing easyconfigs for ictce/5.3.0, series f-k --- .../FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb | 34 ++++++++++++++++ .../f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb | 27 +++++++++++++ .../fixesproto/fixesproto-5.0-ictce-5.3.0.eb | 17 ++++++++ .../f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb | 19 +++++++++ .../f/freetype/freetype-2.4.11-ictce-5.3.0.eb | 19 +++++++++ .../freetype/freetype-2.5.0.1-ictce-5.3.0.eb | 21 ++++++++++ .../g/GDAL/GDAL-1.9.2-ictce-5.3.0.eb | 22 ++++++++++ .../g/GLPK/GLPK-4.48-ictce-5.3.0.eb | 21 ++++++++++ .../g/GLib/GLib-2.34.3-ictce-5.3.0.eb | 19 +++++++++ .../g/GMP/GMP-5.1.1-ictce-5.3.0.eb | 20 ++++++++++ .../g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb | 40 +++++++++++++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb | 16 ++++++++ .../g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb | 18 +++++++++ .../g/g2lib/g2lib-1.4.0-ictce-5.3.0.eb | 20 ++++++++++ .../g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb | 23 +++++++++++ .../g/gzip/gzip-1.6-ictce-5.3.0.eb | 34 ++++++++++++++++ .../h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 21 ++++++++++ .../h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb | 22 ++++++++++ .../h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb | 24 +++++++++++ .../h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb | 22 ++++++++++ .../h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb | 32 +++++++++++++++ .../h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb | 17 ++++++++ .../h/hwloc/hwloc-1.6-ictce-5.3.0.eb | 17 ++++++++ .../h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb | 17 ++++++++ .../h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb | 17 ++++++++ .../i/imake/imake-1.0.5-ictce-5.3.0.eb | 19 +++++++++ .../inputproto/inputproto-2.3-ictce-5.3.0.eb | 17 ++++++++ .../k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb | 17 ++++++++ 28 files changed, 612 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.5-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..c1e3ad55f7 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.1-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'FIAT' +version = '1.1' + +homepage = 'https://launchpad.net/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': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/release-%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ScientificPython', '2.8', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/FIAT' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..97c39edc10 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.2-ictce-5.3.0.eb @@ -0,0 +1,27 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +name = 'FLTK' +version = '1.3.2' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] + +dependencies = [ + ('Tcl', '8.5.12'), + ('Tk', '8.5.12'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config','bin/fluid'], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..550ddb6d6e --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +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-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..5a15cb7719 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +dependencies = [('libXi', '1.7.2')] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb new file mode 100644 index 0000000000..6c789c8bd3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'freetype' +version = '2.4.11' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +sources = [SOURCE_TAR_GZ] + +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-2.5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..d509fdfff7 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.0.1' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.6')] + +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/g/GDAL/GDAL-1.9.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..3cbfbb519a --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-1.9.2-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://download.osgeo.org/gdal/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': ['lib/libgdal.so', 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb new file mode 100644 index 0000000000..c44466fc3b --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'GLPK' +version = '4.48' + +homepage = 'http://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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] + +dependencies = [ + ('GMP', '5.1.1'), +] + +configopts = "--with-gmp" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..ddeef5db37 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +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', '3.0.13'), + ('gettext', '0.18.2'), +] +builddependencies = [('Python', '2.7.3')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..603803b0a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'GMP' +version = '5.1.1' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..6704a1c189 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb @@ -0,0 +1,40 @@ +## +# 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 +## + +easyblock = 'CMakeMake' + +name = 'GROMACS' +version = '4.6.1' + +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': '5.3.0'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] + +builddependencies = [('CMake', '2.8.4')] + +configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" +runtest = 'check' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb new file mode 100644 index 0000000000..4a05725830 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.3.0.eb @@ -0,0 +1,16 @@ +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..f0e6d6e596 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb @@ -0,0 +1,18 @@ +name = 'g2clib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ("C" version).""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +dependencies = [('JasPer', '1.900.1')] + +sources = ['%s-%s.tar' % (name, version)] +source_urls = [homepage] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..5be5a5a476 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'g2lib' +version = '1.4.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +dependencies = [('JasPer', '1.900.1')] + +sources = ['%s-%s.tar' % (name, version)] +source_urls = [homepage] + +patches = ['fix_makefile.patch'] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..071d45e481 --- /dev/null +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.10.0-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'grib_api' +version = '1.10.0' + +homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home' +description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python + programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of + command line tools is also provided to give quick access to GRIB messages.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('JasPer', '1.900.1'), +] + +preconfigopts = 'FC=$F90' +configopts = '--with-jasper=$EBROOTJASPER' + +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb new file mode 100644 index 0000000000..21e29f76c9 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-5.3.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC +# Authors:: Thekla Loizou +# 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_06-19.html +## + +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = ['http://ftpmirror.gnu.org/gzip'] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb new file mode 100644 index 0000000000..6a6f38583d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'HDF' +version = '4.2.8' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'pic': True} + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), + ] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] + +configopts = "--with-szlib=$EBROOTSZIP" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb new file mode 100644 index 0000000000..4923cec819 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = '-serial' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +patches = ['configure_libtool.patch'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb new file mode 100644 index 0000000000..96aaf04223 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'HDF5' +version = '1.8.10-patch1' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', + 'HDF5-1.8.9_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb new file mode 100644 index 0000000000..d1cfae6705 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.11-ictce-5.3.0-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.11' +versionsuffix = '-serial' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +patches = ['configure_libtool.patch'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..cd410ed70d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.1.3' + +homepage = 'http://code.google.com/p/h5py/' +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +source_urls = ['http://h5py.googlecode.com/files/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.10'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..4255032ed4 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = '1.5.1' + +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': 'ictce', 'version': '5.3.0'} + +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/h/hwloc/hwloc-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb new file mode 100644 index 0000000000..f1b284038d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = '1.6' + +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': 'ictce', 'version': '5.3.0'} + +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/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..a5fd17b348 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = '1.6.2' + +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': 'ictce', 'version': '5.3.0'} + +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/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..5abd7ea765 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = "1.7.2" + +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': 'ictce', 'version': '5.3.0'} + +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/imake/imake-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/i/imake/imake-1.0.5-ictce-5.3.0.eb new file mode 100644 index 0000000000..2a9e2558db --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.5-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'imake' +version = '1.0.5' + +homepage = 'http://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it easier to develop software + portably for multiple systems.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://artfiles.org/x.org/pub/individual/util/'] + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['ccmakedep', 'cleanlinks', 'imake', 'makeg', 'mergelib', + 'mkdirhier', 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..554430022b --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +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-ictce-5.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb new file mode 100644 index 0000000000..598911385e --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'kbproto' +version = '1.0.6' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +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' -- GitLab From 54d3e82cd7b561357abd4a1e5084f25849098f52 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 12:01:37 +0100 Subject: [PATCH 092/566] add missing easyconfigs for ictce/5.3.0, series l-o --- .../l/LWM2/LWM2-1.1-ictce-5.3.0.eb | 46 +++++++++++++++++ .../l/libICE/libICE-1.0.8-ictce-5.3.0.eb | 22 ++++++++ .../l/libSM/libSM-1.2.1-ictce-5.3.0.eb | 26 ++++++++++ .../l/libX11/libX11-1.6.1-ictce-5.3.0.eb | 35 +++++++++++++ .../l/libXau/libXau-1.0.8-ictce-5.3.0.eb | 19 +++++++ .../l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb | 22 ++++++++ .../l/libXext/libXext-1.3.2-ictce-5.3.0.eb | 28 ++++++++++ .../libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb | 22 ++++++++ .../l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 25 +++++++++ .../l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb | 23 +++++++++ .../l/libXp/libXp-1.0.2-ictce-5.3.0.eb | 28 ++++++++++ .../l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb | 20 ++++++++ .../l/libXt/libXt-1.1.4-ictce-5.3.0.eb | 34 +++++++++++++ .../l/libidn/libidn-1.27-ictce-5.3.0.eb | 13 +++++ .../l/libpng/libpng-1.5.14-ictce-5.3.0.eb | 22 ++++++++ .../libpng-1.6.3-ictce-5.3.0-zlib-1.2.8.eb | 19 +++++++ .../l/libpng/libpng-1.6.3-ictce-5.3.0.eb | 17 +++++++ .../likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb | 27 ++++++++++ .../l/likwid/likwid-3.0.0-ictce-5.3.0.eb | 24 +++++++++ .../l/lynx/lynx-2.8.7-ictce-5.3.0.eb | 17 +++++++ .../MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb | 30 +++++++++++ .../m/Mesquite/Mesquite-2.3.0-ictce-5.3.0.eb | 13 +++++ ...tplotlib-1.2.1-ictce-5.3.0-Python-2.7.3.eb | 34 +++++++++++++ ...tplotlib-1.3.0-ictce-5.3.0-Python-2.7.5.eb | 38 ++++++++++++++ .../molmod-1.0-ictce-5.3.0-Python-2.7.3.eb | 33 ++++++++++++ .../n/netCDF/netCDF-C++-4.2-ictce-5.3.0.eb | 22 ++++++++ .../numpy-1.8.0-ictce-5.3.0-Python-2.7.5.eb | 26 ++++++++++ .../o/OTF/OTF-1.12.4-ictce-5.3.0.eb | 33 ++++++++++++ .../o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb | 31 +++++++++++ ...OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 51 +++++++++++++++++++ ...OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 51 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb | 21 ++++++++ 32 files changed, 872 insertions(+) create mode 100644 easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.27-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0-zlib-1.2.8.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-C++-4.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.8.0-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..18cafee304 --- /dev/null +++ b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb @@ -0,0 +1,46 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# 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 = "LWM2" +version = "1.1" + +homepage = 'http://www.vi-hps.org/Tools/LWM2.html' +description = """The lightweight measurement module (LWM2) is a low overhead profiler developed + during the course of the HOPSA project. It can profile applications without any modification by + a user. The lightweight measurement module uses a hybrid approach to profile an application. It + samples the profiled application at regular intervals to keep track of application activity. To + keep the overhead low, LWM2 avoids stack unwinding at each application sample. Instead, it utilizes + direct instrumentation to earmark regions of interest in an application. When an application is + sampled, the earmarks are checked to identify the region of application execution. As a result, + LWM2 is able to profile application with reasonable knowledge of application activity while + maintaining low overhead. This hybrid approach also allows LWM2 to keep track of the time spent + by an application in different regions of execution without directly measuring the time in these + regions. The hybrid profiling approach is also used to collect additional dat a of interest for + some specific application activities. This includes the MPI communication calls and the amount of + data transfer, the POSIX file I/O calls and associated data transfers, etc.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/projects/hopsa/lwm2-1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/projects/hopsa/'] + +# compiler toolchain depencies +dependencies = [ + ('PAPI', '5.2.0'), +] + +sanity_check_paths = { + 'files': ["bin/l2freader", ("lib64/liblwm2.a", "lib/liblwm2.a")], + 'dirs': [] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb new file mode 100644 index 0000000000..18f415d55b --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'libICE' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.23'), + ('xtrans', '1.2'), +] + +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-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..a05cea05c8 --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb @@ -0,0 +1,26 @@ +name = 'libSM' +version = '1.2.1' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.8'), +] +builddependencies = [ + ('xproto', '7.0.23'), + ('xtrans', '1.2'), +] + +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/libX11/libX11-1.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..0213c75285 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb @@ -0,0 +1,35 @@ +name = 'libX11' +version = '1.6.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +pythonversion = '-Python-2.7.3' +builddependencies = [ + ('xextproto', '7.2.1'), + ('xcb-proto', '1.7', pythonversion), + ('kbproto', '1.0.6'), + ('inputproto', '2.3'), + ('xproto', '7.0.23'), +] + +dependencies = [ + ('libxcb', '1.8', pythonversion), + ('xtrans', '1.2'), +] + +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-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb new file mode 100644 index 0000000000..c5876f3234 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb new file mode 100644 index 0000000000..7c0ed45c9d --- /dev/null +++ b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'libXaw' +version = '1.0.12' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXaw provides the Athena Widgets toolkit""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libXmu', '1.1.2'), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXaw6.a', 'libXaw7.a', 'libXaw.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..0c0daa5834 --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +name = 'libXext' +version = '1.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto','7.0.23'), + ('libX11', '1.6.1'), + ('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/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..6bf02a2a5f --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.2.1'), +] + +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-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..4679a7f203 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -0,0 +1,25 @@ +name = 'libXi' +version = '1.7.2' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xproto', '7.0.23'), + ('xextproto', '7.2.1'), + ('libXext', '1.3.2'), + ('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' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..9a94fcab36 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'libXmu' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. + libXmuu is a lighter-weight version that does not depend on libXt or libXext""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libXt', '1.1.4'), + ('libXpm', '3.5.11'), +] +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/libXp/libXp-1.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..29bafbff8b --- /dev/null +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +name = 'libXp' +version = '1.0.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +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/libXpm/libXpm-3.5.11-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb new file mode 100644 index 0000000000..08a43f1d0e --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'libXpm' +version = '3.5.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXp provides the X print library.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [('gettext', '0.18.2')] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..929c20cbe1 --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb @@ -0,0 +1,34 @@ +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libSM', '1.2.1'), + ('libICE', '1.0.8'), + ('libX11', '1.6.1'), + ('kbproto', '1.0.6'), + ('xproto', '7.0.23'), +] + +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/l/libidn/libidn-1.27-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.27-ictce-5.3.0.eb new file mode 100644 index 0000000000..cc1ae26187 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.27-ictce-5.3.0.eb @@ -0,0 +1,13 @@ +name = 'libidn' +version = '1.27' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-5.3.0.eb new file mode 100644 index 0000000000..4ef2e44f4a --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'libpng' +version = '1.5.14' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +toolchainopts = {'optarch': True} +configopts = "--with-pic" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': ['bin/libpng-config', 'lib/libpng.a', 'lib/libpng.so', 'lib/pkgconfig/libpng.pc'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0-zlib-1.2.8.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0-zlib-1.2.8.eb new file mode 100644 index 0000000000..fb9f32baf9 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0-zlib-1.2.8.eb @@ -0,0 +1,19 @@ +name = 'libpng' +version = '1.6.3' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +zlibver = '1.2.8' +versionsuffix = '-zlib-%s' % zlibver +dependencies = [('zlib', zlibver)] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..2701d0d2b6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'libpng' +version = '1.6.3' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb new file mode 100644 index 0000000000..3561d3e5e5 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0-pinomp.eb @@ -0,0 +1,27 @@ +name = 'likwid' +version = '3.0.0' +versionsuffix = '-pinomp' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GOOGLECODE_SOURCE] + +patches = ['pinomp-pthread-overload.patch'] + +skipsteps = ['configure'] +makeopts='CC="$CC" CFLAGS="$CFLAGS"' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-features", "bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.so", "lib/liblikwid.a"], + 'dirs': ["man/man1"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..b3687e8cba --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'likwid' +version = '3.0.0' + +homepage = 'http://code.google.com/p/likwid/' +description = """Likwid stands for Like I knew what I am doing. This project contributes easy to use + command line tools for Linux to support programmers in developing high performance multi threaded programs.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GOOGLECODE_SOURCE] + +skipsteps = ['configure'] +makeopts='CC="$CC" CFLAGS="$CFLAGS"' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/likwid-features", "bin/likwid-memsweeper", "bin/likwid-mpirun", "bin/likwid-perfctr", + "bin/likwid-perfscope", "bin/likwid-pin", "bin/likwid-powermeter", "bin/likwid-topology", + "lib/liblikwidpin.so", "lib/liblikwid.a"], + 'dirs': ["man/man1"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb new file mode 100644 index 0000000000..8935b8374f --- /dev/null +++ b/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'lynx' +version = '2.8.7' + +description = "lynx is an alphanumeric display oriented World-Wide Web Client" +homepage = 'http://lynx.isc.org/' + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://lynx.isc.org/release/'] +sources = ['%(name)s%(version)s.tar.bz2'] + +sanity_check_paths = { + 'files': ['bin/lynx'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..9d63283dc3 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.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:: Cedric Laczny , 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_2012-94.html +## + +name = 'MUMmer' +version = '3.23' + +homepage = 'http://mummer.sourceforge.net/' +description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%s%s.tar.gz' % (name, version)] +source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [(perl, perlver)] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-5.3.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..26a922fdfd --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-ictce-5.3.0.eb @@ -0,0 +1,13 @@ +name = 'Mesquite' +version = '2.3.0' + +homepage = 'http://software.sandia.gov/~bktidwe/mesquite.html' +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://software.sandia.gov/~bktidwe/'] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..ab81bf895d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': '5.3.0'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.7'), + ('freetype', '2.4.11'), + ('libpng', '1.5.13'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..08450f7881 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,38 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.0' + +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': '5.3.0'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +zlibver = '1.2.8' +dependencies = [ + (python, pythonversion), + ('zlib', zlibver), + ('freetype', '2.4.10'), + ('libpng', '1.6.3', '-zlib-%s' % zlibver), +] + +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/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..42b1105348 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-C++-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-C++-4.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..1f5199fe78 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-C++-4.2-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +name = 'netCDF-C++' +version = '4.2' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = ['netcdf-cxx-%(version)s.tar.gz'] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +sanity_check_paths = { + 'files': ['include/ncvalues.h', 'include/netcdfcpp.h', 'include/netcdf.hh', 'lib/libnetcdf_c++.a', 'lib/libnetcdf_c++.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.0-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.0-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..c5d0574900 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.0-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.8.0' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..34d46acb15 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "OTF" +version = "1.12.4" +majorsuffix = 'salmon' + +homepage = 'http://www.tu-dresden.de/zih/otf/' +description = """The Open Trace Format is a highly scalable, memory efficient event + trace data format plus support library. It is the standard trace format + for Vampir, and is open for other tools. [NOW OBSOLETE: use OTF2]""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.4salmon.tar.gz +sources = ['%%(name)s-%%(version)s%s.tar.gz' % majorsuffix] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get='] + +# name change in version 1.12.3: "open-trace-format" was "otf" in older versions +# "open-trace-format" => "otf" for versions until 1.12.2 +sanity_check_paths = { + 'files': ["bin/otfconfig", "include/open-trace-format/otf.h", + # note by Bernd Mohr: on some systems libraries end up in lib/ + ("lib64/libopen-trace-format.a", "lib/libopen-trace-format.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..341f324efb --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# 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 = "OTF2" +version = "1.2.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..c32ddbd8d2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -0,0 +1,51 @@ +name = 'OpenBLAS' +version = '0.2.6' + +lapackver = '3.4.2' +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': 'ictce', 'version': '5.3.0'} + +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 = [ + 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +makeopts = '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' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..1ea6e6468c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -0,0 +1,51 @@ +name = 'OpenBLAS' +version = '0.2.8' + +lapackver = '3.4.2' +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': 'ictce', 'version': '5.3.0'} + +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 = [ + # 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +makeopts = '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' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..0d17976392 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.0' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' -- GitLab From a40e13d37bbece2ae0dafec1a25940bd37011a56 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 12:02:25 +0100 Subject: [PATCH 093/566] add missing easyconfigs for ictce/5.3.0, series p-z --- .../p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb | 44 +++++++++++++++++ .../easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb | 48 +++++++++++++++++++ .../p/PP/PP-1.6.4-ictce-5.3.0-Python-2.7.5.eb | 30 ++++++++++++ .../p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb | 30 ++++++++++++ .../p/PSI/PSI-4.0b4-ictce-5.3.0.eb | 28 +++++++++++ .../p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb | 31 ++++++++++++ .../p/PSI/PSI-4.0b5-ictce-5.3.0.eb | 30 ++++++++++++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 23 +++++++++ .../phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb | 35 ++++++++++++++ .../p/pixman/pixman-0.28.2-ictce-5.3.0.eb | 18 +++++++ .../printproto-1.0.5-ictce-5.3.0.eb | 17 +++++++ ...pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb | 32 +++++++++++++ .../easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb | 20 ++++++++ .../SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb | 14 ++++++ .../SCons-2.3.0-ictce-5.3.0-Python-2.7.5.eb | 26 ++++++++++ .../s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb | 35 ++++++++++++++ .../s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb | 34 +++++++++++++ .../Sablotron/Sablotron-1.0.3-ictce-5.3.0.eb | 21 ++++++++ .../s/Silo/Silo-4.9.1-ictce-5.3.0.eb | 20 ++++++++ .../s/Stacks/Stacks-1.03-ictce-5.3.0.eb | 29 +++++++++++ .../s/Stride/Stride-1.0-ictce-5.3.0.eb | 24 ++++++++++ ...kit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb | 28 +++++++++++ .../scipy-0.12.0-ictce-5.3.0-Python-2.7.3.eb | 19 ++++++++ .../sympy-0.7.2-ictce-5.3.0-Python-2.7.3.eb | 32 +++++++++++++ .../t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb | 19 ++++++++ .../w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb | 25 ++++++++++ .../w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb | 28 +++++++++++ .../w/WPS/WPS-3.5-ictce-5.3.0-dmpar.eb | 29 +++++++++++ .../w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb | 29 +++++++++++ .../w/WRF/WRF-3.4.1-ictce-5.3.0-dmpar.eb | 37 ++++++++++++++ .../w/WRF/WRF-3.5.1-ictce-5.3.0-dmpar.eb | 36 ++++++++++++++ ...i2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb | 44 +++++++++++++++++ ...L-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb | 25 ++++++++++ ...XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb | 25 ++++++++++ .../x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb | 17 +++++++ .../xextproto/xextproto-7.2.1-ictce-5.3.0.eb | 23 +++++++++ .../x/xtrans/xtrans-1.2-ictce-5.3.0.eb | 24 ++++++++++ .../YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb | 35 ++++++++++++++ .../yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb | 36 ++++++++++++++ .../z/zsh/zsh-5.0.2-ictce-5.3.0.eb | 16 +++++++ 40 files changed, 1116 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-2.3.0-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb create mode 100644 easybuild/easyconfigs/s/Sablotron/Sablotron-1.0.3-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.12.0-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-0.7.2-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.4.1-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-5.3.0-dmpar.eb create mode 100644 easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..0376287c5e --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-ictce-5.3.0.eb @@ -0,0 +1,44 @@ +## +# 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_07-02.html +## + +name = 'PAPI' +version = '5.2.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb new file mode 100644 index 0000000000..d5d52a3127 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -0,0 +1,48 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "PDT" +version = "3.19" + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..3d4858dc19 --- /dev/null +++ b/easybuild/easyconfigs/p/PP/PP-1.6.4-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'PP' +version = '1.6.4' + +homepage = 'http://www.parallelpython.com/' +description = """PP is a python module which provides mechanism for parallel execution of python code on SMP + (systems with multiple processors or cores) and clusters (computers connected via network).""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.parallelpython.com/downloads/pp/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(namelower)s.py' % pythonshortversion], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb new file mode 100644 index 0000000000..d9bf4f7fd5 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb @@ -0,0 +1,30 @@ +name = 'PSI' +version = '4.0b4' +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': 'ictce', 'version': '5.3.0'} +# not using MPI results in a build relying on multithreaded BLAS solely +toolchainopts = {'usempi': False} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b4-mpi.patch', + 'PSI-4.0b4-thread-pool.patch', +] + +python = 'Python' +pyver = '2.7.3' + +dependencies = [ + (python, pyver), + ('Boost', '1.53.0', '-%s-%s' % (python, pyver)), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb new file mode 100644 index 0000000000..55585c69df --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb @@ -0,0 +1,28 @@ +name = 'PSI' +version = '4.0b4' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b4-mpi.patch', + 'PSI-4.0b4-thread-pool.patch', +] + +python = 'Python' +pyver = '2.7.3' + +dependencies = [ + (python, pyver), + ('Boost', '1.53.0', '-%s-%s' % (python, pyver)), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb new file mode 100644 index 0000000000..5e2d6e7d5e --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb @@ -0,0 +1,31 @@ +name = 'PSI' +version = '4.0b5' +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': 'ictce', 'version': '5.3.0'} +# not using MPI results in a build relying on multithreaded BLAS solely +toolchainopts = {'usempi': False} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-thread-pool.patch', + 'PSI-4.0b5-new-plugin.patch', +] + +python = 'Python' +pyver = '2.7.5' + +dependencies = [ + (python, pyver), + ('Boost', '1.53.0', '-%s-%s' % (python, pyver)), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb new file mode 100644 index 0000000000..324e93c116 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb @@ -0,0 +1,30 @@ +name = 'PSI' +version = '4.0b5' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b5-mpi-memcpy.patch', + 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-thread-pool.patch', + 'PSI-4.0b5-new-plugin.patch', +] + +python = 'Python' +pyver = '2.7.5' + +dependencies = [ + (python, pyver), + ('Boost', '1.53.0', '-%s-%s' % (python, pyver)), +] + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000..68a4b58e99 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -0,0 +1,23 @@ +name = 'Python' +version = '2.5.6' +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +patches = ['python_libffi_int128_icc.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..c9d54a15dd --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.6.4-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'phonopy' +version = '1.6.4' + +homepage = 'http://phonopy.sourceforge.net/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.3' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), + ('lxml', '3.1.2', versionsuffix), + ('PyYAML', '3.10', versionsuffix), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pythonshortversion + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pythonshortversion), pylibdir)], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..f27088d0c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-5.3.0.eb @@ -0,0 +1,18 @@ +name = "pixman" +version = '0.28.2' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb new file mode 100644 index 0000000000..bc10ad3e08 --- /dev/null +++ b/easybuild/easyconfigs/p/printproto/printproto-1.0.5-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +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': 'ictce', 'version': '5.3.0'} + +sanity_check_paths = { + 'files': ['include/X11/extensions/Print.h', 'include/X11/extensions/Printstr.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..bf06ddc40b --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.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': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/pysqlite/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +pyshortver = '2.7' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.1'), +] + +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/q/Qt/Qt-4.8.5-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb new file mode 100644 index 0000000000..e712e4c5a2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'Qt' +version = '4.8.5' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +configopts="-confirm-license -opensource -silent" + +sanity_check_paths = { + 'files': ['lib/libQtCore.so'], + 'dirs': [], +} +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..7bad11e6da --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.0_esmumps-ictce-5.3.0.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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/31832/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.0-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.0-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..35beebb612 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.0-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.0' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..2d87802022 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.1-ictce-5.3.0.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/ +## + +name = 'SQLite' +version = '3.8.1' + +homepage = 'http://www.hwaci.com/sw/sqlite/' +description = "SQLite: SQL Database Engine in a C Library" + +# eg. http://www.hwaci.com/sw/sqlite/2013/sqlite-autoconf-3080100.tar.gz +source_urls = ['http://www.hwaci.com/sw/sqlite/2013'] +sources = ['sqlite-autoconf-%s0%s0%s00.tar.gz' % tuple(version.split('.'))] # very weird way to calculate your filename + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('libreadline', '6.2'), + ('Tcl', '8.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb b/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb new file mode 100644 index 0000000000..711aeda3a7 --- /dev/null +++ b/easybuild/easyconfigs/s/SURF/SURF-1.0-ictce-5.3.0-LINUXAMD64.eb @@ -0,0 +1,34 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'MakeCp' + +name = 'SURF' +version = '1.0' +ARCH = 'LINUXAMD64' +versionsuffix = '-%s' % ARCH + +homepage = 'http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node65.html' +description = "A molecular surface solver, which can be used as rendering method in VMD." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.ks.uiuc.edu/Research/vmd/extsrcs'] +sources = [('%(namelower)s.tar.Z', 'tar -xzf %s')] + +builddependencies = [ + ('makedepend', '1.0.4'), + ('ed', '1.9'), +] + +premakeopts = 'make INCLUDE="-I. -I$EBROOTGCC/lib/gcc/x86_64-unknown-linux-gnu/$EBVERSIONGCC/include" depend && ' +makeopts = ' && mv surf surf_%s' % ARCH + +files_to_copy = [(['surf_%s' % ARCH], "bin")] + +sanity_check_paths = { + 'files': ['bin/surf_%s' % ARCH], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sablotron/Sablotron-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Sablotron/Sablotron-1.0.3-ictce-5.3.0.eb new file mode 100644 index 0000000000..12bb8bfb6e --- /dev/null +++ b/easybuild/easyconfigs/s/Sablotron/Sablotron-1.0.3-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = 'Sablotron' +version = '1.0.3' + +homepage = 'http://sablotron.sourceforge.net/' +description = """Sablotron XML processor""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['Sablot-%(version)s.tar.gz'] + +patches = ['%(name)s-%(version)s_recent-icpc.patch'] + +dependencies = [('expat', '2.1.0')] + +sanity_check_paths = { + 'files': ['bin/sabcmd', 'bin/sablot-config', 'include/sablot.h', 'lib/libsablot.a', 'lib/libsablot.so'], + 'dirs': ['share/doc/html/sablot', 'man'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..672084b8d3 --- /dev/null +++ b/easybuild/easyconfigs/s/Silo/Silo-4.9.1-ictce-5.3.0.eb @@ -0,0 +1,20 @@ +name = 'Silo' +version = '4.9.1' + +homepage = 'https://wci.llnl.gov/codes/silo/' +description = """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = ['https://wci.llnl.gov/codes/silo/silo-%(version)s'] + +configopts = '--disable-silex' + +sanity_check_paths = { + 'files': ['bin/browser', 'bin/silock', 'bin/silodiff', 'bin/silofile', 'lib/libsilo.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb new file mode 100644 index 0000000000..196d2c22e4 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-5.3.0.eb @@ -0,0 +1,29 @@ +name = 'Stacks' +version = '1.03' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://creskolab.uoregon.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +runtest = "check" + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb new file mode 100644 index 0000000000..da61249bcf --- /dev/null +++ b/easybuild/easyconfigs/s/Stride/Stride-1.0-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'MakeCp' + +name = "Stride" +version = "1.0" + +homepage = 'http://structure.usc.edu/stride/' +description = "STRIDE is a program to recognize secondary structural elements in proteins from their atomic coordinates" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/stride/src/'] +sources = ['%(namelower)s.tar.gz' ] + +files_to_copy = [(['stride'], "bin")] + +sanity_check_paths = { + 'files': ['bin/stride'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb new file mode 100644 index 0000000000..fb08bf0088 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = "scikit-learn" +version = "0.14" + +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': 'ictce', 'version': '5.3.0'} +source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.3.0', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.12.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.12.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..a44fd73413 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.12.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.12.0' +versionsuffix = '-Python-2.7.3' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.6.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.2-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..1328146b8e --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.2-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'sympy' +version = '0.7.2' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://sympy.googlecode.com/files'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +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' 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 new file mode 100644 index 0000000000..fa866637b3 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.1-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = 'Tcl' +version = '8.6.1' + +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': 'ictce', 'version': '5.3.0'} + +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/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..eaf41baf93 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb @@ -0,0 +1,25 @@ +name = 'WPS' +version = '3.3.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. 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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.1.3'), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1') + ] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..3dfc001558 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb @@ -0,0 +1,28 @@ +name = 'WPS' +version = '3.4.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. 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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] + +patches = ['WPS_netCDF-Fortran_seperate_path.patch'] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('libpng', '1.5.14'), + ('JasPer','1.900.1') + ] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..daef6c10e6 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.5-ictce-5.3.0-dmpar.eb @@ -0,0 +1,29 @@ +name = 'WPS' +version = '3.5' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. 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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] + +patches = ['WPS_netCDF-Fortran_seperate_path.patch'] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('zlib', '1.2.7'), + ('libpng', '1.6.3'), + ('JasPer', '1.900.1'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..66eecfdfed --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb @@ -0,0 +1,29 @@ +name = 'WPS' +version = '3.5.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. 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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True} + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] + +patches = ['WPS_netCDF-Fortran_seperate_path.patch'] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('zlib', '1.2.7'), + ('libpng', '1.6.3'), + ('JasPer', '1.900.1'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.4.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.4.1-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..227be5752c --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.4.1-ictce-5.3.0-dmpar.eb @@ -0,0 +1,37 @@ +name = 'WRF' +version = '3.4.1' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['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', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.4.1_netCDF-Fortran_separate_path.patch', + 'WRF_FC-output-spec_fix.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-5.3.0-dmpar.eb new file mode 100644 index 0000000000..f02edb4567 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.5.1-ictce-5.3.0-dmpar.eb @@ -0,0 +1,36 @@ +name = 'WRF' +version = '3.5.1' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = ['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', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.5_netCDF-Fortran_separate_path.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..3e35384c19 --- /dev/null +++ b/easybuild/easyconfigs/w/wiki2beamer/wiki2beamer-0.9.5-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,44 @@ +## +# 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/index.html +## + +easyblock = "PythonPackage" + +name = 'wiki2beamer' +version = '0.9.5' + +homepage = 'http://wiki2beamer.sourceforge.net/' +description = """wiki2beamer converts a simple wiki-like syntax to complex LaTeX beamer code. + It's written in python and should run on all *nix platforms. Afraid to loose some LaTeX powers? + Don't worry: you can always fall back to plain LaTeX as wiki2beamer is just a preprocessor.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +# eg. http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5/wiki2beamer-0.9.5.zip/download +sources = ['wiki2beamer-0.9.5.zip'] +source_urls = ['http://sourceforge.net/projects/wiki2beamer/files/wiki2beamer/wiki2beamer-0.9.5','download'] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +start_dir = 'code' + +options = {'modulename': False} + +sanity_check_paths = { + 'files': ["bin/wiki2beamer"], + 'dirs': ["."] + } + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..f91b2703dc --- /dev/null +++ b/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'XML-LibXML' +version = '2.0018' + +homepage = 'http://search.cpan.org/src/SHLOMIF/XML-LibXML-2.0018/' +description = """Perl binding for libxml2""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.cpan.org/modules/by-module/XML/SHLOMIF/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("libxml2", "2.9.0"), +] + +options = {'modulename': 'XML::LibXML'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..e61280523c --- /dev/null +++ b/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'XML-Simple' +version = '2.20' + +homepage = 'http://search.cpan.org/src/GRANTM/XML-Simple-2.20/' +description = """Easily read/write XML in Perl""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.cpan.org/modules/by-module/XML/GRANTM/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("XML-LibXML", "2.0018", versionsuffix), +] + +options = {'modulename': 'XML::Simple'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..b3d975a744 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-ictce-5.3.0.eb @@ -0,0 +1,17 @@ +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] + +sanity_check_paths = { + 'files' : ['include/X11/bitmaps/gray'], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..b6a0c15993 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.2.1-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'xextproto' +version = '7.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +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/xtrans/xtrans-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..11eabbd405 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb @@ -0,0 +1,24 @@ +name = 'xtrans' +version = '1.2' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +sanity_check_paths = { + 'files' : ['include/X11/Xtrans/%s' % x for x in [ + 'transport.c', 'Xtrans.c', 'Xtransdnet.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtransos2.c', + 'Xtranssock.c', 'Xtranstli.c', 'Xtransutil.c' + ] + ], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb new file mode 100644 index 0000000000..30d441b40a --- /dev/null +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PerlModule' + +name = 'YAML-Syck' +version = '1.27' + +homepage = 'http://search.cpan.org/perldoc?YAML%3A%3ASyck' +description = """Fast, lightweight YAML loader and dumper. + This module provides a Perl interface to the libsyck data serialization library.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://www.cpan.org/modules/by-module/YAML'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +perlverextra = '' +versionsuffix = '-%s-%s%s' % (perl, perlver,perlverextra) + +dependencies = [ + (perl, perlver, perlverextra), +] + +options = {'modulename': 'YAML::Syck'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000..e0ef7ac9a4 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'yaff' +version = '1.0' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://users.ugent.be/~tovrstra/yaff'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('h5py', '2.1.3', versionsuffix), + ('matplotlib', '1.2.1', versionsuffix), + ('Cython', '0.19.1', versionsuffix), + ('molmod', '1.0', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortversion], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..942cf2610b --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.0.2-ictce-5.3.0.eb @@ -0,0 +1,16 @@ +name = 'zsh' +version = '5.0.2' + +homepage = 'http://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# skip test that fails when zsh is built in non-terminal environment +# see http://www.zsh.org/mla/users/2003/msg00852.html +configopts = '--with-tcsetpgrp' + +moduleclass = 'tools' -- GitLab From b3f250e9e192d959055192e58f92e7b48f100fb8 Mon Sep 17 00:00:00 2001 From: "Wiktor Jurkowski Wiktor.Jurkowski@uni.lu" Date: Thu, 5 Dec 2013 13:57:27 +0100 Subject: [PATCH 094/566] add GATK-2.6-5 & GATK-2.7-4 --- .../g/GATK/GATK-2.6-5-Java-1.7.0_10.eb | 40 +++++++++++++++++++ .../g/GATK/GATK-2.7-4-Java-1.7.0_10.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb create mode 100644 easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb new file mode 100644 index 0000000000..cd3b27bab6 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# 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 = '2.6-5' + +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 = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb new file mode 100644 index 0000000000..e9bb8a2fb7 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# 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 = '2.7-4' + +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 = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From b6aff27f783dff81b8697e4496251d7b9bbc1a33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Dec 2013 14:35:22 +0100 Subject: [PATCH 095/566] add easyconfig for SAMtools with ictce/5.5.0, clean up corresponding goolf easyconfig --- .../SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb | 6 +- .../s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb | 33 ++++++++ .../SAMtools-0.1.19_Makefile-ncurses.patch | 81 +++++++++++++++++++ .../SAMtools_0.1.19_Makefile-ncurses.patch | 46 ----------- .../s/SAMtools/SAMtools_0.1.19_misc.patch | 49 ----------- 5 files changed, 117 insertions(+), 98 deletions(-) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19_Makefile-ncurses.patch delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb index 06c8c4d00c..3f46ced5c1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb @@ -21,13 +21,13 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_BZ2] -source_urls = [('http://sourceforge.net/projects/samtools/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] -patches = ['SAMtools_0.1.19_Makefile-ncurses.patch','SAMtools_0.1.19_misc.patch'] +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] dependencies = [ ('ncurses', '5.9'), - ('zlib', '1.2.8'), + ('zlib', '1.2.7'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb new file mode 100644 index 0000000000..dd1a4bc9dd --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.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 = 'SAMtools' +version = '0.1.19' + +homepage = 'http://samtools.sourceforge.net/' +description = """SAM (Sequence Alignment/Map) format is a generic format +for storing large nucleotide sequence alignments.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-0.1.19_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19_Makefile-ncurses.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19_Makefile-ncurses.patch new file mode 100644 index 0000000000..c750681820 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19_Makefile-ncurses.patch @@ -0,0 +1,81 @@ +--- samtools-0.1.19/Makefile.orig 2013-03-19 08:48:09.000000000 +0100 ++++ samtools-0.1.19/Makefile 2013-12-05 11:39:20.167885410 +0100 +@@ -12,10 +12,10 @@ + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + bam_tview_curses.o bam_tview_html.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses + + .SUFFIXES:.c .o + .PHONY: all lib +@@ -47,10 +47,10 @@ + $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz ++ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz -lpthread + + bgzf.o:bgzf.c bgzf.h + $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ +@@ -81,10 +81,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ +--- samtools-0.1.19/misc/Makefile.orig 2013-03-19 08:48:09.000000000 +0100 ++++ samtools-0.1.19/misc/Makefile 2013-12-05 11:40:21.979700133 +0100 +@@ -28,19 +28,19 @@ + lib: + + bamcheck:bamcheck.o +- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz ++ $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -L$(EBROOTZLIB)/lib -lz + + bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h + $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c + + ace2sam:ace2sam.o +- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz ++ $(CC) $(CFLAGS) -o $@ ace2sam.o -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -49,10 +49,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch deleted file mode 100644 index 98fd2203b8..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_Makefile-ncurses.patch +++ /dev/null @@ -1,46 +0,0 @@ ---- samtools-0.1.19.orig/Makefile 2013-03-19 08:48:09.000000000 +0100 -+++ samtools-0.1.19/Makefile 2013-11-29 13:17:00.210306930 +0100 -@@ -12,10 +12,10 @@ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ - bam_tview_curses.o bam_tview_html.o - PROG= samtools --INCLUDES= -I. -+INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. - SUBDIRS= . bcftools misc --LIBPATH= --LIBCURSES= -lcurses # -lXCurses -+LIBPATH= -L$(EBROOTZLIB)/lib -+LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses - - .SUFFIXES:.c .o - .PHONY: all lib -@@ -44,13 +44,13 @@ - $(AR) -csru $@ $(LOBJS) - - samtools:lib-recur $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread -+ $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -L$(EBROOTZLIB)/lib -lz -lpthread - - razip:razip.o razf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -+ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz - - bgzip:bgzip.o bgzf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread -+ $(CC) $(CFLAGS) -o $@ $^ -L$(EBROOTZLIB)/lib -lz -lpthread - - bgzf.o:bgzf.c bgzf.h - $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ -@@ -81,10 +81,10 @@ - - - libbam.1.dylib-local:$(LOBJS) -- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz -+ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz - - libbam.so.1-local:$(LOBJS) -- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz - - dylib: - @$(MAKE) cleanlocal; \ diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch b/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch deleted file mode 100644 index b3f2a74519..0000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools_0.1.19_misc.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- samtools-0.1.19.orig/misc/Makefile 2013-03-19 08:48:09.000000000 +0100 -+++ samtools-0.1.19/misc/Makefile 2013-11-29 13:34:10.250913354 +0100 -@@ -5,7 +5,8 @@ - DFLAGS= -D_FILE_OFFSET_BITS=64 - OBJS= - PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck --INCLUDES= -I.. -+INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I.. -+LIBPATH= -L$(EBROOTZLIB)/lib - SUBDIRS= . - - .SUFFIXES:.c .o -@@ -28,19 +29,19 @@ - lib: - - bamcheck:bamcheck.o -- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz -+ $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -L$(EBROOTZLIB)/lib -lz - - bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h - $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c - - ace2sam:ace2sam.o -- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz -+ $(CC) $(CFLAGS) -o $@ ace2sam.o -L$(EBROOTZLIB)/lib -lz - - wgsim:wgsim.o -- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz -+ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz - - md5fa:md5.o md5fa.o md5.h ../kseq.h -- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz -+ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz - - md5sum-lite:md5sum-lite.o - $(CC) $(CFLAGS) -o $@ md5sum-lite.o -@@ -49,10 +50,10 @@ - $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c - - maq2sam-short:maq2sam.c -- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz - - maq2sam-long:maq2sam.c -- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz - - md5fa.o:md5.h md5fa.c - $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c -- GitLab From a203b011be7ed6128f74909abf90b8f09613a3c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Dec 2013 14:58:36 +0100 Subject: [PATCH 096/566] add missing zlib easyconfig for ictce/5.5.0 --- .../z/zlib/zlib-1.2.7-ictce-5.5.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb new file mode 100644 index 0000000000..fd81470bdd --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +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': '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')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 3ce5b6defb5c4264c06fb4ea42c7707490a9d959 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Dec 2013 17:12:30 +0100 Subject: [PATCH 097/566] fix typo in Cufflinks easyconfigs --- .../c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb index b12bdd90da..9ab19f3693 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goalf-1.1.0-no-OFED.eb @@ -29,7 +29,7 @@ dependencies = [ ('zlib', '1.2.7'), ] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS/lib}' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb index 370e22c4e2..717fc21c8b 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-goolf-1.4.10.eb @@ -31,7 +31,7 @@ dependencies = [ patches = ['Cufflinks_GCC-4.7.patch'] -configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS/lib}' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' sanity_check_paths = { -- GitLab From 3f1e68fe6483fac2fe543f4be43a6392e3f199dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Dec 2013 17:13:04 +0100 Subject: [PATCH 098/566] add Cufflinks 2.1.1 ictce/5.5.0 easyconfig + required patch (curtosy @JensTimmerman) --- .../Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb | 43 +++++++++++++++++++ .../Cufflinks-2.1.1_init-error.patch | 34 +++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1_init-error.patch diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..79ace6dbc7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1-ictce-5.5.0.eb @@ -0,0 +1,43 @@ +## +# 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 +# Jens Timmerman (Ghent University) +# 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 = '2.1.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cufflinks.cbcb.umd.edu/downloads/'] + +patches = ['Cufflinks-2.1.1_init-error.patch'] + +dependencies = [ + ('Boost', '1.55.0', '-Python-2.7.6'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.0'), + ('zlib', '1.2.7'), +] + +configopts = '--enable-intel64 --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/c/Cufflinks/Cufflinks-2.1.1_init-error.patch b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1_init-error.patch new file mode 100644 index 0000000000..199023308c --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.1.1_init-error.patch @@ -0,0 +1,34 @@ +# patch by Jens Timmerman (Ghent University) +# discussed here: http://stackoverflow.com/questions/20100602/is-initializing-a-reference-of-type-int-not-const-qualified-with-a-value-o +--- src/rounding.h.orig 2013-11-20 18:03:13.211025464 +0100 ++++ src/rounding.h 2013-11-20 18:03:22.850887431 +0100 +@@ -165,29 +165,6 @@ + } + + //-------------------------------------------------------------------------- +- // round alternate +- // Bias: none for sequential calls +- bool _is_up = false; +- template +- FloatType roundalternate( const FloatType& value, int& is_up = _is_up ) +- { +- if ((is_up != is_up)) +- return roundhalfup( value ); +- return roundhalfdown( value ); +- } +- +- //-------------------------------------------------------------------------- +- // symmetric round alternate +- // Bias: none for sequential calls +- template +- FloatType roundalternate0( const FloatType& value, int& is_up = _is_up ) +- { +- if ((is_up != is_up)) +- return roundhalfup0( value ); +- return roundhalfdown0( value ); +- } +- +- //-------------------------------------------------------------------------- + // round random + // Bias: generator's bias + template -- GitLab From a022f97a27fd2c2b96cffb9a661b6227f0431368 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Dec 2013 17:14:40 +0100 Subject: [PATCH 099/566] add ictce/5.5.0 easyconfigs for Bowtie2, TopHat, GMap, HTSeq + dependencies --- .../Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb | 28 +++++++++++++ .../b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb | 28 +++++++++++++ .../e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb | 26 ++++++++++++ .../g/GMAP/GMAP-2013-11-27-ictce-5.5.0.eb | 23 ++++++++++ .../HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb | 29 +++++++++++++ .../t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb | 42 +++++++++++++++++++ 6 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..ab10ddc3e6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-5.5.0-Python-2.7.6.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': '5.5.0'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch'] + +pythonversion = '2.7.6' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..879efdd95f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -0,0 +1,28 @@ +## +# 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 = 'Bowtie2' +version = '2.1.0' +altversions = ['2.0.0-beta6', '2.0.0-beta7', '2.0.1', '2.0.2', '2.1.0'] + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """Bowtie 2 is an ultrafast and memory-efficient tool + for aligning sequencing reads to long reference sequences.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +# N.B. the download option above -> required for sourceforge + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..fb8adaa95f --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.0-ictce-5.5.0.eb @@ -0,0 +1,26 @@ +## +# 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 = 'Eigen' +version = '3.2.0' + +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': 'ictce', 'version': '5.5.0'} +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/g/GMAP/GMAP-2013-11-27-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.5.0.eb new file mode 100644 index 0000000000..bc43d8e9e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +name = 'GMAP' +version = '2013-11-27' + +homepage = 'http://research-pub.gene.com/gmap/' +description = "A Genomic Mapping and Alignment Program for mRNA and EST Sequences" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = ['%(namelower)s-gsnap-%(version)s.tar.gz'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), +] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gmap", "bin/gsnap"], + 'dirs': [], +} + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000..478d636658 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.5.4p5' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.6' +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' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.eb new file mode 100644 index 0000000000..fe60f11c96 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.10-ictce-5.5.0.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/Luxembourg Centre for Systems Biomedicine +# Authors:: Cedric Laczny , Fotis Georgatos , Jens Timmerman +# License:: 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 = 'TopHat' +version = '2.0.10' + +homepage = 'http://tophat.cbcb.umd.edu/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://tophat.cbcb.umd.edu/downloads/'] + +patches = ['tophat_ictce.patch'] + +dependencies = [ + ('Boost', '1.55.0', '-Python-2.7.6'), + ('SAMtools', '0.1.19'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam=$EBROOTSAMTOOLS' + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +parallel = 1 # not sure for a parallel build + +moduleclass = 'bio' -- GitLab From acd1bb013f7146f999951ed41b4b41065675b7fc Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 21:28:51 +0100 Subject: [PATCH 100/566] init gperftools Signed-off-by: Fotis Georgatos --- .../gperftools/gperftools-2.1-goolf-1.4.10.eb | 26 +++++++++++++++++++ .../gperftools/gperftools-2.1-ictce-5.3.0.eb | 26 +++++++++++++++++++ .../l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 21 +++++++++++++++ .../l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 21 +++++++++++++++ 4 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..a532d7cc6b --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +name = "gperftools" +version = "2.1" + +homepage = 'http://code.google.com/p/gperftools/' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://gperftools.googlecode.com/files'] + +dependencies = [ + ('Automake', '1.13.4'), + ('Autoconf', '2.69'), + ('libtool', '2.4.2'), + ('libunwind', '1.1'), +] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..e7a1a41118 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb @@ -0,0 +1,26 @@ +name = "gperftools" +version = "2.1" + +homepage = 'http://code.google.com/p/gperftools/' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://gperftools.googlecode.com/files'] + +dependencies = [ + ('Automake', '1.13.4'), + ('Autoconf', '2.69'), + ('libtool', '2.4.2'), + ('libunwind', '1.1'), +] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..83cc56ad97 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +name = "libunwind" +version = "1.1" + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..d8952f399c --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -0,0 +1,21 @@ +name = "libunwind" +version = "1.1" + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' -- GitLab From b775329a88d4d797f19c949e63a7016161fa62dd Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 5 Dec 2013 22:19:10 +0100 Subject: [PATCH 101/566] init NEdit, Molekel, h4toh5 Signed-off-by: Fotis Georgatos --- .../h4toh5-2.2.2-linux-x86_64-static.eb | 20 +++++++++++++ .../m/Molekel/Molekel-5.4.0_Linux_x86_64.eb | 20 +++++++++++++ .../n/NEdit/NEdit-5.5-Linux-x86.eb | 28 +++++++++++++++++++ 3 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb create mode 100644 easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb create mode 100644 easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb new file mode 100644 index 0000000000..ba4c7ce505 --- /dev/null +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'h4toh5' +version = '2.2.2' +versionsuffix = '-linux-x86_64-static' + +homepage = 'http://www.hdfgroup.org/h4toh5/' +description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, + as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.hdfgroup.org/ftp/HDF5/tools/h4toh5/bin/h4h5tools-2.2.1-linux-x86_64-static.tar.gz +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/bin' % name] +sources = ['%s-%s%s.tar.gz' % ('h4h5tools', version, versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['h5toh4', 'h5toh4']], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb new file mode 100644 index 0000000000..4d43f45e84 --- /dev/null +++ b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb @@ -0,0 +1,20 @@ +easyblock = "Tarball" + +name = "Molekel" +version = "5.4.0" +versionsuffix = "-Linux_x86_64" + +homepage = "http://molekel.cscs.ch/" +description = """Molekel is an open-source multi-platform molecular visualization program.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +sources = ['molekel_%s_%s.tar.gz' % (version.replace('.', '_'), versionsuffix.lower()[1:])] +source_urls = ['ftp://ftp.cscs.ch/out/molekel/molekel_%(version_major_minor)s'] + +sanity_check_paths = { + 'files': ["bin/Molekel"], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb new file mode 100644 index 0000000000..a94cde2423 --- /dev/null +++ b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb @@ -0,0 +1,28 @@ +easyblock = "Tarball" + +name = "NEdit" +version = "5.5" +versionsuffix = "-Linux-x86" + +homepage = "http://www.nedit.org" +description = """NEdit is a multi-purpose text editor for the X Window System, + which combines a standard, easy to use, graphical user interface with the thorough + functionality and stability required by users who edit text eight hours a day.""" + +toolchain = {'version': 'dummy', 'name': 'dummy'} + +subdir = '_'.join(version.split('-')[0].split('.')) +source_urls = ['http://ftp.vim.org/editors/NEdit/v%s/executables' % subdir ] +sources = ["nedit-%s%s.tar.gz" % (version, versionsuffix)] + +sanity_check_paths = { + 'files': ["nc", "nedit"], + 'dirs': [] +} + +modextrapaths = { + 'PATH': '', + 'MANPATH': '', +} + +moduleclass = 'tools' -- GitLab From e9a462c360a2259ad5397952df78dc0b78978731 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 5 Dec 2013 22:42:31 +0100 Subject: [PATCH 102/566] A few more packages needed for the nano course --- .../p/packmol/packmol-13.234-ictce-4.1.13.eb | 25 +++++++++ .../easyconfigs/p/packmol/packmol-ictce.patch | 51 +++++++++++++++++++ .../TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb | 36 +++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/p/packmol/packmol-ictce.patch create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb new file mode 100644 index 0000000000..edf4eb9e27 --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb @@ -0,0 +1,25 @@ +easyblock = "MakeCp" + +name = 'packmol' +version = '13.243' + +homepage = 'http://www.cmbi.ru.nl/molden/' +description = "Packing Optimization for Molecular Dynamics Simulations" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://packmol.googlecode.com/files'] + +patches = [ + 'packmol-ictce.patch' +] + +files_to_copy = [(['packmol'],'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] + +sanity_check_paths={ + 'files': ['bin/packmol', 'COPYING', 'AUTHORS', 'LICENSE'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/packmol/packmol-ictce.patch b/easybuild/easyconfigs/p/packmol/packmol-ictce.patch new file mode 100644 index 0000000000..78904b7b4c --- /dev/null +++ b/easybuild/easyconfigs/p/packmol/packmol-ictce.patch @@ -0,0 +1,51 @@ +--- Makefile 2011-08-02 20:21:59.000000000 +0200 ++++ ../Makefile 2013-12-05 12:23:41.941714435 +0100 +@@ -19,7 +19,7 @@ + # below to the path of your fortran compiler. The parallel version + # must be compiled with gfortran version 4.2 or greater. + # +-FORTRAN = /usr/bin/gfortran ++FORTRAN = /apps/gent/SL6/sandybridge/software/ifort/2011.13.367/bin/intel64/ifort + # + FORTRAN_PARALLEL = gfortran + # +@@ -35,6 +35,7 @@ + # + # Change the flags of the compilation if you want: + # ++ + SERIALFLAGS = -O3 -ffast-math + # + # Flags for the compilation of the parallel version +@@ -49,6 +50,7 @@ + # + # Get the default fortran compiler + # ++ + ifeq ($(FORTRAN),AUTO) + FORTRAN = $(FC) + endif +@@ -69,7 +71,6 @@ + @echo " Flags: $(SERIALFLAGS) " + @echo " ------------------------------------------------------ " + @$(FORTRAN) $(SERIALFLAGS) $(srcall) $(srcserial) -o packmol +- @chmod +x solvate.tcl + @echo " Packmol succesfully built." + @echo " ------------------------------------------------------ " + # +@@ -83,7 +84,6 @@ + @$(FORTRAN_PARALLEL) $(PARALLELFLAGS) $(srcall) $(srcparallel)\ + -o packmol + @chmod +x ppackmol +- @chmod +x solvate.tcl + @echo " ------------------------------------------------------ " + @echo " Packmol succesfully built. Paralell version available. " + @echo " ------------------------------------------------------ " +@@ -96,7 +96,6 @@ + @echo " Flags: -Wunused" + @echo " ------------------------------------------------------ " + @$(FORTRAN) -Wunused $(srcall) $(srcserial) -o packmol +- @chmod +x solvate.tcl + @echo " ------------------------------------------------------ " + @echo " Packmol succesfully built. " + @echo " ------------------------------------------------------ " diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb new file mode 100644 index 0000000000..4a6e691309 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'TAMkin' +version = '1.0.0' + +homepage = 'http://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%s' % version] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), + ('molmod', '1.0', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; export OMP_NUM_THREADS=1; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; nosetests -v test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pythonshortversion], +} + +moduleclass = 'chem' -- GitLab From d740a03c13e4f3eca8d41f550cb9de54473f9c62 Mon Sep 17 00:00:00 2001 From: Andreas Panteli Date: Fri, 6 Dec 2013 14:38:53 +0200 Subject: [PATCH 103/566] Contribute HPL compiled with iomkl toolchain --- .../easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb new file mode 100644 index 0000000000..bf12551602 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb @@ -0,0 +1,19 @@ +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': 'iomkl', 'version': '4.6.13'} +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 07ae2978876ef405b527bf03e3668e51212637ff Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Dec 2013 16:09:36 +0100 Subject: [PATCH 104/566] Bison: update to 2.7 with ictce-5.5.0 --- .../b/Bison/Bison-2.7-ictce-5.5.0.eb | 20 ++++++++++++++++ .../easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 23 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb new file mode 100644 index 0000000000..5224af1090 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] + +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/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb new file mode 100644 index 0000000000..a66d14fe08 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/m4'] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 0b194f9191ca461bdba8948eacb8cd4de90f8341 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Dec 2013 16:10:01 +0100 Subject: [PATCH 105/566] Flex: updated to 2.5.37 with ictce-5.5.0 --- .../easyconfigs/f/flex/flex-2.5.37-ictce-5.5.0.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.5.0.eb new file mode 100644 index 0000000000..add73d9286 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.5.0.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' -- GitLab From 2157087f4e8f7658b41ca664f4bbd881d2e69da5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Dec 2013 16:10:31 +0100 Subject: [PATCH 106/566] libxc: update to 2.0.1 with ictce-5.5.0 CP2K needs version 2.0.1 --- .../l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..53b0b9a430 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -0,0 +1,31 @@ +name = 'libxc' +version = '2.0.1' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'opt': True} + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --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 15ef08a0a811f36122ce695bd86e051efece9492 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 6 Dec 2013 16:10:59 +0100 Subject: [PATCH 107/566] FFTW: updated to 3.3.3 with ictce-5.5.0 --- .../f/FFTW/FFTW-3.3.3-ictce-5.5.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..0ae947ce7f --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +name = 'FFTW' +version = '3.3.3' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--enable-openmp --with-pic" + +# no quad precision, requires GCC v4.6 or higher +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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' -- GitLab From 6213c487ee673ba31d56528911f2a7c24c452a95 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 7 Dec 2013 01:37:09 +0100 Subject: [PATCH 108/566] init PRACE Signed-off-by: Fotis Georgatos --- .../p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 36 +++++++++++++++++++ .../p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb 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 new file mode 100644 index 0000000000..dedd3bb32d --- /dev/null +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.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/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of HPCBIOS project: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = "Toolchain" + +name = 'PRACE' +version = '20130605' + +homepage = 'http://www.prace-ri.eu/PRACE-Common-Production' +description = """The PRACE Common Production Environment (PCPE) is a set of software tools and libraries + that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment + variables that try to make compilation on all sites as homogeneous and simple as possible.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [ + ('make', '3.82'), + ('Java', '1.7.0_10', '', True), + ('Bash', '4.2'), + ('tcsh', '6.18.01'), + ('Tcl', '8.5.12'), + ('Tk', '8.5.12'), + ('netCDF', '4.1.3'), # this one will also bring in HDF5 + ('Perl', '5.16.3'), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000..a795cc27ab --- /dev/null +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.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/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of HPCBIOS project: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = "Toolchain" + +name = 'PRACE' +version = '20130605' + +homepage = 'http://www.prace-ri.eu/PRACE-Common-Production' +description = """The PRACE Common Production Environment (PCPE) is a set of software tools and libraries + that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment + variables that try to make compilation on all sites as homogeneous and simple as possible.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +dependencies = [ + ('make', '3.82'), + ('Java', '1.7.0_10', '', True), + ('Bash', '4.2'), + ('tcsh', '6.18.01'), + ('Tcl', '8.5.12'), + ('Tk', '8.5.12'), + ('netCDF', '4.1.3'), # this one will also bring in HDF5 + ('Perl', '5.16.3'), +] + +moduleclass = 'toolchain' -- GitLab From 815637d56fd231109d73e11170be7f1024c3dcb7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 7 Dec 2013 11:53:24 +0100 Subject: [PATCH 109/566] init Lua --- .../l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb | 24 +++++++++++++++++++ .../lua-5.1.4.5_Makefile-static-linking.patch | 12 ++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb new file mode 100644 index 0000000000..b5e1297c18 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +name = "Lua" +version = "5.1.4-5" + +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': 'goolf', 'version': '1.4.10'} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +# patches = ['lua-5.1.4.5_Makefile-static-linking.patch'] # buggy on Debian? + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" diff --git a/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch b/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch new file mode 100644 index 0000000000..761bb38436 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch @@ -0,0 +1,12 @@ +diff -ru lua-5.1.4.5.orig/lua/src/Makefile.in lua-5.1.4.5/lua/src/Makefile.in +--- lua-5.1.4.5.orig/lua/src/Makefile.in 2011-02-18 19:49:01.000000000 +0100 ++++ lua-5.1.4.5/lua/src/Makefile.in 2013-06-02 13:22:28.601496000 +0200 +@@ -98,7 +98,7 @@ + $(MAKE) all MYCFLAGS= + + linux: +- $(MAKE) all MYCFLAGS="$(MYCFLAGS) -DLUA_USE_LINUX" MYLIBS="-Wl,-E -ldl @LIBS@ -lncurses" ++ $(MAKE) all MYCFLAGS="$(MYCFLAGS) -DLUA_USE_LINUX" MYLIBS="-Wl,-E -ldl -Wl,-Bstatic @LIBS@ -lncurses -Wl,-Bdynamic" + + macosx: + # $(MAKE) all MYCFLAGS=-DLUA_USE_MACOSX -- GitLab From a2c54f59e9897c874e29ae533ae61b198cac01e1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 7 Dec 2013 11:53:35 +0100 Subject: [PATCH 110/566] init Lmod --- .../l/Lmod/Lmod-5.2-goolf-1.4.10.eb | 22 +++++++++++++++++++ easybuild/easyconfigs/l/Lmod/sourceme | 18 +++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/l/Lmod/sourceme diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..113bfdc903 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb @@ -0,0 +1,22 @@ +name = "Lmod" +version = "5.2" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +dependencies = [("Lua", "5.1.4-5")] + +sanity_check_paths = { + 'files': ["lmod/%s/init/profile" % version], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme new file mode 100644 index 0000000000..4d8c0c4fe7 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -0,0 +1,18 @@ +## Contributed by Fotis Georgatos, as means to help others wishing to ride on Lmod + +PREFIX=/home/users/fgeorgatos/.local/easybuild +PREFIXLUA=$PREFIX/software/lua/5.1.4-5-goolf-1.4.10 +PREFIXLMOD=$PREFIX/software/Lmod/5.2-goolf-1.4.10/lmod/5.2 + +export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH + +## Uncommend this if things don't work as expected +# lua -v +# ls -las `which lua` +# ls -las $PREFIXLMOD/init/profile + +source $PREFIXLMOD/init/profile + +export PAGER=cat # Keep it simple, for a start +export LMOD_IGNORE_CACHE=OHYES # Keep it simple, for a start +export LMOD_COLORIZE=YES # YMMV -- GitLab From 6f4374a17788cb5df8e12d41ae7e12ffbfb247c4 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 7 Dec 2013 12:00:37 +0100 Subject: [PATCH 111/566] finalize script to help transition to Lmod --- easybuild/easyconfigs/l/Lmod/sourceme | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 4d8c0c4fe7..9f5c723975 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -1,6 +1,7 @@ -## Contributed by Fotis Georgatos, as means to help others wishing to ride on Lmod +## Contributed by Fotis Georgatos , as means to help others wishing to ride on Lmod -PREFIX=/home/users/fgeorgatos/.local/easybuild +## Remember to change the following, as per individual case +PREFIX=${PREFIX:-"/home/users/fgeorgatos/.local/easybuild"} PREFIXLUA=$PREFIX/software/lua/5.1.4-5-goolf-1.4.10 PREFIXLMOD=$PREFIX/software/Lmod/5.2-goolf-1.4.10/lmod/5.2 @@ -16,3 +17,5 @@ source $PREFIXLMOD/init/profile export PAGER=cat # Keep it simple, for a start export LMOD_IGNORE_CACHE=OHYES # Keep it simple, for a start export LMOD_COLORIZE=YES # YMMV + +echo "Now, try fi. `module avail -d compiler` and observe output`" -- GitLab From 85ca49764c8907f002f4fab46a521211e2733f29 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Dec 2013 18:41:06 +0100 Subject: [PATCH 112/566] CP2K: updated to version 20131205 --- ...2K-20131205-fix_compile_date_lastcvs.patch | 11 ++++++ .../c/CP2K/CP2K-20131205-ictce-5.5.0.eb | 38 +++++++++++++++++++ .../c/CP2K/ifort-compiler-bug-fix.patch | 12 ++++++ 3 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000..05fe24dd1d --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- cp2k.orig/cp2k/makefiles/Makefile 2012-08-21 14:35:17.000000000 +0300 ++++ cp2k/cp2k/makefiles/Makefile 2013-11-12 12:41:29.361582641 +0200 +@@ -194,7 +194,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g')\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb new file mode 100644 index 0000000000..a4d400d6d0 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '20131205' + +homepage = 'http://cp2k.berlios.de/index.html' +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['CP2K-%(version)s.tar.gz'] + +patches = [ + 'ifort-compiler-bug-fix.patch', + 'CP2K-%(version)s-fix_compile_date_lastcvs.patch', +] + +## use FFTW, with FFTACML there are extra failures in regtests +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.0.1'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# 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: 13/2450 segfault +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch b/easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch new file mode 100644 index 0000000000..20b595d455 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch @@ -0,0 +1,12 @@ +# workaround for ifort bug +# https://groups.google.com/forum/#!topic/cp2k/LorI2Z4pQgc +--- cp2k.orig/cp2k/src/dbcsr_lib/dbcsr_error_handling.F 2013-12-05 11:46:53.201980584 +0100 ++++ cp2k/cp2k/src/dbcsr_lib/dbcsr_error_handling.F 2013-12-05 16:28:45.572524631 +0100 +@@ -20,7 +20,6 @@ + !$ USE OMP_LIB + + IMPLICIT NONE +- PRIVATE + + ! procedures + PUBLIC :: dbcsr_error_set, dbcsr_error_stop, dbcsr_error_print_stack -- GitLab From 33219003c04a1300cf40e869632b2bbe5e19b13b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Dec 2013 18:41:32 +0100 Subject: [PATCH 113/566] CP2K: added version 2.4.0 with ictce-5.5.0 --- .../c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..037d12025a --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb @@ -0,0 +1,40 @@ +name = 'CP2K' +version = '2.4.0' + +homepage = 'http://cp2k.berlios.de/index.html' +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'do_regtest_nocompile.patch', + 'ifort-compiler-bug-fix.patch', + 'CP2K-20131205-fix_compile_date_lastcvs.patch', +] + +## use FFTW, with FFTACML there are extra failures in regtests +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.0.1'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# 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' -- GitLab From 24dc3f1aa69e531db601e8a2c7a25a2260eb1689 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sat, 7 Dec 2013 22:04:02 +0100 Subject: [PATCH 114/566] M4: remove old patch from 1.4.17 --- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index a66d14fe08..bd161358d2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -11,8 +11,6 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/m4'] -patches = ['M4-%(version)s-no-gets.patch'] - configopts = "--enable-cxx" sanity_check_paths = { -- GitLab From 9d40ffed5bebce469b47a83db4676b9084660e70 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 7 Dec 2013 23:02:08 +0100 Subject: [PATCH 115/566] rewire defaults for Lmod towards GCC-4.8.2 --- .../easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb | 22 +++++++++++++++++ easybuild/easyconfigs/l/Lmod/sourceme | 10 ++++---- .../l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb | 24 +++++++++++++++++++ 3 files changed, 52 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb new file mode 100644 index 0000000000..37839b6a29 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb @@ -0,0 +1,22 @@ +name = "Lmod" +version = "5.2" + +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/'] + +dependencies = [("Lua", "5.1.4-5")] + +sanity_check_paths = { + 'files': ["lmod/%s/init/profile" % version], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 9f5c723975..c0d80e79d7 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -1,9 +1,11 @@ ## Contributed by Fotis Georgatos , as means to help others wishing to ride on Lmod +# +# prereq: Lmod/5.2-GCC-4.8.2 ## Remember to change the following, as per individual case -PREFIX=${PREFIX:-"/home/users/fgeorgatos/.local/easybuild"} -PREFIXLUA=$PREFIX/software/lua/5.1.4-5-goolf-1.4.10 -PREFIXLMOD=$PREFIX/software/Lmod/5.2-goolf-1.4.10/lmod/5.2 +PREFIX=${PREFIX:-"$HOME/.local/easybuild"} +PREFIXLUA=$PREFIX/software/lua/5.1.4-5-GCC-4.8.2 +PREFIXLMOD=$PREFIX/software/Lmod/5.2-GCC-4.8.2/lmod/5.2 export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH @@ -18,4 +20,4 @@ export PAGER=cat # Keep it simple, for a start export LMOD_IGNORE_CACHE=OHYES # Keep it simple, for a start export LMOD_COLORIZE=YES # YMMV -echo "Now, try fi. `module avail -d compiler` and observe output`" +echo 'Now, try fi. `module avail -d compiler` and observe output`' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb new file mode 100644 index 0000000000..536d1c4346 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb @@ -0,0 +1,24 @@ +name = "Lua" +version = "5.1.4-5" + +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': '4.8.2'} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +# patches = ['lua-5.1.4.5_Makefile-static-linking.patch'] # buggy on Debian? + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" -- GitLab From 8a95ad43ec51dd182e6c21cfaa39e7f3b08b5916 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 9 Dec 2013 11:26:41 +0100 Subject: [PATCH 116/566] libffi patch is needed after all --- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 ++ .../python-2.7.6_libffi_int128_icc.patch | 27 +++++++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch 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 adc6635723..b27de9a63f 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 @@ -13,6 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] +patches = ['python-%(version)s_libffi_int128_icc.patch'] + # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch b/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch new file mode 100644 index 0000000000..c639c75c09 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch @@ -0,0 +1,27 @@ +diff -ur Python-2.7.4.orig/Modules/_ctypes/libffi/src/x86/ffi64.c Python-2.7.4/Modules/_ctypes/libffi/src/x86/ffi64.c +--- Python-2.7.4.orig/Modules/_ctypes/libffi/src/x86/ffi64.c 2013-04-06 16:02:35.000000000 +0200 ++++ Python-2.7.4/Modules/_ctypes/libffi/src/x86/ffi64.c 2013-05-13 10:28:22.935090082 +0200 +@@ -56,6 +56,8 @@ + UINT128 i128; + }; + ++typedef struct { int64_t m[2]; } __int128_t; ++ + struct register_args + { + /* Registers for argument passing. */ +@@ -507,10 +509,12 @@ + break; + case X86_64_SSE_CLASS: + case X86_64_SSEDF_CLASS: +- reg_args->sse[ssecount++].i64 = *(UINT64 *) a; ++ reg_args->sse[ssecount++].m[0] = *(UINT64 *) a; ++ reg_args->sse[ssecount++].m[1] = 0; + break; + case X86_64_SSESF_CLASS: +- reg_args->sse[ssecount++].i32 = *(UINT32 *) a; ++ reg_args->sse[ssecount++].m[0] = *(UINT32 *) a; ++ reg_args->sse[ssecount++].m[1] = 0; + break; + default: + abort(); -- GitLab From 35c504622aa5e0a784bcdcd93eb5497ab14ef625 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 9 Dec 2013 15:03:40 +0100 Subject: [PATCH 117/566] init ispc & mcpp Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb | 29 ++++++++++++++++++++++ easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb | 29 ++++++++++++++++++++++ easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb | 20 +++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb create mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb create mode 100644 easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb new file mode 100644 index 0000000000..eed358ec55 --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb @@ -0,0 +1,29 @@ + +easyblock = 'Tarball' + +name = 'ispc' +version = '1.3.0' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for "single program, multiple data" (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. https://github.com/downloads/ispc/ispc/ispc-v1.3.0-linux.tar.gz +# or better for later: https://github.com/ispc/ispc/tarball/v1.3.0 +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = ['https://github.com/downloads/ispc/ispc/'] + +sanity_check_paths = { + 'files': ["ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb new file mode 100644 index 0000000000..1cb61c35ec --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb @@ -0,0 +1,29 @@ + +easyblock = 'Tarball' + +name = 'ispc' +version = '1.5.0' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for "single program, multiple data" (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. https://github.com/downloads/ispc/ispc/ispc-v1.5.0-linux.tar.gz +# or better for later: https://github.com/ispc/ispc/tarball/v1.5.0 +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] + +sanity_check_paths = { + 'files': ["ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb b/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb new file mode 100644 index 0000000000..60b167dc2a --- /dev/null +++ b/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb @@ -0,0 +1,20 @@ + +name = 'mcpp' +version = '2.7.2' + +homepage = 'http://mcpp.sourceforge.net/' +description = """MCPP is a portable C/C++ preprocessor, supporting GCC, Visual C++, etc. + Its source is highly configurable and can generate executables of various specs. + It accompanies a validation suite to check preprocessor's conformance and quality exhaustively.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} # rewire towards your favourite compiler + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +sanity_check_paths = { + 'files': ["bin/mcpp"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From 8bcb6cf5d05a27a02f46f9a41dca8ec3070f6e06 Mon Sep 17 00:00:00 2001 From: admin6 Date: Mon, 9 Dec 2013 15:14:11 +0100 Subject: [PATCH 118/566] libffi was fixed but has a different problem, so switched the patch --- .../easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb | 5 ++++- .../p/Python/libffi-3.0.13_include-xmmintrin.patch | 11 +++++++++++ 5 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch 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 7031a25f57..214f9caf18 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 @@ -13,7 +13,7 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +patches = ['libffi-3.0.13_include-xmmintrin.patch'] # python needs bzip2 to build the bz2 package dependencies = [ 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 3f66b26c69..43582a47e8 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 @@ -13,7 +13,7 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +patches = ['libffi-3.0.13_include-xmmintrin.patch'] # python needs bzip2 to build the bz2 package dependencies = [ 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 a7284262e3..9a2a8fbdbb 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 @@ -13,7 +13,7 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +patches = ['libffi-3.0.13_include-xmmintrin.patch'] # python needs bzip2 to build the bz2 package dependencies = [ 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 671d704218..a621200714 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 @@ -13,7 +13,10 @@ scipyversion = '0.13.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = [ + 'libffi-3.0.13_include-xmmintrin.patch', +] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch b/easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch new file mode 100644 index 0000000000..6b03e80c46 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch @@ -0,0 +1,11 @@ +diff -ru Modules/_ctypes/libffi/src/x86/ffi64.c libffi-3.0.13/src/x86/ffi64.c +--- Modules.orig/_ctypes/libffi/src/x86/ffi64.c 2013-03-16 12:19:39.000000000 +0100 ++++ Modules/_ctypes/libffi/src/x86/ffi64.c 2013-08-14 14:42:38.000000000 +0200 +@@ -39,6 +39,7 @@ + #define MAX_SSE_REGS 8 + + #if defined(__INTEL_COMPILER) ++#include "xmmintrin.h" + #define UINT128 __m128 + #else + #if defined(__SUNPRO_C) -- GitLab From 4294153a5db6943ea1d5c528c9a3d4c671e24241 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 9 Dec 2013 22:35:22 +0100 Subject: [PATCH 119/566] add Lua & Lmod for GCC/4.7.2 Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb | 22 +++++++++++++++++++ .../l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb new file mode 100644 index 0000000000..5567974299 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +name = "Lmod" +version = "5.2" + +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': '4.7.2'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +dependencies = [("Lua", "5.1.4-5")] + +sanity_check_paths = { + 'files': ["lmod/%s/init/profile" % version], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb new file mode 100644 index 0000000000..a877d56895 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb @@ -0,0 +1,22 @@ +name = "Lua" +version = "5.1.4-5" + +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': '4.7.2'} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" -- GitLab From e28f79c5eedae6c6575e97cff9e40ccf81ba75ca Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 9 Dec 2013 23:05:57 +0100 Subject: [PATCH 120/566] add ncurses as Lua dep Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb index a877d56895..6089259852 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} 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': [] -- GitLab From e7ac98ba8e16a3b58c18b2b9b5873ec45b50ecb5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 10 Dec 2013 06:15:54 +0100 Subject: [PATCH 121/566] Revert "add ncurses as Lua dep" This reverts commit e28f79c5eedae6c6575e97cff9e40ccf81ba75ca. --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb index 6089259852..a877d56895 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb @@ -14,8 +14,6 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} 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': [] -- GitLab From 413dc7f439069e691eac60b5640c3851f29e1bc0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 10 Dec 2013 14:24:52 +0100 Subject: [PATCH 122/566] CP2K: small change to be compatible with bash 3.x --- .../CP2K/CP2K-20131205-bash-3-comp-fix.patch | 39 +++++++++++++++++++ .../c/CP2K/CP2K-20131205-ictce-5.5.0.eb | 1 + 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch new file mode 100644 index 0000000000..68932901df --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch @@ -0,0 +1,39 @@ +diff -urN cp2k.orig/cp2k/tools/regtesting/do_regtest cp2k/cp2k/tools/regtesting/do_regtest +--- cp2k.orig/cp2k/tools/regtesting/do_regtest 2013-12-05 11:45:55.804241967 +0100 ++++ cp2k/cp2k/tools/regtesting/do_regtest 2013-12-10 14:19:56.913623248 +0100 +@@ -381,7 +381,7 @@ + # echo "cp2k is now ${cp2k_lines} lines .F" + + # Using svn2cl.pl to generate GNU like ChangeLog +- ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_new} &>>${error_description_file} ++ ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_new} 2>&1 >>${error_description_file} + + line1="$(head -n 1 ${changelog})" + nline=$(grep -n "${line1}" ${changelog_new} | head -n 1 | cut -f 1 -d:) +@@ -421,7 +421,7 @@ + echo "svn update tests went fine" + + # Using svn2cl.pl to generate GNU like ChangeLog +- ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_tests_new} &>>${error_description_file} ++ ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_tests_new} 2>&1 >>${error_description_file} + + line1="$(head -n 1 ${changelog_tests})" + nline=$(grep -n "${line1}" ${changelog_tests_new} | head -n 1 | cut -f 1 -d:) +@@ -464,7 +464,7 @@ + # make realclean + if [[ ${quick} != "quick" ]]; then + cd ${dir_base}/${cp2k_dir}/makefiles +- ${make} realclean ${ARCH_SPEC} VERSION=${cp2k_version} &>>${make_out} ++ ${make} realclean ${ARCH_SPEC} VERSION=${cp2k_version} 2>&1 >>${make_out} + if (( $? )); then + echo "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" >>${error_description_file} + cat ${make_out} >>${error_description_file} +@@ -485,7 +485,7 @@ + echo "${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version}" + echo "(make output is written to ${make_out})" + cd ${dir_base}/${cp2k_dir}/makefiles +- ${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version} &>>${make_out} ++ ${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version} 2>&1 >>${make_out} + if (( $? )); then + echo "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" >>${error_description_file} + cat ${make_out} >>${error_description_file} diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb index a4d400d6d0..c42685d01d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb @@ -15,6 +15,7 @@ sources = ['CP2K-%(version)s.tar.gz'] patches = [ 'ifort-compiler-bug-fix.patch', 'CP2K-%(version)s-fix_compile_date_lastcvs.patch', + 'CP2K-%(version)s-bash-3-comp-fix.patch', ] ## use FFTW, with FFTACML there are extra failures in regtests -- GitLab From 634f9f1daac41b2d1622f281e4e842ddcf885efb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2013 18:20:54 +0100 Subject: [PATCH 123/566] explicitly enable MPI in GROMACS goolf(c) easyconfigs, indicate to use external BLAS/LAPACK (?) --- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb | 7 +++++-- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb | 5 ++++- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb index 86275344ab..02fb60a067 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb @@ -21,6 +21,7 @@ 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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz sources = [ @@ -34,11 +35,13 @@ source_urls = [ builddependencies = [('CMake', '2.8.4')] -configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" -runtest = 'check' +configopts = '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' # explicitely disable CUDA support, i.e. avoid that GROMACS find and uses a system-wide CUDA compiler # CUDA and GCC v4.7 don't play well together configopts += ' -DGMX_GPU=OFF' +configopts += "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" +runtest = 'check' + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb index 07428ab1c0..256c0d975a 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb @@ -21,6 +21,7 @@ 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': 'goolfc', 'version': '1.3.12'} +toolchainopts = {'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz sources = [ @@ -34,7 +35,9 @@ source_urls = [ builddependencies = [('CMake', '2.8.4')] -configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" +configopts = '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' + +configopts += "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" runtest = 'check' moduleclass = 'bio' -- GitLab From 161c74eefb69948788b3424b1d378d525973cfff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2013 18:21:13 +0100 Subject: [PATCH 124/566] add ictce-5.5.0 easyconfig for GROMACS v4.6.5 --- .../g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb new file mode 100644 index 0000000000..3e5a3d3c07 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb @@ -0,0 +1,50 @@ +## +# 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 +## + +easyblock = 'CMakeMake' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +configopts = '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" ' +configopts += '-DMKL_LIBRARIES="$EBROOTMKL/mkl/lib/intel64/libmkl.a;$EBROOTMKL/mkl/lib/intel64/libmkl_lapack.a" ' +configopts += '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' + +# explicitely disable CUDA support, i.e. avoid that GROMACS find and uses a system-wide CUDA compiler +configopts += '-DGMX_GPU=OFF ' + +configopts += '-DREGRESSIONTEST_PATH="%(builddir)s/regressiontests-%(version)s" ' +runtest = 'check' + +moduleclass = 'bio' -- GitLab From 363a30273d1521bb31e1192f86cc4b7418718c54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Dec 2013 18:58:24 +0100 Subject: [PATCH 125/566] add easyconfig file for EB v1.9.0 --- .../e/EasyBuild/EasyBuild-1.9.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb new file mode 100644 index 0000000000..30a0e1cfd6 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '1.9.0' + +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/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 b5377b769e14a97069891281a1e7387c5c5a40b3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 11 Dec 2013 16:06:08 +0100 Subject: [PATCH 126/566] Update CP2K to 20131205 and delete 20131205 The bash fix has already been accepted upstream, so upgrade version to that svn. --- .../CP2K/CP2K-20131205-bash-3-comp-fix.patch | 39 ------------------- ...K-20131211-fix_compile_date_lastcvs.patch} | 0 ...-5.5.0.eb => CP2K-20131211-ictce-5.5.0.eb} | 5 +-- 3 files changed, 2 insertions(+), 42 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch rename easybuild/easyconfigs/c/CP2K/{CP2K-20131205-fix_compile_date_lastcvs.patch => CP2K-20131211-fix_compile_date_lastcvs.patch} (100%) rename easybuild/easyconfigs/c/CP2K/{CP2K-20131205-ictce-5.5.0.eb => CP2K-20131211-ictce-5.5.0.eb} (91%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch deleted file mode 100644 index 68932901df..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-bash-3-comp-fix.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -urN cp2k.orig/cp2k/tools/regtesting/do_regtest cp2k/cp2k/tools/regtesting/do_regtest ---- cp2k.orig/cp2k/tools/regtesting/do_regtest 2013-12-05 11:45:55.804241967 +0100 -+++ cp2k/cp2k/tools/regtesting/do_regtest 2013-12-10 14:19:56.913623248 +0100 -@@ -381,7 +381,7 @@ - # echo "cp2k is now ${cp2k_lines} lines .F" - - # Using svn2cl.pl to generate GNU like ChangeLog -- ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_new} &>>${error_description_file} -+ ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_new} 2>&1 >>${error_description_file} - - line1="$(head -n 1 ${changelog})" - nline=$(grep -n "${line1}" ${changelog_new} | head -n 1 | cut -f 1 -d:) -@@ -421,7 +421,7 @@ - echo "svn update tests went fine" - - # Using svn2cl.pl to generate GNU like ChangeLog -- ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_tests_new} &>>${error_description_file} -+ ${dir_base}/${cp2k_dir}/tools/svn2cl/svn2cl.sh --limit 100 -i -o ${changelog_tests_new} 2>&1 >>${error_description_file} - - line1="$(head -n 1 ${changelog_tests})" - nline=$(grep -n "${line1}" ${changelog_tests_new} | head -n 1 | cut -f 1 -d:) -@@ -464,7 +464,7 @@ - # make realclean - if [[ ${quick} != "quick" ]]; then - cd ${dir_base}/${cp2k_dir}/makefiles -- ${make} realclean ${ARCH_SPEC} VERSION=${cp2k_version} &>>${make_out} -+ ${make} realclean ${ARCH_SPEC} VERSION=${cp2k_version} 2>&1 >>${make_out} - if (( $? )); then - echo "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" >>${error_description_file} - cat ${make_out} >>${error_description_file} -@@ -485,7 +485,7 @@ - echo "${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version}" - echo "(make output is written to ${make_out})" - cd ${dir_base}/${cp2k_dir}/makefiles -- ${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version} &>>${make_out} -+ ${make} -j $((maxtasks)) ${ARCH_SPEC} VERSION=${cp2k_version} 2>&1 >>${make_out} - if (( $? )); then - echo "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx" >>${error_description_file} - cat ${make_out} >>${error_description_file} diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-fix_compile_date_lastcvs.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/CP2K-20131205-fix_compile_date_lastcvs.patch rename to easybuild/easyconfigs/c/CP2K/CP2K-20131211-fix_compile_date_lastcvs.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb similarity index 91% rename from easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb rename to easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb index c42685d01d..b04e8859be 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131205-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb @@ -1,5 +1,5 @@ name = 'CP2K' -version = '20131205' +version = '20131211' homepage = 'http://cp2k.berlios.de/index.html' description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular @@ -10,12 +10,11 @@ classical pair and many-body potentials. """ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} -sources = ['CP2K-%(version)s.tar.gz'] +sources = [SOURCE_TAR_BZ2] patches = [ 'ifort-compiler-bug-fix.patch', 'CP2K-%(version)s-fix_compile_date_lastcvs.patch', - 'CP2K-%(version)s-bash-3-comp-fix.patch', ] ## use FFTW, with FFTACML there are extra failures in regtests -- GitLab From 7f8834f06e3a46a0dfc3d367c4d0db561aab15fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 16:28:04 +0100 Subject: [PATCH 127/566] get rid of patch files for Molden, just use makeopts --- .../m/Molden/Molden-5.0-ictce-4.1.13.eb | 5 +---- .../easyconfigs/m/Molden/Molden-5.0-ictce.patch | 15 --------------- .../m/Molden/Molden-5.0-molden-only.patch | 13 ------------- 3 files changed, 1 insertion(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch delete mode 100644 easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb index 76a1b7f50f..ea8f241450 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce-4.1.13.eb @@ -13,10 +13,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['%(namelower)s%(version)s.tar.gz'] source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] -patches = [ - 'Molden-%(version)s-ictce.patch', - 'Molden-%(version)s-molden-only.patch', -] +makeopts = 'CC="$CC" FC="$F90" molden' files_to_copy = [(['molden'],'bin'), 'CopyRight', 'README', 'REGISTER'] diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch b/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch deleted file mode 100644 index 2897b802f0..0000000000 --- a/easybuild/easyconfigs/m/Molden/Molden-5.0-ictce.patch +++ /dev/null @@ -1,15 +0,0 @@ -# Because there is no configure script, one has to specify the compiler manually. -# By Toon Verstraelen ---- molden5.0-orig/makefile 2013-11-28 16:02:04.563545000 +0100 -+++ molden5.0/makefile 2013-11-28 16:08:13.606238000 +0100 -@@ -13,8 +13,8 @@ - # Disregard compiler warnings on rdmolf.f - # - # --CC = cc --FC = gfortran -+CC = icc -+FC = ifort - LIBS = -lX11 -lm - LDR = ${FC} - LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm diff --git a/easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch b/easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch deleted file mode 100644 index feffc8a8e0..0000000000 --- a/easybuild/easyconfigs/m/Molden/Molden-5.0-molden-only.patch +++ /dev/null @@ -1,13 +0,0 @@ -# Only compile the molden binary to keep things simple -# By Toon Verstraelen (toon.verstraelen@ugent.be) ---- molden5.0-orig/makefile 2013-11-28 16:02:04.563545000 +0100 -+++ molden5.0/makefile 2013-11-28 16:08:13.606238000 +0100 -@@ -252,7 +252,7 @@ - # - #LIBSG = -L/usr/X11R6/lib -Wl,-framework -Wl,GLUT -Wl,-framework -Wl,OpenGL -Wl,-framework -Wl,Cocoa -lGLU -lGL -lXmu -lX11 -lm - --all: molden gmolden ambfor/ambfor ambfor/ambmd surf/surf -+all: molden - - - molden: $(OBJS) mpdum.o xwin.o -- GitLab From d632babf1656576780732d9df4907a9aa00817e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 16:28:21 +0100 Subject: [PATCH 128/566] fix typo/style --- .../n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb index 6bd0ab86b5..6f22931653 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.1.13-Python-2.7.3.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] +patches = ['numpy-%(version)s_distutils_multiple-lib-dirs.patch'] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb index b50e725a50..94e60465eb 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.3.2-ictce-5.5.0-Python-2.7.5.eb @@ -22,7 +22,7 @@ patches = [ builddependencies = [('CMake', '2.8.12')] python = "Python" -pythonversion = '2.7.7' +pythonversion = '2.7.5' pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -- GitLab From f2304be427ea5d223449077317dfb02f42433329 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 16:29:23 +0100 Subject: [PATCH 129/566] get rid of patch file for packmol, use makeopts instead --- .../p/packmol/packmol-13.234-ictce-4.1.13.eb | 4 +- .../easyconfigs/p/packmol/packmol-ictce.patch | 51 ------------------- 2 files changed, 1 insertion(+), 54 deletions(-) delete mode 100644 easybuild/easyconfigs/p/packmol/packmol-ictce.patch diff --git a/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb b/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb index edf4eb9e27..839e36a38e 100644 --- a/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/packmol/packmol-13.234-ictce-4.1.13.eb @@ -11,9 +11,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] source_urls = ['https://packmol.googlecode.com/files'] -patches = [ - 'packmol-ictce.patch' -] +makeopts = 'FORTRAN="$F90"' files_to_copy = [(['packmol'],'bin'), 'COPYING', 'AUTHORS', 'LICENSE'] diff --git a/easybuild/easyconfigs/p/packmol/packmol-ictce.patch b/easybuild/easyconfigs/p/packmol/packmol-ictce.patch deleted file mode 100644 index 78904b7b4c..0000000000 --- a/easybuild/easyconfigs/p/packmol/packmol-ictce.patch +++ /dev/null @@ -1,51 +0,0 @@ ---- Makefile 2011-08-02 20:21:59.000000000 +0200 -+++ ../Makefile 2013-12-05 12:23:41.941714435 +0100 -@@ -19,7 +19,7 @@ - # below to the path of your fortran compiler. The parallel version - # must be compiled with gfortran version 4.2 or greater. - # --FORTRAN = /usr/bin/gfortran -+FORTRAN = /apps/gent/SL6/sandybridge/software/ifort/2011.13.367/bin/intel64/ifort - # - FORTRAN_PARALLEL = gfortran - # -@@ -35,6 +35,7 @@ - # - # Change the flags of the compilation if you want: - # -+ - SERIALFLAGS = -O3 -ffast-math - # - # Flags for the compilation of the parallel version -@@ -49,6 +50,7 @@ - # - # Get the default fortran compiler - # -+ - ifeq ($(FORTRAN),AUTO) - FORTRAN = $(FC) - endif -@@ -69,7 +71,6 @@ - @echo " Flags: $(SERIALFLAGS) " - @echo " ------------------------------------------------------ " - @$(FORTRAN) $(SERIALFLAGS) $(srcall) $(srcserial) -o packmol -- @chmod +x solvate.tcl - @echo " Packmol succesfully built." - @echo " ------------------------------------------------------ " - # -@@ -83,7 +84,6 @@ - @$(FORTRAN_PARALLEL) $(PARALLELFLAGS) $(srcall) $(srcparallel)\ - -o packmol - @chmod +x ppackmol -- @chmod +x solvate.tcl - @echo " ------------------------------------------------------ " - @echo " Packmol succesfully built. Paralell version available. " - @echo " ------------------------------------------------------ " -@@ -96,7 +96,6 @@ - @echo " Flags: -Wunused" - @echo " ------------------------------------------------------ " - @$(FORTRAN) -Wunused $(srcall) $(srcserial) -o packmol -- @chmod +x solvate.tcl - @echo " ------------------------------------------------------ " - @echo " Packmol succesfully built. " - @echo " ------------------------------------------------------ " -- GitLab From d1c3a0b404985cd9c9d32c7590872507c99474ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 16:35:55 +0100 Subject: [PATCH 130/566] fix minor style remarks --- .../s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb | 5 +++-- 6 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 6be5a1f63a..12ff2e5188 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] dependencies = [('numpy', '1.6.2', versionsuffix)] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 1e2a06545e..afedbc1537 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] dependencies = [('numpy', '1.6.2', versionsuffix)] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb index ace3c72316..93184d4eaf 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'pic': True} -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] dependencies = [('numpy', '1.6.2', versionsuffix)] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb index b80ca9d761..f76c775805 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] dependencies = [('numpy', '1.6.2', versionsuffix)] diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb index aaa6f260b9..5c1e324243 100644 --- a/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scipy/scipy-0.11.0-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """SciPy is a collection of mathematical algorithms and convenienc toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} -source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%s' % version, 'download')] +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] dependencies = [('numpy', '1.6.2', versionsuffix)] diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb index 4a6e691309..bdf51643a2 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """TAMkin is a post-processing toolkit for normal mode analysis, toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://github.com/molmod/tamkin/releases/download/v%s' % version] +source_urls = ['https://github.com/molmod/tamkin/releases/download/v%(version)s'] sources = [SOURCE_TAR_GZ] python = "Python" @@ -26,7 +26,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; export OMP_NUM_THREADS=1; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; nosetests -v test' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v test' sanity_check_paths = { 'files': [], -- GitLab From c4ba7faba27116d2f6a49f7d2660bf26cd0efd31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 18:18:07 +0100 Subject: [PATCH 131/566] fix typos w.r.t. 2013_sp1 versioning in icc/imkl easyconfigs --- easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index af863bb54e..be5072e46d 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -6,7 +6,7 @@ description = "C and C++ compiler from Intel" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_ccompxe_2013_%(version)s.tgz'] +sources = ['l_ccompxe_%(version)s.tgz'] dontcreateinstalldir = 'True' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index a835fca22a..ca26f636cc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mkl_%(version)s.tgz'] # deps for interface build -compver = '2013.sp1.080' +compver = '2013_sp1.0.080' dependencies = [ ('icc', compver), ('ifort', compver), -- GitLab From f3a89d2fa61f8f278f7dc54a187aa5788bbcf4eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 19:41:15 +0100 Subject: [PATCH 132/566] add easyconfigs for recent icc/ifort/imkl/impi versions --- .../easyconfigs/i/icc/icc-2013_sp1.1.106.eb | 18 +++++++++++ .../i/ifort/ifort-2013_sp1.1.106.eb | 18 +++++++++++ .../easyconfigs/i/imkl/imkl-11.1.1.106.eb | 30 +++++++++++++++++++ .../easyconfigs/i/impi/impi-4.1.2.040.eb | 19 ++++++++++++ 4 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb new file mode 100644 index 0000000000..2e5244fe91 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -0,0 +1,18 @@ +name = 'icc' +version = '2013_sp1.1.106' + +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'] + +# compiler class +moduleclass = 'compiler' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb new file mode 100644 index 0000000000..8d50c3c460 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -0,0 +1,18 @@ +name = 'ifort' +version = '2013_sp1.1.106' + +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'] + +# compiler class +moduleclass = 'compiler' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb new file mode 100644 index 0000000000..3a8d833067 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -0,0 +1,30 @@ +name = 'imkl' +version = '11.1.1.106' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mkl_%(version)s.tgz'] + +# deps for interface build +compver = '2013_sp1.1.106' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.2.040') +] + +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-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb new file mode 100644 index 0000000000..95c8b09cb5 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.2.040' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +moduleclass = 'mpi' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -- GitLab From e60093ea903f0f42b93134c814578feff37a14bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 20:48:58 +0100 Subject: [PATCH 133/566] add easyconfigs for ictce 6.0.0 and 6.1.0 --- easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb | 21 ++++++++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb | 21 ++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb new file mode 100644 index 0000000000..343a214a2c --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '6.0.0' + +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 = '0.080' +compver = '2013_sp1.%s' % suff + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.1.036'), + ('imkl', '11.1.%s' % suff), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb new file mode 100644 index 0000000000..29381078a5 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '6.1.0' + +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 = '1.106' +compver = '2013_sp1.%s' % suff + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.2.040'), + ('imkl', '11.1.%s' % suff), +] + +moduleclass = 'toolchain' -- GitLab From 8e0c0a2ad7b1743f47b805682cf3021de7b294a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2013 21:10:32 +0100 Subject: [PATCH 134/566] add example easyconfigs for HPL with ictce/6.x.0 --- .../easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb | 18 ++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb new file mode 100644 index 0000000000..dad098f322 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.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': 'ictce', 'version': '6.0.0'} +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/HPL/HPL-2.0-ictce-6.1.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb new file mode 100644 index 0000000000..d3a5822e94 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.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': 'ictce', 'version': '6.1.0'} +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 3f5fefe7116e8b108eb669f732588bf387c373db Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 12 Dec 2013 11:25:47 +0100 Subject: [PATCH 135/566] Added GMP 5.1.3 with ictce-5.5.0 and c++ support --- .../g/GMP/GMP-5.1.3-ictce-5.5.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..bbaacb631c --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +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': 'ictce', 'version': '5.5.0'} + +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.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 0bf1cfb225b4065241e2e396f36465eb3c8a5de7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 12 Dec 2013 13:29:40 +0100 Subject: [PATCH 136/566] CP2k: fixed name of patch, should work now --- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb | 2 +- ...ompile_date_lastcvs.patch => fix_compile_date_lastsvn.patch} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CP2K/{CP2K-20131211-fix_compile_date_lastcvs.patch => fix_compile_date_lastsvn.patch} (100%) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb index 037d12025a..b1ca163f20 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb @@ -16,7 +16,7 @@ source_urls = [SOURCEFORGE_SOURCE] patches = [ 'do_regtest_nocompile.patch', 'ifort-compiler-bug-fix.patch', - 'CP2K-20131205-fix_compile_date_lastcvs.patch', + 'fix_compile_date_lastsvn.patch', ] ## use FFTW, with FFTACML there are extra failures in regtests diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb index b04e8859be..61301c6ae4 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb @@ -14,7 +14,7 @@ sources = [SOURCE_TAR_BZ2] patches = [ 'ifort-compiler-bug-fix.patch', - 'CP2K-%(version)s-fix_compile_date_lastcvs.patch', + 'fix_compile_date_lastsvn.patch', ] ## use FFTW, with FFTACML there are extra failures in regtests diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastsvn.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/CP2K-20131211-fix_compile_date_lastcvs.patch rename to easybuild/easyconfigs/c/CP2K/fix_compile_date_lastsvn.patch -- GitLab From f99fdf880b9ad1669b0aebe02f5244a3eee9ec28 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 12 Dec 2013 13:32:25 +0100 Subject: [PATCH 137/566] CHARMM: fixed small errors in easyconfigs --- .../easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb | 5 ++++- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 4 +++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb index 81985c2134..25b23807a7 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb @@ -19,10 +19,13 @@ patches = [ "main-case-fix-%(version)s.patch", ] -#dependencies = [('Gaussian', 'g09_D.01-ictce-5.5.0-amd64-gpfs')] +dependencies = [ +# ('Gaussian', 'g09_D.01-ictce-5.5.0-amd64-gpfs') +] # MKL activated automatically when the MKL is found, same for g09 build_options = ["FULL", "COLFFT", "PIPF"] + # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb index 14e379742a..ca44f64f49 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -20,7 +20,9 @@ patches = [ # if you specify Gaussian, it will be used for the QM part. # if you specify FFTW, it will be used instead of the MKL -dependencies = [('Gaussian', 'g09_D.01', '-amd64-gpfs')] +dependencies = [ +# ('Gaussian', 'g09_D.01', '-amd64-gpfs') +] # MKL activated automatically when the ictce toolchain is used build_options = ["FULL", "COLFFT", "PIPF"] -- GitLab From f851678ad9d6bcfa2e482ce19d08d5d2d4edf8f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Dec 2013 14:13:54 +0100 Subject: [PATCH 138/566] add easyconfig for old impi v3.2.2 --- .../easyconfigs/i/impi/impi-3.2.2.006.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100755 easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb new file mode 100755 index 0000000000..af378447b9 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '3.2.2.006' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +moduleclass = 'mpi' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -- GitLab From f9a2b04b98a5299524c6acec4e93eef5e1a68718 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 13 Dec 2013 00:43:58 +0100 Subject: [PATCH 139/566] cosmetic changes --- easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb | 1 - 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb index d2d1de373c..41829c8d56 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goolf-1.4.10.eb @@ -16,10 +16,11 @@ version = '3.1.4' 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': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb index a703fdda55..0c368ea41a 100644 --- a/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb @@ -21,5 +21,4 @@ dependencies = [ ('GSL', '1.15'), ] - moduleclass = 'lib' -- GitLab From d7c1a7fb408bbef09309b308f319ab799e2d834e Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 13 Dec 2013 00:53:21 +0100 Subject: [PATCH 140/566] cosmetic changes replacing %(version)s as suggested by @fgeorgatos --- .../easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb | 2 +- .../easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb index 13621d0cd0..2b998a05e2 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb @@ -21,6 +21,6 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb index 3d05ff2d7e..958a558f7d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goolf-1.4.10.eb @@ -21,6 +21,6 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb index 9722706459..1b2199f7ad 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-4.0.6.eb @@ -21,6 +21,6 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb index 8827e2e91a..3c1a34a84a 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-ictce-5.3.0.eb @@ -22,6 +22,6 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb index fae87489f0..5eb47f9b01 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-goalf-1.5.12-no-OFED.eb @@ -21,6 +21,6 @@ toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] -sources = ['%s.tar.bz2' % version] +sources = ['%(version)s.tar.bz2'] moduleclass = 'math' -- GitLab From ef6e3f80b487ec4624df50e00d3b88f344a9871e Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 00:32:29 +0100 Subject: [PATCH 141/566] promote Coreutils to v8.22 Signed-off-by: Fotis Georgatos --- ...eutils-8.21-goolf-1.4.10.eb => Coreutils-8.22-goolf-1.4.10.eb} | 0 ...oreutils-8.21-ictce-5.3.0.eb => Coreutils-8.22-ictce-5.3.0.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Coreutils/{Coreutils-8.21-goolf-1.4.10.eb => Coreutils-8.22-goolf-1.4.10.eb} (100%) rename easybuild/easyconfigs/c/Coreutils/{Coreutils-8.21-ictce-5.3.0.eb => Coreutils-8.22-ictce-5.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-goolf-1.4.10.eb rename to easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/c/Coreutils/Coreutils-8.21-ictce-5.3.0.eb rename to easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb -- GitLab From d281a18d69141894592acaf73e0a7ba1e8e9ff9e Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 10:21:17 +0100 Subject: [PATCH 142/566] ini patch Signed-off-by: Fotis Georgatos --- .../Coreutils/Coreutils-8.22-goolf-1.4.10.eb | 6 +++--- .../c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb | 6 +++--- .../c/Coreutils/patch-2.7.1-goolf-1.4.10.eb | 19 +++++++++++++++++++ .../c/Coreutils/patch-2.7.1-ictce-5.3.0.eb | 19 +++++++++++++++++++ 4 files changed, 44 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb index 73aff4d255..71347c1b3f 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = "Coreutils" -version = "8.21" +version = "8.22" 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': 'goolf', 'version': '1.4.10'} -toolchainopts = {'pic': True} +toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftp.gnu.org/gnu/coreutils'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb index c61eaf7004..3a81592a70 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = "Coreutils" -version = "8.21" +version = "8.22" 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': 'ictce', 'version': '5.3.0'} -toolchainopts = {'pic': True} +toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftp.gnu.org/gnu/coreutils'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..21419abe8d --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +name = "patch" +version = "2.7.1" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """Patch takes a patch file containing a difference listing produced by the diff + program and applies those differences to one or more original files, producing patched versions.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +sanity_check_paths = { + 'files': ["bin/patch"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb new file mode 100644 index 0000000000..f8da2a6e5b --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb @@ -0,0 +1,19 @@ +name = "patch" +version = "2.7.1" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """Patch takes a patch file containing a difference listing produced by the diff + program and applies those differences to one or more original files, producing patched versions.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +sanity_check_paths = { + 'files': ["bin/patch"], + 'dirs': [] +} + +moduleclass = 'tools' -- GitLab From c980e3cb03b506a31e49994dbfba0a326430468f Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 10:41:01 +0100 Subject: [PATCH 143/566] improve Coreutils & patch Signed-off-by: Fotis Georgatos --- .../easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb index 71347c1b3f..bd182d78c1 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-goolf-1.4.10.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] sanity_check_paths = { - 'files': ["bin/date", "bin/true"], + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], 'dirs': [] } diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb index 3a81592a70..3eae868790 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.22-ictce-5.3.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] sanity_check_paths = { - 'files': ["bin/date", "bin/true"], + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], 'dirs': [] } diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb index 21419abe8d..2bd4cf1e84 100644 --- a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb @@ -16,4 +16,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'tools' +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb index f8da2a6e5b..d40dfa96e1 100644 --- a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb @@ -16,4 +16,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'tools' +moduleclass = 'devel' -- GitLab From f3acc0a34847cac5cf2084c24a7eecd703105c5a Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 13:32:27 +0100 Subject: [PATCH 144/566] relocate patch easyconfigs where they belong Signed-off-by: Fotis Georgatos --- .../{c/Coreutils => p/patch}/patch-2.7.1-goolf-1.4.10.eb | 0 .../{c/Coreutils => p/patch}/patch-2.7.1-ictce-5.3.0.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{c/Coreutils => p/patch}/patch-2.7.1-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/{c/Coreutils => p/patch}/patch-2.7.1-ictce-5.3.0.eb (100%) diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/patch/patch-2.7.1-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/c/Coreutils/patch-2.7.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/p/patch/patch-2.7.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/patch/patch-2.7.1-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/c/Coreutils/patch-2.7.1-ictce-5.3.0.eb rename to easybuild/easyconfigs/p/patch/patch-2.7.1-ictce-5.3.0.eb -- GitLab From b150879a76107dd13b1b219c9d2c1cd455cd7b86 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 14:21:30 +0100 Subject: [PATCH 145/566] replace with GNU_SOURCE where needed, round #1 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.2.eb | 2 +- .../easyconfigs/a/Autoconf/Autoconf-2.69-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb | 2 +- .../easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.6.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.16.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb | 2 +- .../easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb | 2 +- 85 files changed, 85 insertions(+), 85 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb index fcd7007494..39d449ebf4 100755 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb @@ -6,7 +6,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'GCC', 'version': '4.7.2'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.2.eb index 5211af2bb2..231ec6e1b8 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-4.8.2.eb @@ -10,7 +10,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'GCC', 'version': '4.8.2'} -source_urls = ['http://ftpmirror.gnu.org/%s/' % name.lower()] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goalf-1.1.0-no-OFED.eb index 7b68488129..e0b581ce3d 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb index 82a404f023..a25b326d59 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.0.6.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.0.6.eb index 749be4325e..0a829a5bd2 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.1.13.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.1.13.eb index a41534f1d8..e304f4b331 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.3.0.eb index 22f54366ee..c9ccb7d911 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.0.6.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.0.6.eb index 69549d1d6f..1a58cb138e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.1.13.eb index 30eaae1636..dd1af5cd2f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-4.1.13.eb index 1670d6477e..5954b4a580 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-5.3.0.eb index d46be8f544..cbdb121a82 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.6.5-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb index 9dcd73edef..6cb5d154df 100644 --- a/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ed/ed-1.9-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """GNU ed is a line-oriented text editor.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(name)s/'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files' : ['bin/ed'], diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb index 9ff5eb806d..7e1027f357 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.48-ictce-5.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.2.0'} toolchainopts = {'opt': True, 'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] +source_urls = [GNU_SOURCE] dependencies = [ ('GMP', '5.1.1'), diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb index 4390cf21c4..aa9ed9d6e0 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb index fe17508924..8fbb3b8253 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb @@ -7,7 +7,7 @@ The library provides a wide range of mathematical routines such as random number toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb index acfba35290..d1b3c6c699 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb index 46fb6c2c19..75d1c9681c 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb index 3279101aeb..f649ead9a5 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-5.5.0.eb @@ -8,7 +8,7 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/gsl/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb index 6e1f6d8d88..72bf9736f8 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """GNU gperf is a perfect hash function generator. For a given lis toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://ftpmirror.gnu.org/%s' % name] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb index 2bbf67ad0e..bad261c98a 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-goolf-1.4.10.eb @@ -8,7 +8,7 @@ function is perfect, which means that the hash table has no collisions, and the string comparison only.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://ftpmirror.gnu.org/%s' % name] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb index 63b3d924c1..3a83b14550 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """GNU gperf is a perfect hash function generator. For a given lis toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://ftpmirror.gnu.org/%s' % name] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb index 09e7025757..18fd84fe28 100644 --- a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """GNU gperf is a perfect hash function generator. For a given lis toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://ftpmirror.gnu.org/%s' % name] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb index ae0e87fc42..5457e6d892 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'cgoolf', 'version': '1.1.7'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb index ab8b1bc75e..7949d851ed 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'gmpolf', 'version': '1.4.8'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb index ccba8d9338..acb7e90d49 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb index 5302cfd659..78ba032893 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'goolf', 'version': '1.4.10'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.0.6.eb index 829726e985..5cff62f0ca 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.0.6.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '4.0.6'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.1.13.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.1.13.eb index fe8de65ddb..2fe7409a9e 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-4.1.13.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '4.1.13'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb index dcb790826e..42edcfbbc8 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.5-ictce-5.3.0.eb @@ -20,7 +20,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'ictce', 'version': '5.3.0'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.5.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb index bb3ec5eed9..8aefa658eb 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.10.eb @@ -19,7 +19,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'goolf', 'version': '1.6.10'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 890fe517c0..359b660e46 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 388a3e580b..18fe4059db 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index ba6d6b6505..b64442d4ef 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline'] +source_urls = [GNU_SOURCE] dependencies = [ ('ncurses', '5.9-20130406'), diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 497a7d18be..7c6b657fe5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgoolf', 'version': '1.1.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index d664c36f04..9dab8be0f9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmpolf', 'version': '1.4.8'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 7f81da5c1f..0bf8fe1872 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index b157f2cf21..1eebe810d9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 19e8a88ef4..a7db566606 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 641658be88..1c868a1400 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 30f278107c..d3fdc7906c 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index 5b76aa7d0e..5740dd60f2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 54747712bc..e93ffff0df 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 14784ff7b9..438d259161 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index d2bc153da5..ad79306c27 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 7b174c8d4d..bc74b8856b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -10,7 +10,7 @@ to recall and perhaps reedit those lines, and perform csh-like history expansion toolchain = {'name': 'ictce', 'version' : '5.2.0'} sources = ['readline-%s.tar.gz' % version] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index d309434705..be1364c6ff 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index f2d1625f9b..5a97406731 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7f487221c1..cc11d206f2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iomkl', 'version': '4.6.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index d46fc3ce87..bb973d3cf6 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index e96333ad7a..68860b70ee 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '4.4.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = ['http://ftpmirror.gnu.org/readline/'] +source_urls = [GNU_SOURCE] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb index 286c9ae8c7..a48c5487ad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb index 5f1bea4076..06b9044ce0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] configopts = "--enable-cxx" diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.6.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.6.3.eb index 264b599862..607e6bd0b5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.6.3.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.2.eb index 10a60472cd..0560144686 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.2.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.3.eb index c26aa03e7c..5bb719ac95 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.7.3.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.1.eb index ddb33422fd..55cba29b68 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.1.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb index 5f6973dba4..679d0186cd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb @@ -10,7 +10,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] configopts = "--enable-cxx" diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb index 8e168f546e..81a49cdbe3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb @@ -10,7 +10,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'gmacml', 'version': '1.7.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb index 945533570d..410fbc75ce 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'goalf', 'version' : '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.4.10.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.4.10.eb index 60c923740e..d66d8b9e4e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-goolf-1.4.10.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb index b5c20dbd5d..925e8c70e6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-3.2.2.u3.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb index 6953b94347..c344494bc3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb index c970130d7f..3c8fbd6746 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.3.0.eb index 7b14418a3d..7915e22d2e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb index 1c34adaa26..98f82e41c4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-iqacml-3.7.3.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16.eb index 97181f8563..50af850a5a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16.eb @@ -11,7 +11,7 @@ GNU M4 also has built-in functions for including files, running shell commands, toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] patches = ['M4-%(version)s-no-gets.patch'] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index bd58d4c9be..ad58285a85 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'GCC', 'version': '4.7.2'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index edddf1e97a..f972b6a4ff 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'GCC', 'version': '4.7.3'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 910be3e324..5f56a55621 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'GCC', 'version': '4.8.1'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index edda66f1dc..15745294d9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'gmpolf', 'version': '1.4.8'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index fbc61c03f9..38b356d5e1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index ec0e28d989..947e8e3afa 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 82a5ffa96a..4084c938c1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 246b288ce1..33bb21037f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index e4ac4f446a..5a698183f4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'goolfc', 'version': '1.3.12'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index c5f6b9a107..c0284ad94f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 0d526d6fbb..95388cfc5b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '4.0.10'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 523dca81d9..731485e77b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 4cc75a29d9..8cb79c351b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index ab29dec4fe..fb1f4e9935 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -8,7 +8,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'ictce', 'version': '5.2.0'} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 60209824d7..020778b318 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index c4b928cee8..a81155369d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 6648a8a7ab..9963e053c2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'iomkl', 'version': '4.6.13'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index 2b469fedf6..decfe9bc04 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -9,7 +9,7 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index 0395e1a010..f4b42632c9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -9,7 +9,7 @@ description = """The Ncurses (new curses) library is a free software emulation o toolchain = {'name': 'iqacml', 'version': '4.4.13'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] moduleclass = 'devel' -- GitLab From f8e71d864378a2e24f613e7e31edc1237acc75d1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 14:22:29 +0100 Subject: [PATCH 146/566] replace with GNU_SOURCE where needed, round #2 Signed-off-by: Fotis Georgatos --- .../easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.13.4-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb | 2 +- easybuild/easyconfigs/b/Bison/Bison-2.7.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb | 2 +- .../b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-5.0.5-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-5.0.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb | 2 +- .../easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb | 2 +- .../easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb | 2 +- .../easyconfigs/g/gettext/gettext-0.18.2-goalf-1.1.0-no-OFED.eb | 2 +- .../g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb | 2 +- easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/l/libidn/libidn-1.27-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-5.3.0.eb | 2 +- .../l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb | 2 +- .../l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb | 2 +- .../l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb | 2 +- .../p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/p/parallel/parallel-20130122-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb | 2 +- .../easyconfigs/p/parallel/parallel-20130122-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb | 2 +- 97 files changed, 97 insertions(+), 97 deletions(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb index 5708912031..8dced5a5fc 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-goolf-1.4.10.eb @@ -16,7 +16,7 @@ version = '1.13.4' homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -source_urls = ['http://ftp.gnu.org/gnu/automake'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-4.1.13.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-4.1.13.eb index e6a35fdebc..4ce71128df 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-4.1.13.eb @@ -16,7 +16,7 @@ version = '1.13.4' homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -source_urls = ['http://ftp.gnu.org/gnu/automake'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb index a6aed31760..e10d946779 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.3.0.eb @@ -16,7 +16,7 @@ version = '1.13.4' homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -source_urls = ['http://ftp.gnu.org/gnu/automake'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb index 38cd369b16..6a66db0401 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-GCC-4.8.2.eb @@ -18,7 +18,7 @@ description = "Automake: GNU Standards-compliant Makefile generator" toolchain = {'name': 'GCC', 'version': '4.8.2'} -source_urls = ['http://ftp.gnu.org/gnu/automake'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] dependencies = [('Autoconf', '2.69')] diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb index aae867d2af..f1ed26f41e 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ description = """a2ps-4.14: Formats an ascii file for printing on a postscript p toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/a2ps'] +source_urls = [GNU_SOURCE] dependencies = [ ('gettext', '0.18.2'), diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb index 85c12af224..85a8aac89e 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb @@ -16,7 +16,7 @@ description = """a2ps-4.14: Formats an ascii file for printing on a postscript p toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/a2ps'] +source_urls = [GNU_SOURCE] dependencies = [ ('gettext', '0.18.2'), diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb index 5f8b190cff..1a8b5ec4d6 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb @@ -16,7 +16,7 @@ description = """a2ps-4.14: Formats an ascii file for printing on a postscript p toolchain = {'version': '4.0.6', 'name': 'ictce'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/a2ps'] +source_urls = [GNU_SOURCE] dependencies = [ ('gettext', '0.18.2'), diff --git a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb index 442f9c380e..8b4d01b9b2 100644 --- a/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb @@ -17,7 +17,7 @@ description = """a2ps-4.14: Formats an ascii file for printing on a postscript p toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/a2ps'] +source_urls = [GNU_SOURCE] dependencies = [ ('gettext', '0.18.2'), diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb index 359650da74..8ffbecad50 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-goalf-1.1.0-no-OFED.eb @@ -21,7 +21,7 @@ description = """Bash is an sh-compatible command language interpreter that exec toolchain = {'name' : 'goalf', 'version' : '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files': ["bin/bash"], diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb index ebae0731f4..d4a53daa14 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-goolf-1.4.10.eb @@ -21,7 +21,7 @@ description = """Bash is an sh-compatible command language interpreter that exec toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files': ["bin/bash"], diff --git a/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb index 953596556a..0863522494 100644 --- a/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bash/Bash-4.2-ictce-5.3.0.eb @@ -21,7 +21,7 @@ description = """Bash is an sh-compatible command language interpreter that exec toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files': ["bin/bash"], diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb index b06f0de448..4422c069ef 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-GCC-4.6.3.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb index 07ff8400be..31520c710c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-gmacml-1.7.0.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'gmacml', 'version': '1.7.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-goalf-1.1.0-no-OFED.eb index aa3f8448b3..f26bcc8110 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb index 827c4f0330..aba6ec1fef 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-goolf-1.4.10.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-3.2.2.u3.eb index c6a21e310e..10fc9ef68a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-3.2.2.u3.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb index eeb7f3e8bb..9c14def61f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.5-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb index 8e67117ad4..8744cbb56a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.1.3.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb index 42be6e0154..ec2d8ec231 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ClangGCC-1.2.3.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.2.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.2.eb index 8db1f625f0..585ea2ac96 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.2.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.3.eb index c713bcbe68..e3ee605bb0 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.7.3.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.1.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.1.eb index e24eef4f7e..f8873239d9 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-GCC-4.8.1.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.4.10.eb index a770800fdf..8be6a9e305 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.4.10.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb index f26e4c67a1..8043e00d5c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb index 82ddbeb0ac..9cbcbb84e1 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7.eb index e6eb380e33..e1f74e5158 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7.eb @@ -8,7 +8,7 @@ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.16')] 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 add5f24592..24e4efa236 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 @@ -17,7 +17,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" sources = ['binutils-%s.tar.bz2' % version] -source_urls = ['http://ftp.gnu.org/gnu/binutils'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} 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 17866810c4..bf43692811 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 @@ -17,7 +17,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" sources = ['binutils-%s.tar.bz2' % version] -source_urls = ['http://ftp.gnu.org/gnu/binutils'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {'pic': True} 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 9ccfe20342..e7bcf8437d 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 @@ -17,7 +17,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" sources = ['binutils-%s.tar.bz2' % version] -source_urls = ['http://ftp.gnu.org/gnu/binutils'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb index c5754639f5..59124fc81f 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ homepage = 'http://www.gnu.org/software/cflow/' description = """cflow-1.4: Code-path flow analyzer for C""" sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/cflow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb index ec677bbfc5..2fa549427b 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-goolf-1.4.10.eb @@ -15,7 +15,7 @@ homepage = 'http://www.gnu.org/software/cflow/' description = """cflow-1.4: Code-path flow analyzer for C""" sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/cflow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb index 48b62c0de5..626c573418 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-4.0.6.eb @@ -15,7 +15,7 @@ homepage = 'http://www.gnu.org/software/cflow/' description = """cflow-1.4: Code-path flow analyzer for C""" sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/cflow'] +source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} diff --git a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb index 1dadcc0504..a6c4166eee 100644 --- a/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/c/cflow/cflow-1.4-ictce-5.3.0.eb @@ -15,7 +15,7 @@ homepage = 'http://www.gnu.org/software/cflow/' description = """cflow-1.4: Code-path flow analyzer for C""" sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/cflow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb index 5371caa2fa..5c1247c5f6 100644 --- a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ version = '3.2' description = """Diffutils: GNU diff utilities - find the differences between files""" homepage = 'http://www.gnu.org/software/diffutils/diffutils.html' -source_urls = ['http://ftp.gnu.org/gnu/diffutils'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb index 216a96d6a7..182d829f0f 100644 --- a/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Diffutils/Diffutils-3.2-ictce-5.3.0.eb @@ -16,7 +16,7 @@ version = '3.2' description = """Diffutils: GNU diff utilities - find the differences between files""" homepage = 'http://www.gnu.org/software/diffutils/diffutils.html' -source_urls = ['http://ftp.gnu.org/gnu/diffutils'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb index 7d2ab705af..0160acc4c4 100644 --- a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-goolf-1.4.10.eb @@ -16,7 +16,7 @@ version = '4.2.33' homepage = 'http://www.gnu.org/software/findutils/findutils.html' description = "findutils: The GNU find, locate, updatedb, and xargs utilities" -source_urls = ['http://ftp.gnu.org/gnu/findutils'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb index 6baac60dd5..b2d360c185 100644 --- a/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/findutils/findutils-4.2.33-ictce-5.3.0.eb @@ -16,7 +16,7 @@ version = '4.2.33' homepage = 'http://www.gnu.org/software/findutils/findutils.html' description = "findutils: The GNU find, locate, updatedb, and xargs utilities" -source_urls = ['http://ftp.gnu.org/gnu/findutils'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb index c9c21b7554..add5752ac7 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmpolf-1.1.6.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb index d398023614..1825890778 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.1.12rc1.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb index 058c22bab1..db088b8956 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgmvolf-1.2.7.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb index 0d0649160d..14dca7818e 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-cgoolf-1.1.7.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'cgoolf', 'version': '1.1.7'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb index 3c952396b7..e54d658dee 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12.eb @@ -18,7 +18,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'gmvolf', 'version': '1.7.12'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb index ee93ab0e55..bb25a5e621 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-gmvolf-1.7.12rc1.eb @@ -18,7 +18,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb index b559961469..7814ec1eba 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb index 0f50e5f84d..e2199ba071 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-7.5.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "GDB-7.5.1: The GNU Project Debugger" sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gdb/'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goalf-1.1.0-no-OFED.eb index 6d6c21ad76..2706aa7486 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """GMP is a free library for arbitrary precision arithmetic, toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +source_urls = [GNU_SOURCE] runtest = 'check' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goolf-1.4.10.eb index e24d3871de..c9123d61f7 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-goolf-1.4.10.eb @@ -7,7 +7,7 @@ operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +source_urls = [GNU_SOURCE] runtest = 'check' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb index 03244c62e3..3c7c8b1566 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """GMP is a free library for arbitrary precision arithmetic, toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +source_urls = [GNU_SOURCE] runtest = 'check' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-5.3.0.eb index aa308839e7..8fdf71fe7e 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """GMP is a free library for arbitrary precision arithmetic, toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +source_urls = [GNU_SOURCE] runtest = 'check' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.2.0.eb index c0dac1a452..af2d9401ca 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-5.2.0.eb @@ -8,7 +8,7 @@ operating on signed integers, rational numbers, and floating point numbers. """ toolchain = {'name': 'ictce', 'version': '5.2.0'} sources = [SOURCELOWER_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/gmp'] +source_urls = [GNU_SOURCE] runtest = 'check' diff --git a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb index 616810aa15..adc07319fe 100644 --- a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ version = '4.0.2' homepage = 'http://www.gnu.org/software/gawk/gawk.html' description = "gawk: GNU awk" -source_urls = ['http://ftp.gnu.org/gnu/gawk'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb index c32d5a7da3..2f7e0cf882 100644 --- a/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gawk/gawk-4.0.2-ictce-5.3.0.eb @@ -16,7 +16,7 @@ version = '4.0.2' homepage = 'http://www.gnu.org/software/gawk/gawk.html' description = "gawk: GNU awk" -source_urls = ['http://ftp.gnu.org/gnu/gawk'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb index 7aa8ebc89f..2d9e22b986 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb index a02af5a472..74ed768df4 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb index 7b771be38b..4bcc26447a 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb index 6a75826e5b..a32268bf8f 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'cgoolf', 'version': '1.1.7'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb index 93247f5f1a..1fede7e4c6 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmpolf-1.4.8.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'gmpolf', 'version': '1.4.8'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb index 60cb87e25e..87753bfbc9 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb index f6924ebc7b..b9cff2211e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gmvolf-1.7.12rc1.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goalf-1.1.0-no-OFED.eb index be1d80eb14..c26723dfec 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb index f99a141fdb..35cded15c6 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-gompi-1.4.12-no-OFED.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb index a3b70c032f..8c7cc9b4b8 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-goolf-1.4.10.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.0.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.0.6.eb index acbb710e53..3eddb0a6d2 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.0.6.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb index 34e274c6bd..56598b375e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-4.1.13.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb index 530e6833bb..be4e49be17 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.2.0.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'ictce', 'version': '5.2.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb index e49e2e384b..3c2d60cef2 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2-ictce-5.3.0.eb @@ -9,7 +9,7 @@ and documentation""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://ftp.gnu.org/pub/gnu/%(name)s'] +source_urls = [GNU_SOURCE] configopts = '--without-emacs' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb index 90e6fd9442..9596baa7ba 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] dependencies = [ ('libtool', '2.4.2'), diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb index ed99bdaf7b..215f5b7322 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb @@ -7,7 +7,7 @@ the official extension language for the GNU operating system.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] dependencies = [ ('libtool', '2.4.2'), diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb index 09c8aa8e51..517a4e5549 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] dependencies = [ ('libtool', '2.4.2'), diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb index 9b84ed765c..13223b7897 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['%s-%s.tar.gz' % (name.lower(), version)] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] dependencies = [ ('libtool', '2.4.2'), diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb index c6b02f870f..0d0a354c13 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb @@ -7,7 +7,7 @@ Libidn's purpose is to encode and decode internationalized domain names.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.27-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libidn/libidn-1.27-goolf-1.4.10.eb index befb705dc8..ce8871841a 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.27-goolf-1.4.10.eb @@ -7,7 +7,7 @@ Libidn's purpose is to encode and decode internationalized domain names.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb index 494ea997a3..175e451374 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,6 @@ description = """GNU libtool is a generic library support script. Libtool hides toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goolf-1.4.10.eb index 1b2d459320..f40fb3df88 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goolf-1.4.10.eb @@ -7,6 +7,6 @@ behind a consistent, portable interface.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb index 16e021b019..ff247a01fc 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb @@ -8,6 +8,6 @@ description = """GNU libtool is a generic library support script. Libtool hides toolchain = {'name': 'ictce', 'version' : '4.0.6'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb index b8e328774b..5002055bd1 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb @@ -8,6 +8,6 @@ description = """GNU libtool is a generic library support script. Libtool hides toolchain = {'name': 'ictce', 'version' : '4.1.13'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-5.3.0.eb index f8c23c3025..04bf2df64f 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-5.3.0.eb @@ -9,6 +9,6 @@ description = """GNU libtool is a generic library support script. Libtool hides toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb index 56bdff5bcc..f7e4bcfbbd 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """This library provides functions for manipulating Unicode string toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files' : ['lib/libunistring.a', 'lib/libunistring.so', 'include/unistring'] + diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb index 5a3efb3ea5..fd4a8b980c 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb @@ -7,7 +7,7 @@ according to the Unicode standard.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] sanity_check_paths = { 'files' : ['lib/libunistring.a', 'lib/libunistring.so', 'include/unistring'] + diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb index dec6140666..9b68839fba 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """This library provides functions for manipulating Unicode string toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] patches = ['libunistring_icc_builtin_nan-inf.patch'] diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb index 6c3d6347d8..c8fd88eb0f 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """This library provides functions for manipulating Unicode string toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +source_urls = [GNU_SOURCE] patches = ['libunistring_icc_builtin_nan-inf.patch'] diff --git a/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb b/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb index 4adee4b622..33ab4efa80 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = "make-3.82: GNU version of make utility" # fi. http://ftp.gnu.org/gnu/make/make-3.82.tar.gz sources = ['make-%(version)s.tar.bz2'] -source_urls = ['http://ftp.gnu.org/gnu/make'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb index 61ce56f41f..98d8a738b6 100644 --- a/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-3.82-ictce-5.3.0.eb @@ -18,7 +18,7 @@ description = "make-3.82: GNU version of make utility" # fi. http://ftp.gnu.org/gnu/make/make-3.82.tar.gz sources = ['make-%(version)s.tar.bz2'] -source_urls = ['http://ftp.gnu.org/gnu/make'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} 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 26569c2f16..d19fa1d165 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 @@ -17,7 +17,7 @@ homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/parallel'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} 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 85e087b41e..ec06e9c7cc 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 @@ -17,7 +17,7 @@ homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/parallel'] +source_urls = [GNU_SOURCE] 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 cf5a965b2d..2a63fe61d3 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 @@ -17,7 +17,7 @@ homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/parallel'] +source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} 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 47bd8f12e9..8de6c29485 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 @@ -17,7 +17,7 @@ homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/parallel'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb index eb4db79fe2..107caabf86 100644 --- a/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RCS/RCS-5.7-goolf-1.4.10.eb @@ -17,7 +17,7 @@ homepage = 'http://www.cs.purdue.edu/homes/trinkle/RCS/' description = "RCS: GNU Revision Control System - version control software" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/rcs'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb index 779cdb65cd..d2cd389f5e 100644 --- a/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/RCS/RCS-5.7-ictce-5.3.0.eb @@ -17,7 +17,7 @@ homepage = 'http://www.cs.purdue.edu/homes/trinkle/RCS/' description = "RCS: GNU Revision Control System - version control software" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/rcs'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb index a4d66cc836..b67b65616a 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/stow/stow.html' description = """Stow-1.3.3: Maps several separate packages into a tree without merging them""" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/stow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb index cc9ff2a153..3e5a453e42 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-goolf-1.4.10.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/stow/stow.html' description = """Stow-1.3.3: Maps several separate packages into a tree without merging them""" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/stow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb index b098bdf237..911acb7f10 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-4.0.6.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/stow/stow.html' description = """Stow-1.3.3: Maps several separate packages into a tree without merging them""" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/stow'] +source_urls = [GNU_SOURCE] toolchain = {'version': '4.0.6', 'name': 'ictce'} diff --git a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb index 28ac7d91ae..1c4d3c3cc5 100644 --- a/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/Stow/Stow-1.3.3-ictce-5.3.0.eb @@ -17,7 +17,7 @@ homepage = 'http://www.gnu.org/software/stow/stow.html' description = """Stow-1.3.3: Maps several separate packages into a tree without merging them""" sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/stow'] +source_urls = [GNU_SOURCE] toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb index 36d6a8effc..a50ed96b52 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb @@ -16,7 +16,7 @@ version = '1.26' homepage = 'http://www.gnu.org/software/tar/tar.html' description = "tar: The GNU tape archiver" -source_urls = ['http://ftp.gnu.org/gnu/tar'] +source_urls = [GNU_SOURCE] sources = ['tar-%s.tar.bz2' % version] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb index 9714f94ef0..72c6d238a9 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-goolf-1.4.10.eb @@ -16,7 +16,7 @@ version = '1.26' homepage = 'http://www.gnu.org/software/tar/tar.html' description = "tar: The GNU tape archiver" -source_urls = ['http://ftp.gnu.org/gnu/tar'] +source_urls = [GNU_SOURCE] sources = ['tar-%s.tar.bz2' % version] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-4.0.6.eb index 5e707fde52..dc4a806ac5 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-4.0.6.eb @@ -16,7 +16,7 @@ version = '1.26' homepage = 'http://www.gnu.org/software/tar/tar.html' description = "tar: The GNU tape archiver" -source_urls = ['http://ftp.gnu.org/gnu/tar'] +source_urls = [GNU_SOURCE] sources = ['tar-%s.tar.bz2' % version] toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb index 0444d484d5..5b4cb4045a 100644 --- a/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tar/Tar-1.26-ictce-5.3.0.eb @@ -16,7 +16,7 @@ version = '1.26' homepage = 'http://www.gnu.org/software/tar/tar.html' description = "tar: The GNU tape archiver" -source_urls = ['http://ftp.gnu.org/gnu/tar'] +source_urls = [GNU_SOURCE] sources = ['tar-%s.tar.bz2' % version] -- GitLab From e66219647a156fcee22d8bdefaf569415a104ee1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 14 Dec 2013 14:31:36 +0100 Subject: [PATCH 147/566] replace with GNU_SOURCE where needed, round #3 Signed-off-by: Fotis Georgatos --- .../f/freetype/freetype-2.4.10-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.0.6.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.10-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb | 2 +- .../f/freetype/freetype-2.4.11-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.11-ictce-3.2.2.u3.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.11-ictce-4.1.13.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb | 2 +- .../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb | 2 +- 15 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goalf-1.1.0-no-OFED.eb index 46fc41bf4b..0933ebbe50 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb index 0d83aa6521..13f7275f3e 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-goolf-1.4.10.eb @@ -9,7 +9,7 @@ servers, font conversion tools, text image generation tools, and many other prod toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.0.6.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.0.6.eb index 57c645e55f..d8180f31a0 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.1.13.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.1.13.eb index 23c5e15dba..6cd7f858d2 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb index 5771475460..115ca243f3 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.10-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goalf-1.1.0-no-OFED.eb index 05ced29532..00039d8f1d 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goalf-1.1.0-no-OFED.eb @@ -9,7 +9,7 @@ servers, font conversion tools, text image generation tools, and many other prod toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb index 87014fb205..1df33cbab7 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-goolf-1.4.10.eb @@ -9,7 +9,7 @@ servers, font conversion tools, text image generation tools, and many other prod toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-3.2.2.u3.eb index 181648612e..b99078235a 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-3.2.2.u3.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-4.1.13.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-4.1.13.eb index 1b32b32fb6..6187e6b9ba 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb index f82be0c8cb..b585104cab 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.4.11-iqacml-3.7.3.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'iqacml', 'version': '3.7.3'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb index a3b5de75a2..e9d9036e94 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.0.1-ictce-5.5.0.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://download.savannah.gnu.org/releases/freetype/'] +source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] dependencies = [('libpng', '1.6.6')] diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb index dd04511798..dc8684e20b 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb @@ -5,7 +5,7 @@ homepage = 'http://www.gnu.org/software/libmatheval/' description = """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.""" -source_urls = ['http://ftp.gnu.org/gnu/libmatheval/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index b24bc59f04..cb89a94544 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -5,7 +5,7 @@ homepage = 'http://www.gnu.org/software/libmatheval/' description = """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.""" -source_urls = ['http://ftp.gnu.org/gnu/libmatheval/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb index 7b46f2830c..d043ee8cce 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb @@ -5,7 +5,7 @@ homepage = 'http://www.gnu.org/software/libmatheval/' description = """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.""" -source_urls = ['http://ftp.gnu.org/gnu/libmatheval/'] +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index c3709d8e78..1a22f67f60 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -5,7 +5,7 @@ homepage = 'http://www.gnu.org/software/libmatheval/' description = """GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.""" -source_urls = ['http://ftp.gnu.org/gnu/libmatheval/'] +source_urls = [GNU_SOURCE] sources = ['%s-%s.tar.gz' % (name.lower(), version)] -- GitLab From 8e1c9d8d2902a957c6b4e353732895d22815a166 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Dec 2013 21:25:06 +0100 Subject: [PATCH 148/566] rework goolfc/2.6.10 easyconfigs using gcccuda subtoolchain, add GROMACS easyconfig for goolfc/2.6.10 --- .../Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb | 24 +++++++++++ .../Automake/Automake-1.14-gcccuda-2.6.10.eb | 31 ++++++++++++++ .../c/CMake/CMake-2.8.4-goolfc-2.6.10.eb | 20 ++++++++++ ...-1.6.10.eb => FFTW-3.3.3-gompic-2.6.10.eb} | 2 +- .../g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb | 40 +++++++++++++++++++ .../easyconfigs/g/gcccuda/gcccuda-2.6.10.eb | 17 ++++++++ .../easyconfigs/g/gompic/gompic-1.6.10.eb | 29 -------------- .../easyconfigs/g/gompic/gompic-2.6.10.eb | 19 +++++++++ .../{goolfc-2.0.10.eb => goolfc-2.6.10.eb} | 17 +++----- .../h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb | 17 ++++++++ .../m/M4/M4-1.4.16-gcccuda-2.6.10.eb | 22 ++++++++++ .../n/ncurses/ncurses-5.9-goolfc-2.6.10.eb | 15 +++++++ ...nBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb} | 2 +- ....22.eb => OpenMPI-1.7.3-gcccuda-2.6.10.eb} | 6 +-- ...pic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb} | 2 +- 15 files changed, 214 insertions(+), 49 deletions(-) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.14-gcccuda-2.6.10.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.3-gompic-1.6.10.eb => FFTW-3.3.3-gompic-2.6.10.eb} (95%) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb delete mode 100644 easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb rename easybuild/easyconfigs/g/goolfc/{goolfc-2.0.10.eb => goolfc-2.6.10.eb} (72%) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb => OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb} (96%) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb => OpenMPI-1.7.3-gcccuda-2.6.10.eb} (88%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb => ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb} (92%) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..3dbedef6bb --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-gcccuda-2.6.10.eb @@ -0,0 +1,24 @@ +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': 'gcccuda', 'version': '2.6.10'} + +source_urls = ['http://ftpmirror.gnu.org/%s/' % name.lower()] +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-gcccuda-2.6.10.eb b/easybuild/easyconfigs/a/Automake/Automake-1.14-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..60bb667379 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.14-gcccuda-2.6.10.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:: 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/ +## + +name = 'Automake' +version = "1.14" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'gcccuda', 'version': '2.6.10'} + +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/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb new file mode 100644 index 0000000000..42fa53cb42 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.4-goolfc-2.6.10.eb @@ -0,0 +1,20 @@ +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': 'goolfc', 'version': '2.6.10'} + +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/FFTW/FFTW-3.3.3-gompic-1.6.10.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb similarity index 95% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb index 7dd42f220e..e3193217ca 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-1.6.10.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompic-2.6.10.eb @@ -5,7 +5,7 @@ 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': 'gompic', 'version': '1.6.10'} +toolchain = {'name': 'gompic', 'version': '2.6.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb new file mode 100644 index 0000000000..40a4d861ce --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb @@ -0,0 +1,40 @@ +## +# 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 +## + +easyblock = 'CMakeMake' + +name = 'GROMACS' +version = '4.6.1' + +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': 'goolfc', 'version': '2.6.10'} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +sources = [ + SOURCELOWER_TAR_GZ, + 'regressiontests-%(version)s.tar.gz', +] +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] + +builddependencies = [('CMake', '2.8.4')] + +configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" +runtest = 'check' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb new file mode 100644 index 0000000000..d75a89f110 --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb @@ -0,0 +1,17 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2.6.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# compiler toolchain dependencies +dependencies = [ + ('GCC', '4.8.2'), + ('CUDA', '5.5.22'), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb b/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb deleted file mode 100644 index 525fd48b04..0000000000 --- a/easybuild/easyconfigs/g/gompic/gompic-1.6.10.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "Toolchain" - -name = 'gompic' -version = '1.6.10' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, - including OpenMPI for MPI support.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -compname = 'GCC' -compver = '4.8.2' -comp = (compname, compver) - -mpilib = 'OpenMPI' -mpiver = '1.7.3' - -cudaname = 'CUDA' -cudaver = '5.5.22' -cudasuffix = '-' + cudaname + '-' + cudaver - -# compiler toolchain dependencies -dependencies = [ - comp, - (mpilib, mpiver, cudasuffix, comp), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb b/easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb new file mode 100644 index 0000000000..d0cc8743ce --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2.6.10.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2.6.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# compiler toolchain dependencies +dependencies = [ + ('GCC', '4.8.2'), # part of gcccuda + ('CUDA', '5.5.22'), # part of gcccuda + ('OpenMPI', '1.7.3', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2.6.10.eb similarity index 72% rename from easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb rename to easybuild/easyconfigs/g/goolfc/goolfc-2.6.10.eb index 549e0bec37..345bc66c03 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2.0.10.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2.6.10.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'goolfc' -version = '2.0.10' +version = '2.6.10' homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including @@ -9,19 +9,11 @@ description = """GCC based compiler toolchain __with CUDA support__, and includi toolchain = {'name': 'dummy', 'version': 'dummy'} -comp_name = 'GCC' -comp_version = '4.8.2' -comp = (comp_name, comp_version) - # toolchain used to build goolfc dependencies comp_mpi_tc_name = 'gompic' -comp_mpi_tc_ver = '1.6.10' +comp_mpi_tc_ver = version comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) -cudaname = 'CUDA' -cudaver = '5.5.22' -cudasuffix = '-' + cudaname + '-' + cudaver - blaslib = 'OpenBLAS' blasver = '0.2.8' blassuff = '-LAPACK-3.4.2' @@ -31,8 +23,9 @@ blas = '-%s-%s%s' % (blaslib, blasver, blassuff) # we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain # because of toolchain preperation functions dependencies = [ - comp, # part of gompic - ('OpenMPI', '1.7.3', cudasuffix, comp), # part of gompic, which includes also CUDA + ('GCC', '4.8.2'), # part of gompic + ('CUDA', '5.5.22'), # part of gompic + ('OpenMPI', '1.7.3', '', ('gcccuda', version)), # part of gompic (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.3', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..f554e7a62a --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb @@ -0,0 +1,17 @@ +name = 'hwloc' +version = "1.7.2" + +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': 'gcccuda', 'version': '2.6.10'} + +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/m/M4/M4-1.4.16-gcccuda-2.6.10.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..2175e7a770 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb @@ -0,0 +1,22 @@ +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': 'gcccuda', 'version': '2.6.10'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/m4'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb new file mode 100644 index 0000000000..4e33e95089 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.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': 'goolfc', 'version': '2.6.10'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/%(name)s'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb index dfef0b31c1..59919ca91a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompic-2.6.10-LAPACK-3.4.2.eb @@ -7,7 +7,7 @@ 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': 'gompic', 'version': '1.6.10'} +toolchain = {'name': 'gompic', 'version': '2.6.10'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb similarity index 88% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 64159cacf9..7912a2d94c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2-CUDA-5.5.22.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -1,11 +1,10 @@ name = 'OpenMPI' version = "1.7.3" -versionsuffix = '-CUDA-5.5.22' homepage = 'http://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" -toolchain = {'name': 'GCC', 'version': '4.8.2'} +toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] @@ -17,7 +16,6 @@ builddependencies = [ dependencies = [ ('hwloc', '1.7.2'), - ('CUDA', '5.5.22', '', True), ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' @@ -36,5 +34,3 @@ sanity_check_paths = { } moduleclass = 'mpi' - -patches = ['openmpi-mca-params.conf-1.4.5-local.patch', 'pax_disable.patch'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb similarity index 92% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb index 0bc94ce1d6..77f58e7b27 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2.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': 'gompic', 'version': '1.6.10'} +toolchain = {'name': 'gompic', 'version': '2.6.10'} toolchainopts = {'pic': True} source_urls = [homepage] -- GitLab From 80035a6fa645d59f9c8b30b7b38bbaca6a032970 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 16 Dec 2013 22:30:16 +0100 Subject: [PATCH 149/566] change gromacs version from 4.6.1 to 4.6.5 Signed-off-by: Fotis Georgatos --- ...-4.6.1-goolfc-2.6.10.eb => GROMACS-4.6.5-goolfc-2.6.10.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-4.6.1-goolfc-2.6.10.eb => GROMACS-4.6.5-goolfc-2.6.10.eb} (94%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb similarity index 94% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb index 40a4d861ce..5c6e6ac80d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb @@ -14,7 +14,7 @@ easyblock = 'CMakeMake' name = 'GROMACS' -version = '4.6.1' +version = '4.6.5' homepage = 'http://www.gromacs.org' description = """GROMACS is a versatile package to perform molecular dynamics, @@ -22,7 +22,7 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'goolfc', 'version': '2.6.10'} -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz sources = [ SOURCELOWER_TAR_GZ, 'regressiontests-%(version)s.tar.gz', -- GitLab From e306e498766a1717fec6255650631c1fba48ba95 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 17 Dec 2013 00:55:52 +0100 Subject: [PATCH 150/566] promote version of hwloc from 1.7.2 to 1.8 Signed-off-by: Fotis Georgatos --- ...wloc-1.7.2-gcccuda-2.6.10.eb => hwloc-1.8-gcccuda-2.6.10.eb} | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/hwloc/{hwloc-1.7.2-gcccuda-2.6.10.eb => hwloc-1.8-gcccuda-2.6.10.eb} (98%) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb similarity index 98% rename from easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb index f554e7a62a..16ef9ff42e 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8-gcccuda-2.6.10.eb @@ -1,5 +1,5 @@ name = 'hwloc' -version = "1.7.2" +version = "1.8" 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/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 7912a2d94c..9198983666 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 @@ -15,7 +15,7 @@ builddependencies = [ ] dependencies = [ - ('hwloc', '1.7.2'), + ('hwloc', '1.8'), ] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' -- GitLab From 54191fc3b951d9086b090e3a18535bd9ea9b375e Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 17 Dec 2013 01:27:56 +0100 Subject: [PATCH 151/566] add netloc and its dep Jansson Signed-off-by: Fotis Georgatos --- .../j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb | 28 +++++++++++++++++++ .../n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb | 25 +++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb create mode 100644 easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..cc9e526be3 --- /dev/null +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb @@ -0,0 +1,28 @@ +name = 'Jansson' +version = "2.5" + +homepage = 'http://www.digip.org/jansson/' +description = """Jansson is a C library for encoding, decoding and manipulating JSON data. + Its main features and design principles are: + * Simple and intuitive API and data model + * Comprehensive documentation + * No dependencies on other libraries + * Full Unicode support (UTF-8) + * Extensive test suite""" + +toolchain = {'name': 'gcccuda', 'version': '2.6.10'} + +# fi. https://github.com/akheron/jansson/archive/2.5.zip +source_urls = ['https://github.com/akheron/jansson/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Autoconf', '2.69')] + +preconfigopts = 'autoreconf -i && ' + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb new file mode 100644 index 0000000000..b8c85aae37 --- /dev/null +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb @@ -0,0 +1,25 @@ +name = 'netloc' +version = "0.5" +versionsuffix = "beta" + +homepage = 'http://www.open-mpi.org/software/netloc' +description = """The Portable Network Locality (netloc) software package provides + network topology discovery tools, and an abstract representation of those networks + topologies for a range of network types and configurations. + It is provided as a companion to the Portable Hardware Locality (hwloc) package.""" + +toolchain = {'name': 'gcccuda', 'version': '2.6.10'} + +dependencies = [ + ('hwloc', '1.8'), + ('Jansson', '2.5'), +] + +configopts = '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support + +# fi. http://www.open-mpi.org/software/netloc/v0.5/downloads/netloc-0.5.tar.gz +source_urls = [ homepage + '/v%(version_major_minor)s/downloads'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' -- GitLab From 023402da37d72bb2e2b0398ee0cf9226f952f556 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 17 Dec 2013 01:32:18 +0100 Subject: [PATCH 152/566] also do runtest for jansson Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb index cc9e526be3..5bc100cb87 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb @@ -25,4 +25,6 @@ sanity_check_paths = { 'dirs': ['include'], } +runtest = 'check' + moduleclass = 'devel' -- GitLab From 9d66a446c8f643f4bbd1375e2ca5f6f01e24d885 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 17 Dec 2013 13:11:34 +0100 Subject: [PATCH 153/566] added BEDTools-2.18.1-goolf-1.4.10.eb --- .../BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb 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 new file mode 100644 index 0000000000..47e6beb8fd --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +name = 'BEDTools' +version = '2.18.1' + +easyblock = 'MakeCp' + +homepage = "https://github.com/arq5x/bedtools2" +description = """A powerful toolset for genome arithmetic.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/archive/'] + +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': [], +} + +moduleclass = 'bio' -- GitLab From b3cbdbcfe394a489e8d5828ea7470aba9b55b835 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 17 Dec 2013 13:51:34 +0100 Subject: [PATCH 154/566] cutadapt-1.3-goolf-1.4.10 --- .../cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 33 +++++++++++++++++++ .../cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb 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 new file mode 100644 index 0000000000..a13b2285f2 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.3' + +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 = ['http://cutadapt.googlecode.com/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.3' +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/calign.so',], + 'dirs': [], +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000..df852e5316 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,33 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.3' + +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 = ['http://cutadapt.googlecode.com/files/'] +sources = ['%(namelower)s-%(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','lib/python2.7/site-packages/cutadapt/calign.so',], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 0d89376b5c4a52b18e462f3ee01c00b7fd5f95ef Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 17 Dec 2013 15:22:24 +0100 Subject: [PATCH 155/566] CHARMM: updated to remarks in PR --- ...7b2-ictce-5.5.0-nompi.eb => CHARMM-37b2-ictce-5.5.0-mt.eb} | 2 +- easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch | 1 + easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch | 4 +++- easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch | 1 + 4 files changed, 6 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CHARMM/{CHARMM-37b2-ictce-5.5.0-nompi.eb => CHARMM-37b2-ictce-5.5.0-mt.eb} (97%) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb similarity index 97% rename from easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb rename to easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index 25b23807a7..cd544770d0 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-nompi.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -2,7 +2,7 @@ name = "CHARMM" version = "37b2" -versionsuffix = "nompi" +versionsuffix = "-mt" homepage = "http://www.charmm.org" description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile diff --git a/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch b/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch index 3ec2563cdb..e2261c3173 100644 --- a/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch +++ b/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch @@ -1,4 +1,5 @@ # fix a error in the main +# By Ward Poelmans diff -ur c37b2.orig/source/charmm/charmm_main.src c37b2/source/charmm/charmm_main.src --- c37b2.orig/source/charmm/charmm_main.src 2013-02-11 06:27:24.000000000 +0100 +++ c37b2/source/charmm/charmm_main.src 2013-12-03 16:30:45.539579132 +0100 diff --git a/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch b/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch index 2365077555..291948be88 100644 --- a/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch +++ b/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch @@ -1,4 +1,6 @@ -# fixes compile error. Always display the warning +# fixes compile error: for some reason, ifort fails on this (possibly compiler bug) +# As a solution, we always display the warning +# By Ward Poelmans diff -ur c37b2.orig/source/squantm/sqnt_qm2_ewald.src c37b2/source/squantm/sqnt_qm2_ewald.src --- c37b2.orig/source/squantm/sqnt_qm2_ewald.src 2012-07-17 01:08:32.000000000 +0200 +++ c37b2/source/squantm/sqnt_qm2_ewald.src 2013-12-03 14:11:46.945196858 +0100 diff --git a/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch b/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch index deb270dfb2..1bfab91ec4 100644 --- a/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch +++ b/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch @@ -1,4 +1,5 @@ # lets use the flags the EB sets for us +# By Ward Poelmans diff -ur c37b2.orig/build/UNX/Makefile_em64t c37b2/build/UNX/Makefile_em64t --- c37b2.orig/build/UNX/Makefile_em64t 2012-07-10 14:06:18.000000000 +0200 +++ c37b2/build/UNX/Makefile_em64t 2013-12-03 15:35:18.997245768 +0100 -- GitLab From 3686f7ec5fb7737dbf5e3ce95deff7275a66cdd6 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Dec 2013 15:39:53 +0100 Subject: [PATCH 156/566] added vsc-base and vsc-mympirun --- .../easyconfigs/v/vsc-base/vsc-base-1.6.9.eb | 19 +++++++++++++++ .../v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 23 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb new file mode 100644 index 0000000000..3f28389ec6 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb @@ -0,0 +1,19 @@ +easyblock = 'VersionIndependendPythonPackage' +name = 'vsc-base' +version = '1.6.9' + +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-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb new file mode 100644 index 0000000000..12fd4698df --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependendPythonPackage' +name = 'vsc-mympirun' +version = '3.2.1' + +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-mympirun/archive/', +] + +dependencies = [('vsc-base', '1.6.9')] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +moduleclass = 'tools' -- GitLab From 31a869b31314c3ac7ced7ce5d3d3e5dc67abc63d Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 17 Dec 2013 15:53:15 +0100 Subject: [PATCH 157/566] CHARMM: remove g09 dep --- .../c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb | 5 ----- .../easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb | 4 ---- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 6 ------ 3 files changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb index 75a0e78635..6a211df95b 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb @@ -17,11 +17,6 @@ patches = [ "main-case-fix-%(version)s.patch", ] -# if you specify Gaussian, it will be used for the QM part. -dependencies = [ -# ('Gaussian', 'g09_D.01', '-amd64-gpfs'), -] - # FFTW will automatically be used because of the toolchain build_options = ["FULL", "COLFFT", "PIPF"] diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index cd544770d0..446ccaff83 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -19,10 +19,6 @@ patches = [ "main-case-fix-%(version)s.patch", ] -dependencies = [ -# ('Gaussian', 'g09_D.01-ictce-5.5.0-amd64-gpfs') -] - # MKL activated automatically when the MKL is found, same for g09 build_options = ["FULL", "COLFFT", "PIPF"] diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb index ca44f64f49..dec6c5408f 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -18,12 +18,6 @@ patches = [ "main-case-fix-%(version)s.patch", ] -# if you specify Gaussian, it will be used for the QM part. -# if you specify FFTW, it will be used instead of the MKL -dependencies = [ -# ('Gaussian', 'g09_D.01', '-amd64-gpfs') -] - # MKL activated automatically when the ictce toolchain is used build_options = ["FULL", "COLFFT", "PIPF"] -- GitLab From 88855caf526a3eb075d873b0ab565b87d0581341 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 17 Dec 2013 15:55:25 +0100 Subject: [PATCH 158/566] CHARMM: updated build options to new easyblock We now use a string instead of list. --- .../easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb | 2 +- easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb index 6a211df95b..928c867d0a 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-goalf-1.5.12-no-OFED.eb @@ -18,7 +18,7 @@ patches = [ ] # FFTW will automatically be used because of the toolchain -build_options = ["FULL", "COLFFT", "PIPF"] +build_options = "FULL COLFFT PIPF" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb index 446ccaff83..3485ce9ee9 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0-mt.eb @@ -20,7 +20,7 @@ patches = [ ] # MKL activated automatically when the MKL is found, same for g09 -build_options = ["FULL", "COLFFT", "PIPF"] +build_options = "FULL COLFFT PIPF" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb index dec6c5408f..81f90923f0 100644 --- a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-ictce-5.5.0.eb @@ -19,7 +19,7 @@ patches = [ ] # MKL activated automatically when the ictce toolchain is used -build_options = ["FULL", "COLFFT", "PIPF"] +build_options = "FULL COLFFT PIPF" # Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce system_size = "medium" -- GitLab From 65e38573905733815ba69b5e9ad7815ce4194b5c Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Dec 2013 16:52:45 +0100 Subject: [PATCH 159/566] reverted bump of distribute in Python-3.2.3-ictce-5.3.0.eb --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) 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 66d906e00a..ad55ab0b99 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 @@ -24,9 +24,10 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], - }), + ('distribute', '0.6.26', { + 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'modulename': 'setuptools', + ) ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), -- GitLab From eb901afacac6994003ca3f8edeb3089d33fc8e3b Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Dec 2013 16:55:31 +0100 Subject: [PATCH 160/566] reverted bump of distribute in Python-3.2.3-ictce-5.3.0.eb --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) 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 ad55ab0b99..647a552ff9 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 @@ -24,6 +24,8 @@ dependencies = [ # order is important! exts_list = [ + # This should actually be bumped to 'setuptools', '1.4.1' see + # https://github.com/hpcugent/easybuild-easyconfigs/pull/563#discussion-diff-8024693R27 ('distribute', '0.6.26', { 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', -- GitLab From f99d9423ffbe519ea62a7b9e60e7eb74de17b062 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Tue, 17 Dec 2013 18:01:22 +0100 Subject: [PATCH 161/566] added , --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 647a552ff9..8c0e2e548c 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 @@ -29,7 +29,7 @@ exts_list = [ ('distribute', '0.6.26', { 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', - ) + ), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), -- GitLab From 4fe121d20a99fcaf794b5ca74d79c36117368d85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:31:45 +0100 Subject: [PATCH 162/566] style fixes in HDF easyconfigs --- .../h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 8 ++++---- .../h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 8 ++++---- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 8 ++++---- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 10 +++++----- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 8 ++++---- 6 files changed, 25 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 4280af21ba..ca672a8ed9 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index b4ea04cfdb..ac9ee252e4 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -7,10 +7,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index b18ddf73bb..66fffd032c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 2914eadfc9..341fa0c50d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -9,10 +9,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('Szip', '2.1'), - ] + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index 6a6f38583d..4f8fd04bf4 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -8,13 +8,13 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), - ('Szip', '2.1'), - ] + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/] configopts = "--with-szlib=$EBROOTSZIP" diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 1706cf2d0c..63497c73fd 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -8,10 +8,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), - ('Szip', '2.1'), - ] + ('flex', '2.5.37'), + ('Bison', '2.7'), + ('Szip', '2.1'), +] sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -- GitLab From da92bce9baab0c0b8f07fb9858cdab8338b2ca8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:39:04 +0100 Subject: [PATCH 163/566] style fixes in MUMmer easyconfigs --- .../m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb | 7 ++++--- .../m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb | 8 +++++--- .../easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb | 8 +++++--- easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb | 7 ++++--- .../m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb | 8 +++++--- .../m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb | 7 ++++--- easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb | 7 ++++--- 7 files changed, 31 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb index 2c1a1daf0a..8ad0e5e710 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb @@ -14,12 +14,13 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb index e610d327ac..cc1c5b9528 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10-Perl-5.16.3.eb @@ -14,12 +14,14 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb index 68e6cd4aaf..3a1c6157f6 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goolf-1.4.10.eb @@ -14,11 +14,13 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb index 9a5bbfccf4..ee85659115 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb @@ -14,12 +14,13 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb index a8ee9f8f89..b85beabd73 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb @@ -14,12 +14,14 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" + toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb index 9d63283dc3..6148c2da6e 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0-Perl-5.16.3.eb @@ -14,13 +14,14 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb index 03ba013834..e11bf5f61d 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-5.3.0.eb @@ -14,13 +14,14 @@ name = 'MUMmer' version = '3.23' homepage = 'http://mummer.sourceforge.net/' -description = """MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.""" +description = """MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s%s.tar.gz' % (name, version)] -source_urls = [('http://sourceforge.net/projects/mummer/files/%s/%s/' % (name.lower(), version), 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] moduleclass = 'bio' -- GitLab From 8e94ee6aaf0c6219ddeaddafe006a52a9eb7d9a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:40:23 +0100 Subject: [PATCH 164/566] style fixes in molmod easyconfigs --- .../m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb | 3 ++- .../m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb index 2521556c73..08d2e9759c 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-goolf-1.4.10-Python-2.7.3.eb @@ -23,7 +23,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb index 7f4ed72e6c..e697762256 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb @@ -23,7 +23,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb index 42b1105348..221229e3a6 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -23,7 +23,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], -- GitLab From d4582d95448aa68e8fd8aff374659a3c2d8c8d50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:42:16 +0100 Subject: [PATCH 165/566] style fixes in OTF easyconfigs --- easybuild/easyconfigs/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb | 3 +-- easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb index e2416b4554..23a2067ba3 100644 --- a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-gompi-1.4.12-no-OFED.eb @@ -8,7 +8,6 @@ ## name = "OTF" version = "1.12.4" -majorsuffix = 'salmon' homepage = 'http://www.tu-dresden.de/zih/otf/' description = """The Open Trace Format is a highly scalable, memory efficient event @@ -18,7 +17,7 @@ description = """The Open Trace Format is a highly scalable, memory efficient ev toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} # http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.4salmon.tar.gz -sources = ['%%(name)s-%%(version)s%s.tar.gz' % majorsuffix] +sources = ['%(name)s-%(version)ssalmon.tar.gz'] source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get='] # name change in version 1.12.3: "open-trace-format" was "otf" in older versions diff --git a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb index 34d46acb15..0d0f9bbf97 100644 --- a/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF/OTF-1.12.4-ictce-5.3.0.eb @@ -8,7 +8,6 @@ ## name = "OTF" version = "1.12.4" -majorsuffix = 'salmon' homepage = 'http://www.tu-dresden.de/zih/otf/' description = """The Open Trace Format is a highly scalable, memory efficient event @@ -18,7 +17,7 @@ description = """The Open Trace Format is a highly scalable, memory efficient ev toolchain = {'name': 'ictce', 'version': '5.3.0'} # http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.4salmon.tar.gz -sources = ['%%(name)s-%%(version)s%s.tar.gz' % majorsuffix] +sources = ['%(name)s-%(version)ssalmon.tar.gz'] source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get='] # name change in version 1.12.3: "open-trace-format" was "otf" in older versions -- GitLab From 75f1a8faa41682641d8260a4c0fc97f5fce8596f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:44:34 +0100 Subject: [PATCH 166/566] style fixes in OpenBLAS easyconfigs --- .../o/OpenBLAS/OpenBLAS-0.2.6-cgmpich-1.1.6-LAPACK-3.4.2.eb | 2 +- .../OpenBLAS-0.2.6-cgmvapich2-1.1.12rc1-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.2.7-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-cgompi-1.1.7-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb | 2 +- .../OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmpich-1.1.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmpich-1.1.6-LAPACK-3.4.2.eb index 4c5aa495a3..3d70563ce7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmpich-1.1.6-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmpich-1.1.6-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.1.12rc1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.1.12rc1-LAPACK-3.4.2.eb index 7edb3a4acf..a34682d998 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.1.12rc1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.1.12rc1-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.2.7-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.2.7-LAPACK-3.4.2.eb index 02701dd4c9..5d51f5f66c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.2.7-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgmvapich2-1.2.7-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgompi-1.1.7-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgompi-1.1.7-LAPACK-3.4.2.eb index f2e81ac46b..f7fcbb964f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgompi-1.1.7-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-cgompi-1.1.7-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb index 12c01f0dfb..70c17c320e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb index 894db5aef6..7689f17f2e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gmvapich2-1.7.12rc1-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb index c7072566fc..500a1a4501 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index 95abb118d2..ada05e324e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index c32ddbd8d2..cf3256ea5a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index 6692010d4e..57cde75cef 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - # 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index 1ea6e6468c..50eb836081 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -26,7 +26,7 @@ source_urls = [ ] patches = [ - # 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), -- GitLab From e9cfb35c4d426fd2fb1d8f285062b71b8cd7688d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:45:42 +0100 Subject: [PATCH 167/566] remove OpenBLAS Makefile patch for recent OpenBLAS versions --- .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 1 - .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index 57cde75cef..005cd85340 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -26,7 +26,6 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index 50eb836081..15f2df5280 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -26,7 +26,6 @@ source_urls = [ ] patches = [ - 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), -- GitLab From 9532cc5255f1a1f97aaac0649e59b0bc38b0a9c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:47:41 +0100 Subject: [PATCH 168/566] style fixes in PSI easyconfigs --- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb | 4 ++-- easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb | 4 ++-- 10 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb index 257d8f97ad..d3cae5bf6c 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb @@ -4,8 +4,8 @@ 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.""" + 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': 'ictce', 'version': '4.1.13'} # not using MPI results in a build relying on multithreaded BLAS solely diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb index 78a59d7159..0325be769c 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb @@ -3,8 +3,8 @@ version = '4.0b4' 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.""" + 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': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb index d9bf4f7fd5..ea25a8f6c0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb @@ -4,8 +4,8 @@ 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.""" + 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': 'ictce', 'version': '5.3.0'} # not using MPI results in a build relying on multithreaded BLAS solely diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb index 55585c69df..9d5ff82601 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb @@ -3,8 +3,8 @@ version = '4.0b4' 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.""" + 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': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb index baeac81b77..aaa504d53c 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb @@ -4,8 +4,8 @@ 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.""" + 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': 'goalf', 'version': '1.5.12-no-OFED'} # not using MPI results in a build relying on multithreaded BLAS solely diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb index 99696fe235..6882ac49f0 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb @@ -3,8 +3,8 @@ version = '4.0b5' 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.""" + 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': 'goalf', 'version': '1.5.12-no-OFED'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb index 5e2d6e7d5e..51a7d52ca8 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb @@ -4,8 +4,8 @@ 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.""" + 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': 'ictce', 'version': '5.3.0'} # not using MPI results in a build relying on multithreaded BLAS solely diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb index 324e93c116..7ded97c33e 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb @@ -3,8 +3,8 @@ version = '4.0b5' 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.""" + 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': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb index 33a7817cd8..089a136deb 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb @@ -4,8 +4,8 @@ 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.""" + 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': 'ictce', 'version': '5.5.0'} # not using MPI results in a build relying on multithreaded BLAS solely diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb index 6c090df7b7..863bb18040 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb @@ -3,8 +3,8 @@ version = '4.0b5' 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.""" + 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': 'ictce', 'version': '5.5.0'} toolchainopts = {'usempi': True} -- GitLab From 380b8da7fe4c877ad429dadef8386c94cbe04635 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:52:04 +0100 Subject: [PATCH 169/566] style fixes in scikit-learn easyconfigs --- .../scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb | 1 + .../s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb index 5e0d6b5e2f..4e7c9c3f6d 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb @@ -10,6 +10,7 @@ it provides versatile tools for data mining and analysis in any field of science It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} + source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb index fb08bf0088..d7df74419b 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -11,6 +11,7 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] + sources = [SOURCE_TAR_GZ] python = "Python" -- GitLab From de6644c6cecb5a281b829de88d6325e9186cbf0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:56:39 +0100 Subject: [PATCH 170/566] style fixes in WPS easyconfigs --- .../w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb | 10 +++++----- .../w/WPS/WPS-3.3.1-goolf-1.4.10-dmpar.eb | 2 +- .../w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb | 10 +++++----- .../easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb | 10 +++++----- .../w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb | 12 ++++++------ .../w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb | 12 ++++++------ .../easyconfigs/w/WPS/WPS-3.4-ictce-5.3.0-dmpar.eb | 12 ++++++------ .../easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb | 12 ++++++------ .../w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb | 12 ++++++------ 9 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb index 66840bc3fb..bf9ebc38cd 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb @@ -16,10 +16,10 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.1.3'), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.1.3'), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goolf-1.4.10-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goolf-1.4.10-dmpar.eb index d191598cb4..cf9f032fe1 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goolf-1.4.10-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-goolf-1.4.10-dmpar.eb @@ -19,7 +19,7 @@ dependencies = [ ('WRF', version, versionsuffix), ('netCDF', '4.1.3'), ('libpng', '1.5.11'), - ('JasPer', '1.900.1') + ('JasPer', '1.900.1'), ] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb index 16a3c57158..8431eafd57 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-3.2.2.u3-dmpar.eb @@ -16,10 +16,10 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.1.3'), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.1.3'), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb index eaf41baf93..9a70c0a0be 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.3.1-ictce-5.3.0-dmpar.eb @@ -16,10 +16,10 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.1.3'), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.1.3'), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb index df3c22e073..9e0cde67a1 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4-goalf-1.1.0-no-OFED-dmpar.eb @@ -20,11 +20,11 @@ versionsuffix = '-%s' % buildtype netcdf_version = '4.2' dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', netcdf_version), - ('netCDF-Fortran', netcdf_version), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', netcdf_version), + ('netCDF-Fortran', netcdf_version), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb index 0f57f30f8f..ceaf726698 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-3.2.2.u3-dmpar.eb @@ -20,11 +20,11 @@ versionsuffix = '-%s' % buildtype netcdf_version = '4.2' dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', netcdf_version), - ('netCDF-Fortran', netcdf_version), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', netcdf_version), + ('netCDF-Fortran', netcdf_version), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-5.3.0-dmpar.eb index d43822d6cd..ef8b3b3cc6 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-5.3.0-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4-ictce-5.3.0-dmpar.eb @@ -19,11 +19,11 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.2.1.1'), - ('netCDF-Fortran', '4.2'), - ('libpng', '1.5.11'), - ('JasPer', '1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('libpng', '1.5.11'), + ('JasPer', '1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb index 3dfc001558..a520db3494 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-ictce-5.3.0-dmpar.eb @@ -18,11 +18,11 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.2.1.1'), - ('netCDF-Fortran', '4.2'), - ('libpng', '1.5.14'), - ('JasPer','1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('libpng', '1.5.14'), + ('JasPer','1.900.1'), +] moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb index a4441004d5..a11ffd3dd5 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.4.1-iqacml-3.7.3-dmpar.eb @@ -18,11 +18,11 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, versionsuffix), - ('netCDF', '4.2.1.1'), - ('netCDF-Fortran', '4.2'), - ('libpng', '1.5.14'), - ('JasPer','1.900.1') - ] + ('WRF', version, versionsuffix), + ('netCDF', '4.2.1.1'), + ('netCDF-Fortran', '4.2'), + ('libpng', '1.5.14'), + ('JasPer','1.900.1'), +] moduleclass = 'geo' -- GitLab From d3f733d7471402d34537f7b7328b0138ac6e2098 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 20:59:19 +0100 Subject: [PATCH 171/566] style fixes in yaff easyconfigs --- .../easyconfigs/y/yaff/yaff-1.0-goolf-1.4.10-Python-2.7.3.eb | 3 ++- .../easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb | 3 ++- .../easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0-goolf-1.4.10-Python-2.7.3.eb index 15ffe15aee..18d7701786 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0-goolf-1.4.10-Python-2.7.3.eb @@ -26,7 +26,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb index a08ebd67d7..cdf3df85de 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-4.1.13-Python-2.7.3.eb @@ -26,7 +26,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb index e0ef7ac9a4..ed6b897594 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.0-ictce-5.3.0-Python-2.7.3.eb @@ -26,7 +26,8 @@ dependencies = [ ] # disable tests that require X11 by specifying "backend: agg" in matplotlibrc -runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; python setup.py build_ext -i; nosetests -v' +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' sanity_check_paths = { 'files': [], -- GitLab From 0f270d08fbcee7ff203d80bb18d2933eb4719bfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 21:09:08 +0100 Subject: [PATCH 172/566] fix typo in HDF easyconfig + missing style fix --- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index 4f8fd04bf4..2035306c6a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -14,7 +14,7 @@ dependencies = [ ] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] configopts = "--with-szlib=$EBROOTSZIP" diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 63497c73fd..5a9f8c793a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -14,7 +14,7 @@ dependencies = [ ] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] configopts = "--with-szlib=$EBROOTSZIP" -- GitLab From 5dbadd375ee39afcb51c219dbcd6b3674d11e35f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Dec 2013 22:27:31 +0100 Subject: [PATCH 173/566] fix HDF v4.2.7 deps --- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 66fffd032c..d0446b5752 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -8,8 +8,8 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), + ('flex', '2.5.35'), + ('Bison', '2.5'), ('Szip', '2.1'), ] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 341fa0c50d..1ad7d6ac5c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -9,8 +9,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} dependencies = [ - ('flex', '2.5.37'), - ('Bison', '2.7'), + ('flex', '2.5.35'), + ('Bison', '2.5'), ('Szip', '2.1'), ] -- GitLab From 0b60f34ab8dd8ebc7c28bf17b8f788962de3d621 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 18 Dec 2013 01:49:16 +0100 Subject: [PATCH 174/566] removed CBLAS for ictce-5.3.0 Signed-off-by: Fotis Georgatos --- .../c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb deleted file mode 100644 index 41a61d1d6f..0000000000 --- a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-ictce-5.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'CBLAS' -version = '20110120' - -homepage = 'http://www.netlib.org/blas/' -description = "C interface to the BLAS" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.netlib.org/blas/blast-forum/'] -sources = ['cblas.tgz'] - -patches = ['CBLAS_shared-lib.patch'] - -makeopts = 'all shared' - -# parallel build fails occasionally -parallel = 1 - -runtest = 'runtst' - -moduleclass = 'numlib' -- GitLab From 57276b9feee33eec08ff8d3cfbc90da5b7e357f6 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 18 Dec 2013 01:57:29 +0100 Subject: [PATCH 175/566] remove GROMACS-4.6.1-ictce-5.3.0.eb Signed-off-by: Fotis Georgatos --- .../g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb deleted file mode 100644 index 6704a1c189..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0.eb +++ /dev/null @@ -1,40 +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 -## - -easyblock = 'CMakeMake' - -name = 'GROMACS' -version = '4.6.1' - -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': '5.3.0'} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.tar.gz', -] -source_urls = [ - 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources - 'http://gerrit.gromacs.org/download/', # regression tests sources -] - -builddependencies = [('CMake', '2.8.4')] - -configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" -runtest = 'check' - -moduleclass = 'bio' -- GitLab From fe5e3a0c96055c7bb04b4a66036120bd307058c7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 18 Dec 2013 02:08:45 +0100 Subject: [PATCH 176/566] remove OpenSSL-1.0.0-ictce-5.3.0.eb Signed-off-by: Fotis Georgatos --- .../o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb deleted file mode 100644 index 0d17976392..0000000000 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.0-ictce-5.3.0.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'OpenSSL' -version = '1.0.0' - -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': 'ictce', 'version': '5.3.0'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.openssl.org/source/'] - -dependencies = [('zlib', '1.2.7')] - -# makefile is not suitable for parallel build -parallel = 1 -runtest = 'test' - -moduleclass = 'system' -- GitLab From b13d24039db8f0036a7c2df5a21e5adb604399bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 07:44:46 +0100 Subject: [PATCH 177/566] mark flex/Bison as build dependencies of Doxygen rather than actual deps --- .../d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb | 4 ++-- .../easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb | 2 +- .../easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb | 4 ++-- 11 files changed, 21 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb index a617a2a35e..94124552fa 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb index d5037c4b63..50e6f2e0f5 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb @@ -10,7 +10,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [('flex', '2.5.35'), - ('Bison', '2.5')] +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5'), +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb index f8cc37f0d7..2b4093a0c4 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb index 134c1f4a23..6fe341a2e4 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb index 32150d37b1..0a291437d5 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb index 69ca07e3c9..46e392d855 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb index 433f76db8e..4e0322abc4 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.37'), ('Bison', '2.6.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb index 064fa6f372..2793cce845 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.37'), ('Bison', '2.6.5'), - ] +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb index 9962c84d18..9b648008e6 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.37'), ('Bison', '2.7'), ] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb index 1af9922e91..b9145b9d9d 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.37'), ('Bison', '2.7'), ] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb index a3abb79c1b..17c6df3ade 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb @@ -10,9 +10,9 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = ['%(namelower)s-%(version)s.src.tar.gz'] source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] -dependencies = [ +builddependencies = [ ('flex', '2.5.37'), ('Bison', '2.7'), - ] +] moduleclass = 'devel' -- GitLab From d6da9522cdb67ed12c2fbaac42b70686205cdd89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 07:47:44 +0100 Subject: [PATCH 178/566] style fixes for g2clib easyconfigs --- .../g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb | 6 +++--- .../easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb | 6 +++--- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb | 7 +++---- .../easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb | 6 +++--- .../easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb | 6 +++--- 6 files changed, 18 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb index dbced3e64b..1f22264a23 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder ("C" version).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb index 40a9844a04..f03d5ac65f 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb @@ -6,11 +6,11 @@ description = """Library contains GRIB2 encoder/decoder ("C" version).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb index 6626ea0412..e5c7bb899d 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder ("C" version).""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb index 1e29860282..64379dcbec 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb @@ -4,15 +4,14 @@ version = '1.2.3' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder ("C" version).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb index 42f32bafc7..cd304a31b0 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder ("C" version).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb index 36b9488a21..568873fa47 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder ("C" version).""" toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + # parallel build tends to fail parallel = 1 -- GitLab From 2e8ab8413c76971179430c0abfd54d6344ebfa9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 07:48:59 +0100 Subject: [PATCH 179/566] style fixes for g2lib easyconfigs --- .../easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb | 6 +++--- easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb | 6 +++--- .../easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb | 6 +++--- easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb | 7 +++---- easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb | 6 +++--- easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb | 6 +++--- 6 files changed, 18 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb index cd9cd1eda9..0ab3fe63d5 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder and search/indexing rout toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb index d471cd44b2..afcd635a41 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goolf-1.4.10.eb @@ -6,11 +6,11 @@ description = """Library contains GRIB2 encoder/decoder and search/indexing rout toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb index 7012aa01db..5f3786879f 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder and search/indexing rout toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb index c7e5c2c63f..0cce533391 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-5.3.0.eb @@ -4,15 +4,14 @@ version = '1.2.4' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb index 73e2caf3fb..6afe34db8d 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder and search/indexing rout toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb index 7e04bd54d3..deaffbea8e 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb @@ -7,11 +7,11 @@ description = """Library contains GRIB2 encoder/decoder and search/indexing rout toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True} -dependencies = [('JasPer', '1.900.1')] - -sources = ['%s-%s.tar' % (name, version)] +sources = [SOURCE_TAR] source_urls = [homepage] +dependencies = [('JasPer', '1.900.1')] + patches = ['fix_makefile.patch'] # parallel build tends to fail -- GitLab From cbb3cbae5e18cd0f976cb6efb37b9648194f0dca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 07:51:25 +0100 Subject: [PATCH 180/566] style fixes for HDF, HDF5 and libjpeg-turbo easyconfigs --- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 4 +++- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 3 ++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 3 ++- .../easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb | 2 +- .../l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb | 3 ++- 8 files changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 6c4821a391..2afcef011a 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -2,7 +2,8 @@ name = 'HDF' version = '4.2.7-patch1' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index 1ca5d08181..ddec0bbdd1 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -2,7 +2,9 @@ name = 'HDF' version = '4.2.7-patch1' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index d71e54280e..7bf50ddd9d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -2,7 +2,8 @@ name = 'HDF' version = '4.2.7-patch1' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index df3727db52..8e8c3a76f4 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -2,8 +2,8 @@ name = 'HDF' version = '4.2.7-patch1' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" - +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index 12c89a77b4..0810f8a775 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -2,7 +2,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index a83caaaf0c..8cf209069c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -2,7 +2,8 @@ name = 'HDF' version = '4.2.8' homepage = 'http://www.hdfgroup.org/products/hdf4/' -description = """HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.""" +description = """HDF (also known as HDF4) is a library and multi-object file format for storing + and managing data between machines.""" toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True, 'pic': True} diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb index b1532bad95..3003f14877 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('zlib', '1.2.7'), - ('Szip','2.1'), + ('Szip', '2.1'), ] configopts = "--enable-gpfs --enable-threadsafe --enable-production " diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb index a8b098068f..60866e8337 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb @@ -5,7 +5,8 @@ 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': 'ictce', 'version': '4.1.13'} # tweaked by EasyBuild (was: {'name': 'ictce', 'version': '4.0.10'}) + +toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] -- GitLab From 3df653d3bc60220322c94432e145094e787a0b13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 09:06:54 +0100 Subject: [PATCH 181/566] make sure patch file is used in all M4 easyconfigs --- easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb | 2 ++ easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb index 5f1bea4076..104b577f90 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/m4'] +patches = ['M4-%(version)s-no-gets.patch'] + configopts = "--enable-cxx" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb index 5f6973dba4..175c5e78af 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-GCC-4.8.2.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/m4'] +patches = ['M4-%(version)s-no-gets.patch'] + configopts = "--enable-cxx" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb index 2175e7a770..68b005dc52 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftpmirror.gnu.org/m4'] +patches = ['M4-%(version)s-no-gets.patch'] + configopts = "--enable-cxx" sanity_check_paths = { -- GitLab From d77982820ce717aa5b8d75b617baeda086602074 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 18 Dec 2013 10:04:43 +0100 Subject: [PATCH 182/566] fixed syntax error --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 8c0e2e548c..5153420960 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 @@ -29,7 +29,7 @@ exts_list = [ ('distribute', '0.6.26', { 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', - ), + }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], }), -- GitLab From 1ee53df508027c952830b8d65d2708c201459fdd Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 18 Dec 2013 10:15:10 +0100 Subject: [PATCH 183/566] fixed indentation --- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) 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 a13b2285f2..5a8435dee3 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 @@ -8,7 +8,11 @@ name = 'cutadapt' version = '1.3' 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. """ +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'} -- GitLab From c4b321bd47cb6b464e3a6d068dc37c6bf993143e Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 18 Dec 2013 10:17:27 +0100 Subject: [PATCH 184/566] fix indent second eb file --- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) 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 df852e5316..abd9e43447 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 @@ -8,7 +8,11 @@ name = 'cutadapt' version = '1.3' 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. """ +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'} -- GitLab From 0497c9179046d56d1807df138ca1fb8029a5aa73 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 18 Dec 2013 12:09:19 +0100 Subject: [PATCH 185/566] remove p/Python/Python-2.5.6-ictce-5.3.0-bare.eb Signed-off-by: Fotis Georgatos --- .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb 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 deleted file mode 100644 index 68a4b58e99..0000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'Python' -version = '2.5.6' -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': 'ictce', 'version': '5.3.0'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] - -patches = ['python_libffi_int128_icc.patch'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.7'), - ('libreadline', '6.2'), - ('ncurses', '5.9'), -] - -moduleclass = 'lang' -- GitLab From 33c02f771e4897116b3712178c78c2816c9272b1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 18 Dec 2013 12:15:56 +0100 Subject: [PATCH 186/566] CP2K: reworked after remarks. --- ...tsvn.patch => CP2K-2.4.0-fix_compile_date_lastsvn.patch} | 0 easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb | 5 ++--- easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb | 6 +++--- ...fix.patch => CP2K-20131211-ifort-compiler-bug-fix.patch} | 0 easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb | 6 +++--- 5 files changed, 8 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/c/CP2K/{fix_compile_date_lastsvn.patch => CP2K-2.4.0-fix_compile_date_lastsvn.patch} (100%) rename easybuild/easyconfigs/c/CP2K/{ifort-compiler-bug-fix.patch => CP2K-20131211-ifort-compiler-bug-fix.patch} (100%) diff --git a/easybuild/easyconfigs/c/CP2K/fix_compile_date_lastsvn.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-fix_compile_date_lastsvn.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/fix_compile_date_lastsvn.patch rename to easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-fix_compile_date_lastsvn.patch diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb index b1ca163f20..ff604547cf 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb @@ -15,11 +15,10 @@ source_urls = [SOURCEFORGE_SOURCE] patches = [ 'do_regtest_nocompile.patch', - 'ifort-compiler-bug-fix.patch', - 'fix_compile_date_lastsvn.patch', + 'CP2K-20131211-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -## use FFTW, with FFTACML there are extra failures in regtests dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.0.1'), diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb index 61301c6ae4..1d06d1dfc9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb @@ -10,14 +10,14 @@ classical pair and many-body potentials. """ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} +# Uses a svn checkout from 20131211 (r13439) sources = [SOURCE_TAR_BZ2] patches = [ - 'ifort-compiler-bug-fix.patch', - 'fix_compile_date_lastsvn.patch', + 'CP2K-20131211-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', ] -## use FFTW, with FFTACML there are extra failures in regtests dependencies = [ ('Libint', '1.1.4'), ('libxc', '2.0.1'), diff --git a/easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ifort-compiler-bug-fix.patch similarity index 100% rename from easybuild/easyconfigs/c/CP2K/ifort-compiler-bug-fix.patch rename to easybuild/easyconfigs/c/CP2K/CP2K-20131211-ifort-compiler-bug-fix.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb index 53b0b9a430..7b83d19f9b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-5.5.0.eb @@ -5,12 +5,12 @@ 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': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True} +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + configopts = 'FC="$F77" FCFLAGS="$FFLAGS" FCCPP="$F77 -E" --enable-shared' # From the libxc mailing list -- GitLab From c9853b0fd0a089a05911daf9d2ea0aa74afe5e94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 20:35:43 +0100 Subject: [PATCH 187/566] various style and consistency fixes across Python easyconfigs, don't use icc patch for GCC-based builds --- .../Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 2 -- .../Python/Python-2.5.6-goolf-1.4.10-bare.eb | 2 -- .../p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 4 ++- .../Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 1 + .../p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 1 + .../p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 1 + .../Python-2.7.3-goalf-1.1.0-no-OFED.eb | 1 + .../p/Python/Python-2.7.3-goolf-1.4.10.eb | 1 + .../p/Python/Python-2.7.3-ictce-4.0.6.eb | 1 + .../p/Python/Python-2.7.3-iomkl-4.6.13.eb | 4 +-- .../Python-2.7.5-goalf-1.5.12-no-OFED.eb | 2 -- .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 3 --- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 3 ++- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 5 ++-- .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 3 ++- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 4 +-- .../Python-3.2.3-goalf-1.1.0-no-OFED.eb | 5 ++-- .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 5 ++-- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 5 ++-- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 -- .../python-2.7.6_libffi_int128_icc.patch | 27 ------------------- ...python-2.7_libffi-include-xmmintrin.patch} | 0 23 files changed, 30 insertions(+), 55 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch rename easybuild/easyconfigs/p/Python/{libffi-3.0.13_include-xmmintrin.patch => python-2.7_libffi-include-xmmintrin.patch} (100%) 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 8831f1a81b..9ab4e226d2 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 @@ -11,8 +11,6 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python_libffi_int128_icc.patch'] - dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), 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 f626304d89..d72d837ddd 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 @@ -11,8 +11,6 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python_libffi_int128_icc.patch'] - dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), 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 40021bd464..0964225cd4 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 @@ -19,7 +19,9 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), -]# order is important! +] + +# order is important! exts_list = [ ('setuptools', '0.6c11', { 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], 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 84f064c627..2abbb4a82c 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 a38b2c3f31..10d8fa9b8f 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 c89425f2de..fdfab00748 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 1155745345..84035e978d 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 1f0a6d0a81..e19b57db63 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 3b07a66bff..d9fb7984f4 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 @@ -22,6 +22,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 95ba9a38e7..ee9593c250 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 @@ -8,8 +8,7 @@ toolchain = {'name': 'iomkl', 'version': '4.6.13'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} numpyversion = '1.6.1' -scipyversion = '0.11.0' -pytablesversion = '2.4.0' +scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] @@ -23,6 +22,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ] + # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 2447f7bc5d..dc003dc8ce 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 @@ -13,8 +13,6 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), 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 7c65b339df..3d4ede9ed0 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 @@ -13,8 +13,6 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), @@ -23,7 +21,6 @@ dependencies = [ ('ncurses', '5.9'), ] - # order is important! exts_list = [ ('setuptools', '0.6c11', { 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 214f9caf18..780f5d4768 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 @@ -13,7 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['libffi-3.0.13_include-xmmintrin.patch'] +# 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 = [ 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 43582a47e8..59cc853852 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 @@ -13,7 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['libffi-3.0.13_include-xmmintrin.patch'] +# 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 = [ 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 9a2a8fbdbb..2632828fea 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 @@ -7,13 +7,14 @@ description = "Python is a programming language that lets you work more quickly toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -numpyversion = '1.7.1' +numpyversion = '1.7.0' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['libffi-3.0.13_include-xmmintrin.patch'] +# 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 = [ 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 a510ac66d6..81a392ff98 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 @@ -13,7 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python-%(version)s_libffi_int128_icc.patch'] +# 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 = [ 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 a621200714..a66adf51e6 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 @@ -14,9 +14,7 @@ source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] # libffi build in python is still broken, see http://bugs.python.org/issue4130 -patches = [ - 'libffi-3.0.13_include-xmmintrin.patch', -] +patches = ['python-2.7_libffi-include-xmmintrin.patch'] # python needs bzip2 to build the bz2 package dependencies = [ 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 fb7852574b..ceea0be3dc 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 @@ -23,8 +23,9 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + ('distribute', '0.6.26', { + 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'modulename': 'setuptools', }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], 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 c42562dc72..525d37410a 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 @@ -23,8 +23,9 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + ('distribute', '0.6.26', { + 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'modulename': 'setuptools', }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], 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 9422982772..a56d8bfda5 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 @@ -23,8 +23,9 @@ dependencies = [ # order is important! exts_list = [ - ('setuptools', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + ('distribute', '0.6.26', { + 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'modulename': 'setuptools', }), ('pip', '1.1', { 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], 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 5153420960..0bd2f902ad 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 @@ -24,8 +24,6 @@ dependencies = [ # order is important! exts_list = [ - # This should actually be bumped to 'setuptools', '1.4.1' see - # https://github.com/hpcugent/easybuild-easyconfigs/pull/563#discussion-diff-8024693R27 ('distribute', '0.6.26', { 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', diff --git a/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch b/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch deleted file mode 100644 index c639c75c09..0000000000 --- a/easybuild/easyconfigs/p/Python/python-2.7.6_libffi_int128_icc.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff -ur Python-2.7.4.orig/Modules/_ctypes/libffi/src/x86/ffi64.c Python-2.7.4/Modules/_ctypes/libffi/src/x86/ffi64.c ---- Python-2.7.4.orig/Modules/_ctypes/libffi/src/x86/ffi64.c 2013-04-06 16:02:35.000000000 +0200 -+++ Python-2.7.4/Modules/_ctypes/libffi/src/x86/ffi64.c 2013-05-13 10:28:22.935090082 +0200 -@@ -56,6 +56,8 @@ - UINT128 i128; - }; - -+typedef struct { int64_t m[2]; } __int128_t; -+ - struct register_args - { - /* Registers for argument passing. */ -@@ -507,10 +509,12 @@ - break; - case X86_64_SSE_CLASS: - case X86_64_SSEDF_CLASS: -- reg_args->sse[ssecount++].i64 = *(UINT64 *) a; -+ reg_args->sse[ssecount++].m[0] = *(UINT64 *) a; -+ reg_args->sse[ssecount++].m[1] = 0; - break; - case X86_64_SSESF_CLASS: -- reg_args->sse[ssecount++].i32 = *(UINT32 *) a; -+ reg_args->sse[ssecount++].m[0] = *(UINT32 *) a; -+ reg_args->sse[ssecount++].m[1] = 0; - break; - default: - abort(); diff --git a/easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch b/easybuild/easyconfigs/p/Python/python-2.7_libffi-include-xmmintrin.patch similarity index 100% rename from easybuild/easyconfigs/p/Python/libffi-3.0.13_include-xmmintrin.patch rename to easybuild/easyconfigs/p/Python/python-2.7_libffi-include-xmmintrin.patch -- GitLab From 2385ee7086c957b392e4eacbe53b72076ab9e128 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Dec 2013 22:42:31 +0100 Subject: [PATCH 188/566] paycheck is not compatible with Python 3.x --- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 3 --- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 3 --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 3 --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 3 --- 4 files changed, 12 deletions(-) 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 ceea0be3dc..b87c0b57d2 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 @@ -45,9 +45,6 @@ exts_list = [ ('mpi4py', '1.3', { '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/'], }), 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 525d37410a..f9770acdad 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 @@ -45,9 +45,6 @@ exts_list = [ ('mpi4py', '1.3', { '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/'], }), 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 a56d8bfda5..022930c2e7 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 @@ -45,9 +45,6 @@ exts_list = [ ('mpi4py', '1.3', { '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/'], }), 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 0bd2f902ad..b8f230e44e 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 @@ -46,9 +46,6 @@ exts_list = [ ('mpi4py', '1.3', { '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/'], }), -- GitLab From 5411cdccbc8eaed7af1f772528fa0ae39debef70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 08:50:37 +0100 Subject: [PATCH 189/566] remove patches for Python versions <= 2.7.3 with ictce 5.2.0 or up (incompatibility issue was fixed in Intel compilers) --- easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.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 -- 3 files changed, 6 deletions(-) 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 5defdd9ca7..6f70a20147 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 @@ -11,8 +11,6 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python_libffi_int128_icc.patch'] - dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), 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 9250403c43..4da1f6b6ef 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 @@ -13,8 +13,6 @@ scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), 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 17649568df..6f098b9e79 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 @@ -13,8 +13,6 @@ scipyversion = '0.10.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = ['%(name)s-%(version)s.tgz'] -patches = ['python_libffi_int128_icc.patch'] - # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), -- GitLab From 1a39df304c30af6d966d27b845a2c9679ebc6f5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 08:55:05 +0100 Subject: [PATCH 190/566] add easyconfig for Python 2.7.6 with goolf --- .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb 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 new file mode 100644 index 0000000000..28d55c2c9b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -0,0 +1,82 @@ +name = 'Python' +version = '2.7.6' + +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': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.0' +scipyversion = '0.13.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.4.2', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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')], + }), + ('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', '0.19.2', { + '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', '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' -- GitLab From 628bf0997be84d7fc4fcd0db7f227e7866c6d42c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 09:28:54 +0100 Subject: [PATCH 191/566] call set_tmpdir so tempfile is initialized like in an actual eb run --- test/easyconfigs/easyconfigs.py | 1 + 1 file changed, 1 insertion(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3925e6ada3..b729fca376 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -60,6 +60,7 @@ class EasyConfigTest(TestCase): # 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')) + config.set_tmpdir() del eb_go log = fancylogger.getLogger("EasyConfigTest", fname=False) -- GitLab From c87579caf8f4f3e56681ed81283d618c319f4080 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 09:29:58 +0100 Subject: [PATCH 192/566] minor style fixes in numpy 1.6.2 goolf easyconfig --- .../n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb index 8106dc54bf..a018a5b44d 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb @@ -7,12 +7,13 @@ a powerful N-dimensional array object, sophisticated (broadcasting) functions, t 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': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] -patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] +patches = ['numpy-%(version)s_distutils_multiple-lib-dirs.patch'] python = 'Python' pyver = '2.7.3' -- GitLab From f6f22a13550903cc550ce35788112404861fa0be Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 19 Dec 2013 10:47:38 +0100 Subject: [PATCH 193/566] VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb --- ...CFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..3bf776b509 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,38 @@ +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'VCFtools' +version = '0.1.11' + +easyblock = 'MakeCp' + +homepage = "http://vcftools.sourceforge.net/" +description = """The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin","lib"] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'vcftools', 'vcf-sort', 'vcf-stats', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From d45a7aef06f60eda9feeba6c560f3d7bd64328fc Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 19 Dec 2013 10:51:35 +0100 Subject: [PATCH 194/566] fixed indentation in vcftools eb file --- .../v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb index 3bf776b509..6f90845017 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb @@ -8,7 +8,10 @@ version = '0.1.11' easyblock = 'MakeCp' homepage = "http://vcftools.sourceforge.net/" -description = """The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. """ +description = """The aim of VCFtools is to provide + methods for working with VCF files: validating, + merging, comparing and calculate some basic population + genetic statistics. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} -- GitLab From ed95ea0abf2549f7ab6c840cfb39dca0af82f5a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 11:20:36 +0100 Subject: [PATCH 195/566] add goolf easyconfigs for numpy v1.7.1 and scipy v1.13.0 --- .../numpy-1.7.1-goolf-1.4.10-Python-2.7.3.eb | 26 +++ ...py-1.7.1_distutils_multiple-lib-dirs.patch | 202 ++++++++++++++++++ .../scipy-0.13.0-goolf-1.4.10-Python-2.7.3.eb | 19 ++ 3 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.7.1-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch create mode 100644 easybuild/easyconfigs/s/scipy/scipy-0.13.0-goolf-1.4.10-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..a02cfbdf02 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.7.1' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-%(version)s_distutils_multiple-lib-dirs.patch'] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch b/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch new file mode 100644 index 0000000000..12501c6754 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1_distutils_multiple-lib-dirs.patch @@ -0,0 +1,202 @@ +diff -ru numpy-1.7.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.7.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.7.0.orig/numpy/distutils/fcompiler/__init__.py 2013-02-09 22:04:55.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/fcompiler/__init__.py 2013-05-13 10:40:59.806346107 +0200 +@@ -626,7 +626,11 @@ + 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 -ru numpy-1.7.0.orig/numpy/distutils/system_info.py numpy-1.7.0/numpy/distutils/system_info.py +--- numpy-1.7.0.orig/numpy/distutils/system_info.py 2013-02-09 22:04:56.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/system_info.py 2013-05-13 10:48:49.063599772 +0200 +@@ -588,7 +588,7 @@ + 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, '') +@@ -630,6 +630,23 @@ + 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. +@@ -643,6 +660,18 @@ + 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 = [] +@@ -653,6 +682,9 @@ + 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) +@@ -668,6 +700,19 @@ + 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. + +@@ -709,6 +754,22 @@ + 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. +@@ -944,7 +1005,7 @@ + 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) ++ info = self.check_libs2_all(lib_dirs, mkl_libs) + if info is None: + return + dict_append(info, +@@ -1008,16 +1069,13 @@ + 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 +@@ -1096,7 +1154,7 @@ + info = {} + atlas_libs = self.get_libs('atlas_libs', + self._lib_names + self._lib_atlas) +- atlas = self.check_libs2(lib_dirs, atlas_libs, []) ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs, []) + if atlas is None: + return + include_dirs = self.get_include_dirs() +@@ -1144,7 +1202,7 @@ + lib_dirs = self.get_lib_dirs() + + lapack_libs = self.get_libs('lapack_libs', self._lib_names) +- info = self.check_libs(lib_dirs, lapack_libs, []) ++ info = self.check_libs_all(lib_dirs, lapack_libs, []) + if info is None: + return + info['language'] = 'f77' +@@ -1521,7 +1579,7 @@ + lib_dirs = self.get_lib_dirs() + + blas_libs = self.get_libs('blas_libs', self._lib_names) +- info = self.check_libs(lib_dirs, blas_libs, []) ++ info = self.check_libs_all(lib_dirs, blas_libs, []) + if info is None: + return + info['language'] = 'f77' # XXX: is it generally true? +Only in numpy-1.7.0/numpy/distutils: system_info.py.orig +Only in numpy-1.7.0/numpy/distutils: system_info.py.rej +diff -ru numpy-1.7.0.orig/numpy/distutils/unixccompiler.py numpy-1.7.0/numpy/distutils/unixccompiler.py +--- numpy-1.7.0.orig/numpy/distutils/unixccompiler.py 2013-02-09 22:04:55.000000000 +0100 ++++ numpy-1.7.0/numpy/distutils/unixccompiler.py 2013-05-13 10:40:59.833592000 +0200 +@@ -109,3 +109,12 @@ + + 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/s/scipy/scipy-0.13.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/scipy/scipy-0.13.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000..a1047f4733 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.13.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.13.0' +versionsuffix = '-Python-2.7.3' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.7.1', versionsuffix), +] + +moduleclass = 'math' -- GitLab From 68b078518030bbc72aa6707546ad403684392cc2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 14:23:26 +0100 Subject: [PATCH 196/566] remove XML-LibXML and XML-Simple easyconfigs, build doesn't work --- ...L-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb | 25 ------------------- ...XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb | 25 ------------------- 2 files changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb delete mode 100644 easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb deleted file mode 100644 index f91b2703dc..0000000000 --- a/easybuild/easyconfigs/x/XML/XML-LibXML-2.0018-ictce-5.3.0-Perl-5.16.3.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PerlModule' - -name = 'XML-LibXML' -version = '2.0018' - -homepage = 'http://search.cpan.org/src/SHLOMIF/XML-LibXML-2.0018/' -description = """Perl binding for libxml2""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://www.cpan.org/modules/by-module/XML/SHLOMIF/'] -sources = [SOURCE_TAR_GZ] - -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) - -dependencies = [ - (perl, perlver), - ("libxml2", "2.9.0"), -] - -options = {'modulename': 'XML::LibXML'} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb deleted file mode 100644 index e61280523c..0000000000 --- a/easybuild/easyconfigs/x/XML/XML-Simple-2.20-ictce-5.3.0-Perl-5.16.3.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PerlModule' - -name = 'XML-Simple' -version = '2.20' - -homepage = 'http://search.cpan.org/src/GRANTM/XML-Simple-2.20/' -description = """Easily read/write XML in Perl""" - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://www.cpan.org/modules/by-module/XML/GRANTM/'] -sources = [SOURCE_TAR_GZ] - -perl = 'Perl' -perlver = '5.16.3' -versionsuffix = '-%s-%s' % (perl, perlver) - -dependencies = [ - (perl, perlver), - ("XML-LibXML", "2.0018", versionsuffix), -] - -options = {'modulename': 'XML::Simple'} - -moduleclass = 'data' -- GitLab From 08621517c4b42bea17227593c85e20457a7879ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Dec 2013 15:15:40 +0100 Subject: [PATCH 197/566] remove Qt easyconfig, build seems broken --- .../easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb deleted file mode 100644 index e712e4c5a2..0000000000 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-5.3.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -name = 'Qt' -version = '4.8.5' - -homepage = 'http://qt-project.org/' -description = "Qt is a comprehensive cross-platform C++ application framework." - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] -sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] - -dependencies = [('GLib', '2.34.3')] - -configopts="-confirm-license -opensource -silent" - -sanity_check_paths = { - 'files': ['lib/libQtCore.so'], - 'dirs': [], -} -moduleclass = 'devel' -- GitLab From 461e6cd654eaf35585c8532788ccd6ea10acb7e4 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 20 Dec 2013 11:16:17 +0100 Subject: [PATCH 198/566] small style changes --- .../v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb index 6f90845017..a5053fd3e9 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb @@ -26,15 +26,12 @@ dependencies = [ (perl, perlver), ] -files_to_copy = ["bin","lib"] +files_to_copy = ["bin", "lib"] modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} sanity_check_paths = { - 'files': ['bin/%s' % x for x in [ - 'vcftools', 'vcf-sort', 'vcf-stats', - ] - ], + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], 'dirs': [], } -- GitLab From 5b9e9771fbebbd968f0bc878d3c8d1e61106417d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2013 20:15:16 +0100 Subject: [PATCH 199/566] use '-seq' versionsuffix for existing GROMACS easyconfigs and explicitely disable OpenMPI and MPI support, and -mt, -mpi and -hybrid variants (that work) --- ...10.eb => GROMACS-4.6.1-goolf-1.4.10-mt.eb} | 27 +++++-------- .../GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb | 38 +++++++++++++++++++ ...2.eb => GROMACS-4.6.1-goolfc-1.3.12-mt.eb} | 23 +++++------ .../GROMACS-4.6.1-goolfc-1.3.12-seq.eb | 38 +++++++++++++++++++ .../GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb | 38 +++++++++++++++++++ .../GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb | 38 +++++++++++++++++++ ...0.eb => GROMACS-4.6.5-goolfc-2.6.10-mt.eb} | 20 +++++----- .../GROMACS-4.6.5-goolfc-2.6.10-seq.eb | 38 +++++++++++++++++++ ...eb => GROMACS-4.6.5-ictce-5.5.0-hybrid.eb} | 26 ++++--------- .../GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb | 38 +++++++++++++++++++ .../g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb | 38 +++++++++++++++++++ .../GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb | 38 +++++++++++++++++++ .../g/GSL/GSL-1.15-goolf-1.4.10.eb | 1 + .../easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb | 1 - .../g/GSL/GSL-1.16-goolf-1.4.10.eb | 16 ++++++++ .../g/GSL/GSL-1.16-goolfc-1.3.12.eb | 16 ++++++++ .../g/GSL/GSL-1.16-goolfc-2.6.10.eb | 16 ++++++++ 17 files changed, 387 insertions(+), 63 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-4.6.1-goolf-1.4.10.eb => GROMACS-4.6.1-goolf-1.4.10-mt.eb} (67%) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb rename easybuild/easyconfigs/g/GROMACS/{GROMACS-4.6.1-goolfc-1.3.12.eb => GROMACS-4.6.1-goolfc-1.3.12-mt.eb} (75%) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb rename easybuild/easyconfigs/g/GROMACS/{GROMACS-4.6.5-goolfc-2.6.10.eb => GROMACS-4.6.5-goolfc-2.6.10-mt.eb} (82%) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb rename easybuild/easyconfigs/g/GROMACS/{GROMACS-4.6.5-ictce-5.5.0.eb => GROMACS-4.6.5-ictce-5.5.0-hybrid.eb} (62%) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb similarity index 67% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb index 02fb60a067..f4e21dcbfc 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb @@ -10,38 +10,29 @@ # 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 ## - -easyblock = 'CMakeMake' - name = 'GROMACS' version = '4.6.1' +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.""" + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': False} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.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', '2.8.4')] - -configopts = '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' - -# explicitely disable CUDA support, i.e. avoid that GROMACS find and uses a system-wide CUDA compiler -# CUDA and GCC v4.7 don't play well together -configopts += ' -DGMX_GPU=OFF' +dependencies = [('GSL', '1.16')] -configopts += "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" -runtest = 'check' +builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb new file mode 100644 index 0000000000..08aece5c97 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.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 = '4.6.1' +versionsuffix = '-seq' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': False, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb similarity index 75% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb index 256c0d975a..9d83bacb7b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb @@ -10,34 +10,29 @@ # 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 ## - -easyblock = 'CMakeMake' - name = 'GROMACS' version = '4.6.1' +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.""" + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'goolfc', 'version': '1.3.12'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': False} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.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', '2.8.4')] - -configopts = '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' +dependencies = [('GSL', '1.16')] -configopts += "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" -runtest = 'check' +builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb new file mode 100644 index 0000000000..5a0b2360e9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.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 = '4.6.1' +versionsuffix = '-seq' + +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': 'goolfc', 'version': '1.3.12'} +toolchainopts = {'openmp': False, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb new file mode 100644 index 0000000000..4cfd2d6698 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.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 = '4.6.5' +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb new file mode 100644 index 0000000000..7b464a0529 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.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 = '4.6.5' +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': False, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb similarity index 82% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb index 5c6e6ac80d..651f7be69d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb @@ -10,31 +10,29 @@ # 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 ## - -easyblock = 'CMakeMake' - name = 'GROMACS' version = '4.6.5' +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.""" + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'goolfc', 'version': '2.6.10'} +toolchainopts = {'openmp': True, 'usempi': False} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.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', '2.8.4')] +dependencies = [('GSL', '1.16')] -configopts = "-DREGRESSIONTEST_PATH='%(builddir)s/regressiontests-%(version)s'" -runtest = 'check' +builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb new file mode 100644 index 0000000000..63c1d1b695 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.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 = '4.6.5' +versionsuffix = '-seq' + +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': 'goolfc', 'version': '2.6.10'} +toolchainopts = {'openmp': False, 'usempi': False} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb similarity index 62% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb index 3e5a3d3c07..6b7c7754fa 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb @@ -10,41 +10,29 @@ # 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 ## - -easyblock = 'CMakeMake' - name = 'GROMACS' version = '4.6.5' +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.""" + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz -sources = [ - SOURCELOWER_TAR_GZ, - 'regressiontests-%(version)s.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', +] dependencies = [('GSL', '1.16')] builddependencies = [('CMake', '2.8.12')] -configopts = '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" ' -configopts += '-DMKL_LIBRARIES="$EBROOTMKL/mkl/lib/intel64/libmkl.a;$EBROOTMKL/mkl/lib/intel64/libmkl_lapack.a" ' -configopts += '-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_MPI=ON -DGMX_X11=OFF ' - -# explicitely disable CUDA support, i.e. avoid that GROMACS find and uses a system-wide CUDA compiler -configopts += '-DGMX_GPU=OFF ' - -configopts += '-DREGRESSIONTEST_PATH="%(builddir)s/regressiontests-%(version)s" ' -runtest = 'check' - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb new file mode 100644 index 0000000000..e3aec07320 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-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 = '4.6.5' +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'openmp': False, '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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb new file mode 100644 index 0000000000..12cb6865b7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.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 = '4.6.5' +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': '5.5.0'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb new file mode 100644 index 0000000000..15d5a0a5a9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.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 = '4.6.5' +versionsuffix = '-seq' + +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': '5.5.0'} +toolchainopts = {'openmp': False, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb index fe17508924..f42e966bda 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-goolf-1.4.10.eb @@ -4,6 +4,7 @@ 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': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb index 46fb6c2c19..455dbe52ed 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-5.3.0.eb @@ -5,7 +5,6 @@ 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': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb new file mode 100644 index 0000000000..2d05bc4775 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolf-1.4.10.eb @@ -0,0 +1,16 @@ +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb new file mode 100644 index 0000000000..c792614359 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb @@ -0,0 +1,16 @@ +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': 'goolfc', 'version': '1.3.12'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb new file mode 100644 index 0000000000..db182f74d8 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb @@ -0,0 +1,16 @@ +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': 'goolfc', 'version': '2.6.10'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' -- GitLab From b7cfde0e375ac2d99567e525bf91f1b450adbc1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Dec 2013 20:32:22 +0100 Subject: [PATCH 200/566] add missing CMake easyconfig as build dep for GROMACS --- .../c/CMake/CMake-2.8.12-goolf-1.4.10.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.4.10.eb new file mode 100644 index 0000000000..0eb9ee7abd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolf-1.4.10.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'goolf', 'version': '1.4.10'} + +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 e0438a1c3f60dd3fd998ec22595cd72af63c1e57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:22:45 +0100 Subject: [PATCH 201/566] fix versionsuffix for GROMACS goolf -mt easyconfig --- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb index 4cfd2d6698..79cf87d0ba 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb @@ -12,7 +12,7 @@ ## name = 'GROMACS' version = '4.6.5' -versionsuffix = '-hybrid' +versionsuffix = '-mt' homepage = 'http://www.gromacs.org' description = """GROMACS is a versatile package to perform molecular dynamics, -- GitLab From db0aeace94779c081350c79971936232551ba1eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:27:00 +0100 Subject: [PATCH 202/566] remove -seq and -mpi variants, -mt and -hybrid will do --- .../GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb | 38 ------------------- .../GROMACS-4.6.1-goolfc-1.3.12-seq.eb | 38 ------------------- .../GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb | 38 ------------------- .../GROMACS-4.6.5-goolfc-2.6.10-seq.eb | 38 ------------------- .../GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb | 38 ------------------- .../GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb | 38 ------------------- 6 files changed, 228 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb deleted file mode 100644 index 08aece5c97..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-seq.eb +++ /dev/null @@ -1,38 +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 = '4.6.1' -versionsuffix = '-seq' - -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': 'goolf', 'version': '1.4.10'} -toolchainopts = {'openmp': False, 'usempi': False} - -# 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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.4')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb deleted file mode 100644 index 5a0b2360e9..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-seq.eb +++ /dev/null @@ -1,38 +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 = '4.6.1' -versionsuffix = '-seq' - -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': 'goolfc', 'version': '1.3.12'} -toolchainopts = {'openmp': False, 'usempi': False} - -# 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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.4')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb deleted file mode 100644 index 7b464a0529..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-seq.eb +++ /dev/null @@ -1,38 +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' -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': 'goolf', 'version': '1.4.10'} -toolchainopts = {'openmp': False, 'usempi': False} - -# 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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.12')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb deleted file mode 100644 index 63c1d1b695..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-seq.eb +++ /dev/null @@ -1,38 +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' -versionsuffix = '-seq' - -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': 'goolfc', 'version': '2.6.10'} -toolchainopts = {'openmp': False, 'usempi': False} - -# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.4')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb deleted file mode 100644 index e3aec07320..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mpi.eb +++ /dev/null @@ -1,38 +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' -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': 'ictce', 'version': '5.5.0'} -toolchainopts = {'openmp': False, '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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.12')] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb deleted file mode 100644 index 15d5a0a5a9..0000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-seq.eb +++ /dev/null @@ -1,38 +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' -versionsuffix = '-seq' - -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': '5.5.0'} -toolchainopts = {'openmp': False, 'usempi': False} - -# 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', -] - -dependencies = [('GSL', '1.16')] - -builddependencies = [('CMake', '2.8.12')] - -moduleclass = 'bio' -- GitLab From 88634a3b3d0a7f8c402fad3adadcb95201fd9d46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:30:32 +0100 Subject: [PATCH 203/566] add GROMACS easyconfigs for various toolchains, both -mt and -hybrid versions --- .../GROMACS-4.6.1-goolf-1.4.10-hybrid.eb | 38 +++++++++++++++++ .../GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb | 38 +++++++++++++++++ .../GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb | 41 +++++++++++++++++++ .../GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb | 41 +++++++++++++++++++ .../GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb | 41 +++++++++++++++++++ .../GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb | 41 +++++++++++++++++++ ...ROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb | 38 +++++++++++++++++ .../GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb | 38 +++++++++++++++++ .../GROMACS-4.6.5-goolf-1.4.10-hybrid.eb | 41 +++++++++++++++++++ .../GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb | 40 ++++++++++++++++++ 10 files changed, 397 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb new file mode 100644 index 0000000000..a57097dec7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.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 = '4.6.1' +versionsuffix = '-hyrid' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True, '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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb new file mode 100644 index 0000000000..4c518648ee --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.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 = '4.6.1' +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': 'goolfc', 'version': '1.3.12'} +toolchainopts = {'openmp': True, '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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb new file mode 100644 index 0000000000..b14c93b641 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.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 / 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' +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': 'gmpolf', 'version': '1.4.8'} +toolchainopts = {'openmp': True, '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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +#configopts = "-DGMX_TEST_NUMBER_PROCS=1" +#parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb new file mode 100644 index 0000000000..65217db71e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.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 / 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' +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': 'gmpolf', 'version': '1.4.8'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +#configopts = "-DGMX_TEST_NUMBER_PROCS=1" +#parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb new file mode 100644 index 0000000000..b3862d7bc7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.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 / 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' +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': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'openmp': True, '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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +#configopts = "-DGMX_TEST_NUMBER_PROCS=1" +#parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb new file mode 100644 index 0000000000..f2d0ddfb74 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.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 / 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' +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': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +#configopts = "-DGMX_TEST_NUMBER_PROCS=1" +#parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb new file mode 100644 index 0000000000..538c0a560c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.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 = '4.6.5' +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': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'openmp': True, '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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb new file mode 100644 index 0000000000..ed12feb1c9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.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 = '4.6.5' +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': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb new file mode 100644 index 0000000000..c23c74d646 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.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 / 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' +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True, '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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +#configopts = "-DGMX_TEST_NUMBER_PROCS=1" +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb new file mode 100644 index 0000000000..21eb75235b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb @@ -0,0 +1,40 @@ +## +# 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' +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': 'goolfc', 'version': '2.6.10'} +toolchainopts = {'openmp': True, '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', +] + +#dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.12')] + +configopts = "-DGMX_TEST_NUMBER_PROCS=16" + +moduleclass = 'bio' -- GitLab From 1ee222f13de31a4aa773b047e76d02411e0b6b2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:45:46 +0100 Subject: [PATCH 204/566] fix typo --- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb index a57097dec7..39b40704bf 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb @@ -12,7 +12,7 @@ ## name = 'GROMACS' version = '4.6.1' -versionsuffix = '-hyrid' +versionsuffix = '-hybrid' homepage = 'http://www.gromacs.org' description = """GROMACS is a versatile package to perform molecular dynamics, -- GitLab From afefc373af0f78e2b4d09c591b94892fc1d071d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:46:06 +0100 Subject: [PATCH 205/566] add ictce/5.3.0 easyconfigs for GROMACS v4.6.1 --- .../GROMACS-4.6.1-ictce-5.3.0-hybrid.eb | 38 +++++++++++++++++++ .../g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb new file mode 100644 index 0000000000..2950040b1b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.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 = '4.6.1' +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'openmp': True, '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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb new file mode 100644 index 0000000000..964c5c848d --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.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 = '4.6.1' +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': '5.3.0'} +toolchainopts = {'openmp': True, 'usempi': False} + +# 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', +] + +dependencies = [('GSL', '1.16')] + +builddependencies = [('CMake', '2.8.4')] + +moduleclass = 'bio' -- GitLab From c1591e72c39aec02a901f257b6f23e7fc3d6f85a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 11:46:17 +0100 Subject: [PATCH 206/566] fix HPCBIOS GROMACS entries --- .../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 1a2ccc532c..86ef1ed180 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 @@ -41,7 +41,7 @@ dependencies = [ ('FASTX-Toolkit', '0.0.13.2'), ('FSL', '4.1.9'), ('GLIMMER', '3.02b'), - ('GROMACS', '4.6.1'), + ('GROMACS', '4.6.1', '-hybrid'), ('HH-suite', '2.0.16'), ('HMMER', '3.0'), ('Infernal', '1.1rc1'), 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 1d4aeb5a5a..a7271f599b 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 @@ -41,7 +41,7 @@ dependencies = [ ('FASTX-Toolkit', '0.0.13.2'), ('FSL', '4.1.9'), ('GLIMMER', '3.02b'), -# ('GROMACS', '4.6.1'), + ('GROMACS', '4.6.1', '-hybrid'), ('HMMER', '3.0'), # ('HH-suite', '2.0.16'), ('Infernal', '1.1rc1'), 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 d087f2d6bd..8b2a4995ff 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 @@ -27,7 +27,7 @@ dependencies = [ ('BLAST', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('ClustalW2', '2.1'), - ('GROMACS', '4.6.1'), + ('GROMACS', '4.6.1', '-hybrid'), ('HMMER', '3.0'), ('MrBayes', '3.1.2'), ('mpiBLAST', '1.6.0'), 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 1ea5f64544..dc22e82ed1 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 @@ -27,7 +27,7 @@ dependencies = [ ('BLAST', '2.2.28', '-Python-2.7.3'), ('BWA', '0.6.2'), ('ClustalW2', '2.1'), -# ('GROMACS', '4.6.1'), + ('GROMACS', '4.6.1', '-hybrid'), ('HMMER', '3.0'), ('MrBayes', '3.1.2'), ('mpiBLAST', '1.6.0'), -- GitLab From 45992aaee94a429c961a07ad0007a8eab2443d16 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 21 Dec 2013 12:48:53 +0100 Subject: [PATCH 207/566] fix permissions for impi-3.2.2.006.eb Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb old mode 100755 new mode 100644 -- GitLab From 227fa6212979aa392c1bbface00ef88f206d0b35 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 21 Dec 2013 12:50:42 +0100 Subject: [PATCH 208/566] add ictce/6.2.0 paraphernalia Signed-off-by: Fotis Georgatos --- .../easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb | 18 ++++++++++++++++ easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb | 21 +++++++++++++++++++ .../easyconfigs/i/impi/impi-4.1.3.045.eb | 19 +++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb new file mode 100644 index 0000000000..ea2e3bdfd7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.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': 'ictce', 'version': '6.2.0'} +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/i/ictce/ictce-6.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb new file mode 100644 index 0000000000..973e6ab44a --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '6.2.0' + +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 = '1.106' +compver = '2013_sp1.%s' % suff + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.3.045'), + ('imkl', '11.1.%s' % suff), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb new file mode 100644 index 0000000000..99968e9833 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.3.045' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +moduleclass = 'mpi' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") -- GitLab From a8bb286893e62d56a4e830f89fc29ede6307236f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 14:25:03 +0100 Subject: [PATCH 209/566] drop GSL dependencies, doesn't always work as expected --- .../g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb | 2 -- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb | 2 -- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb | 2 -- .../easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb | 5 ----- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb | 5 ----- .../g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb | 5 ----- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb | 5 ----- .../g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb | 2 -- .../g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb | 5 ----- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb | 4 ---- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb | 2 -- .../g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb | 2 -- .../easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb | 2 -- 18 files changed, 53 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb index 39b40704bf..2c32c1c216 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-hybrid.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb index f4e21dcbfc..7304cc5789 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolf-1.4.10-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb index 4c518648ee..d6f38ccfbb 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb index 9d83bacb7b..caa9471e7c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb index 2950040b1b..6dcbff4c39 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-hybrid.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb index 964c5c848d..605b8ed69d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-ictce-5.3.0-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb index b14c93b641..bbf71787ee 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb @@ -31,11 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -#configopts = "-DGMX_TEST_NUMBER_PROCS=1" -#parallel = 1 - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb index 65217db71e..72e6d81f6c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb @@ -31,11 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -#configopts = "-DGMX_TEST_NUMBER_PROCS=1" -#parallel = 1 - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb index b3862d7bc7..45f81add29 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb @@ -31,11 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -#configopts = "-DGMX_TEST_NUMBER_PROCS=1" -#parallel = 1 - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb index f2d0ddfb74..6d1ed16eee 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb @@ -31,11 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -#configopts = "-DGMX_TEST_NUMBER_PROCS=1" -#parallel = 1 - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb index 538c0a560c..afe1fbe21b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb index ed12feb1c9..e9d5d04c88 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb index c23c74d646..73c56d433b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-hybrid.eb @@ -31,11 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -#configopts = "-DGMX_TEST_NUMBER_PROCS=1" -parallel = 1 - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb index 79cf87d0ba..e5cfaf5826 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolf-1.4.10-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb index 21eb75235b..839eb005c2 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb @@ -31,10 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -#dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] -configopts = "-DGMX_TEST_NUMBER_PROCS=16" - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb index 651f7be69d..060e0556d6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.4')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb index 6b7c7754fa..1f91b84ea4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-hybrid.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb index 12cb6865b7..b04177b611 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-ictce-5.5.0-mt.eb @@ -31,8 +31,6 @@ sources = [ 'regressiontests-%(version)s.tar.gz', ] -dependencies = [('GSL', '1.16')] - builddependencies = [('CMake', '2.8.12')] moduleclass = 'bio' -- GitLab From 73a9234b7bfd65f526bc7266c2b106dc807eeb18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 14:27:21 +0100 Subject: [PATCH 210/566] add missing CMake easyconfigs --- .../c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb | 20 +++++++++++++++++++ .../c/CMake/CMake-2.8.12-gmvolf-1.7.12.eb | 20 +++++++++++++++++++ .../CMake/CMake-2.8.12-goalf-1.1.0-no-OFED.eb | 20 +++++++++++++++++++ .../c/CMake/CMake-2.8.12-goolfc-2.6.10.eb | 20 +++++++++++++++++++ 4 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmvolf-1.7.12.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb new file mode 100644 index 0000000000..29decbc378 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmpolf-1.4.8.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'gmpolf', 'version': '1.4.8'} + +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/CMake/CMake-2.8.12-gmvolf-1.7.12.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmvolf-1.7.12.eb new file mode 100644 index 0000000000..4e80c3b739 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-gmvolf-1.7.12.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'gmvolf', 'version': '1.7.12'} + +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/CMake/CMake-2.8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..4371f8b627 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'goalf', 'version': '1.1.0-no-OFED'} + +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/CMake/CMake-2.8.12-goolfc-2.6.10.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb new file mode 100644 index 0000000000..3b0a2eaf8c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-goolfc-2.6.10.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': 'goolfc', 'version': '2.6.10'} + +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 9eabe0d3b5766b6a026ebfcf973ea8db6d1e5ec6 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 21 Dec 2013 14:46:09 +0100 Subject: [PATCH 211/566] demote ictce-6.2.0 to ictce-6.1.5 Signed-off-by: Fotis Georgatos --- .../easyconfigs/i/ictce/{ictce-6.2.0.eb => ictce-6.1.5.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/i/ictce/{ictce-6.2.0.eb => ictce-6.1.5.eb} (96%) diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb similarity index 96% rename from easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb rename to easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb index 973e6ab44a..47215eb1bc 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'ictce' -version = '6.2.0' +version = '6.1.5' 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.""" -- GitLab From 8919cf9fed98894eb0534c87be716f990d2809e2 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 21 Dec 2013 15:34:58 +0100 Subject: [PATCH 212/566] bumped versions of ictce/6.x --- .../ictce/{ictce-6.0.0.eb => ictce-6.0.5.eb} | 2 +- easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb | 21 ------------------- .../easyconfigs/i/imkl/imkl-11.1.1.106.eb | 2 +- 3 files changed, 2 insertions(+), 23 deletions(-) rename easybuild/easyconfigs/i/ictce/{ictce-6.0.0.eb => ictce-6.0.5.eb} (96%) delete mode 100644 easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.0.5.eb similarity index 96% rename from easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb rename to easybuild/easyconfigs/i/ictce/ictce-6.0.5.eb index 343a214a2c..7fd907fdff 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.0.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.0.5.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'ictce' -version = '6.0.0' +version = '6.0.5' 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.""" diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb deleted file mode 100644 index 29381078a5..0000000000 --- a/easybuild/easyconfigs/i/ictce/ictce-6.1.0.eb +++ /dev/null @@ -1,21 +0,0 @@ -easyblock = "Toolchain" - -name = 'ictce' -version = '6.1.0' - -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 = '1.106' -compver = '2013_sp1.%s' % suff - -dependencies = [ - ('icc', compver), - ('ifort', compver), - ('impi', '4.1.2.040'), - ('imkl', '11.1.%s' % suff), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index 3a8d833067..6c2f677c6c 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -16,7 +16,7 @@ compver = '2013_sp1.1.106' dependencies = [ ('icc', compver), ('ifort', compver), - ('impi', '4.1.2.040') + ('impi', '4.1.3.045') ] dontcreateinstalldir = 'True' -- GitLab From 49a241d477b0799708b558aa652d57af1273d7e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 15:52:22 +0100 Subject: [PATCH 213/566] put moduleclass at bottom of impi easyconfigs, fix toolchains in HPL ictce-6.x easyconfigs --- .../h/HPL/{HPL-2.0-ictce-6.0.0.eb => HPL-2.0-ictce-6.0.5.eb} | 0 .../h/HPL/{HPL-2.0-ictce-6.2.0.eb => HPL-2.0-ictce-6.1.5.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/h/HPL/{HPL-2.0-ictce-6.0.0.eb => HPL-2.0-ictce-6.0.5.eb} (100%) rename easybuild/easyconfigs/h/HPL/{HPL-2.0-ictce-6.2.0.eb => HPL-2.0-ictce-6.1.5.eb} (100%) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.0.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.2.0.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb -- GitLab From f54c26cd4c69c539dea4ab1126d72db9be6a2b0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 15:58:20 +0100 Subject: [PATCH 214/566] put moduleclass at bottom of impi easyconfigs, fix toolchains in HPL ictce-6.x easyconfigs --- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb | 2 +- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb | 2 +- easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb | 4 ++-- easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb | 4 ++-- 11 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb index dad098f322..ab34c97e0c 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.0.5.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': 'ictce', 'version': '6.0.0'} +toolchain = {'name': 'ictce', 'version': '6.0.5'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb index ea2e3bdfd7..91a1cadef9 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.5.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': 'ictce', 'version': '6.2.0'} +toolchain = {'name': 'ictce', 'version': '6.1.5'} toolchainopts = {'optarch': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index af378447b9..5f35cd6834 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index c1fe77fbb7..437532bb49 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -11,8 +11,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_pu_%(version)s.tgz'] -moduleclass = 'mpi' - dontcreateinstalldir = 'True' # license file @@ -20,3 +18,5 @@ import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") m32 = True + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index 02fa80a736..a551f57786 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_pu_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 3e513a018f..4830b5c3c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -12,10 +12,10 @@ sources = ['l_mpi_p_%(version)s.tgz'] patches = ['impi_4.x_productsdb.patch'] -moduleclass = 'mpi' - 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/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 72b72e75d9..839fe8f604 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 5d906bc72f..875b582066 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index a6158d1a06..97c88ff999 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 95c8b09cb5..839d937043 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - 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/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index 99968e9833..d31c2924c8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['l_mpi_p_%(version)s.tgz'] -moduleclass = 'mpi' - dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' -- GitLab From 3b7cdfc94178d4f1da7e5ac8ab07a3c673b04b05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 16:01:44 +0100 Subject: [PATCH 215/566] fix remark --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb | 4 ++-- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb | 4 ++-- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb | 4 ++-- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb | 4 ++-- easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index dc75cc5bc6..39be41a74e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -5,8 +5,8 @@ version = '1.7.0' 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.""" + written in Python that allows you to install software in a structured, + repeatable and robust way.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 4474ca43e8..1fe6136b55 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -5,8 +5,8 @@ version = '1.8.0' 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.""" + written in Python that allows you to install software in a structured, + repeatable and robust way.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index 59a2b57db8..629ec16acb 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -5,8 +5,8 @@ version = '1.8.1' 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.""" + written in Python that allows you to install software in a structured, + repeatable and robust way.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index 13f2a0d294..15551872f9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -5,8 +5,8 @@ version = '1.8.2' 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.""" + written in Python that allows you to install software in a structured, + repeatable and robust way.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 30a0e1cfd6..4047b50760 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -5,8 +5,8 @@ version = '1.9.0' 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.""" + written in Python that allows you to install software in a structured, + repeatable and robust way.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -- GitLab From 148722268f4fde5f318572b0f8ac9e5b074fa29f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Dec 2013 16:08:04 +0100 Subject: [PATCH 216/566] remove HPL for non-existing ictce/6.1.0 --- .../easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb deleted file mode 100644 index d3a5822e94..0000000000 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-6.1.0.eb +++ /dev/null @@ -1,18 +0,0 @@ -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': 'ictce', 'version': '6.1.0'} -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 4d120e2d4994bcbb17091894a656d259c4af1675 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 11:57:20 +0100 Subject: [PATCH 217/566] minor style fixes in Java and ErlangOTP easyconfigs --- .../e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb | 5 +---- .../easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 7 +------ easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb | 2 +- easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb | 2 +- easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb | 2 +- easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb | 2 +- easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb | 2 +- 7 files changed, 7 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb index 819ddd9b6b..84aa14f3cb 100644 --- a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2-no-Java.eb @@ -6,18 +6,15 @@ homepage = 'http://www.erlang.org/' description = """Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] configopts = '--without-javac ' -patches = [] sanity_check_paths = { 'files': ['bin/erl'], - 'dirs': ['lib/erlang/bin', 'lib/erlang/lib'] - + 'dirs': ['lib/erlang/bin', 'lib/erlang/lib'], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 0415fc7a1c..14f196cbec 100644 --- a/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -4,9 +4,7 @@ version = 'R16B02' homepage = 'http://www.erlang.org/' description = """Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system.""" - toolchain = {'name': 'GCC', 'version': '4.7.2'} -toolchainopts = {} # toolchain options, e.g. opt, pic, usempi, optarch, ... sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] @@ -14,13 +12,10 @@ source_urls = ['http://www.erlang.org/download'] builddependencies = [('Java','1.7.0_45','',True)] configopts = '--with-javac ' -patches = [] sanity_check_paths = { 'files': ['bin/erl'], - 'dirs': ['lib/erlang/bin', 'lib/erlang/lib', - 'lib/erlang/lib/jinterface-1.5.8'] # Note java dependency - + 'dirs': ['lib/erlang/bin', 'lib/erlang/lib', 'lib/erlang/lib/jinterface-1.5.8'], } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb index 2b21438ebc..aab1041c12 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb @@ -7,7 +7,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -## download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +# 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] diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb index a2c3b24e5a..5c86c312a9 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb @@ -7,7 +7,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -## download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +# 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] diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb index a103ca3d47..dbfbd84991 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb @@ -7,7 +7,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -## download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +# 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] diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb index a5fd350c4b..cf9d4f4b74 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb @@ -7,7 +7,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -## download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +# 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] diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb index 592d650cab..3387dbbb89 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb @@ -7,7 +7,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -## download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html +# 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] -- GitLab From 40a1f2870bf1e462d28727c5b5c8cf9287fc55a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 13:57:38 +0100 Subject: [PATCH 218/566] minor style fix in GATK easyconfigs, add easyconfig for v2.8-1 --- .../g/GATK/GATK-2.5-2-Java-1.7.0_10.eb | 2 +- .../g/GATK/GATK-2.6-5-Java-1.7.0_10.eb | 2 +- .../g/GATK/GATK-2.7-4-Java-1.7.0_10.eb | 2 +- .../g/GATK/GATK-2.8-1-Java-1.7.0_10.eb | 40 +++++++++++++++++++ 4 files changed, 43 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index 0c47f958a0..4c9f63f9c5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -25,7 +25,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel toolchain = {'name': 'dummy', 'version': 'dummy'} # download manually from http://www.broadinstitute.org/gatk/download -sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] java = 'Java' javaver = '1.7.0_10' diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index cd3b27bab6..833388f606 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -25,7 +25,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel toolchain = {'name': 'dummy', 'version': 'dummy'} # download manually from http://www.broadinstitute.org/gatk/download -sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] java = 'Java' javaver = '1.7.0_10' diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index e9bb8a2fb7..c75c22094b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -25,7 +25,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel toolchain = {'name': 'dummy', 'version': 'dummy'} # download manually from http://www.broadinstitute.org/gatk/download -sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] java = 'Java' javaver = '1.7.0_10' diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb new file mode 100644 index 0000000000..c3a788ffe2 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# 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 = '2.8-1' + +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_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' -- GitLab From 64688082ee34530c0113acfc99f2954cc06b6dc3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 14:03:43 +0100 Subject: [PATCH 219/566] minor style fixes in Libint easyconfig --- .../easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb index 6f64e7b117..df7ae20900 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb @@ -15,10 +15,10 @@ source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'dow configopts = "--with-pic --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':[] - } + '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 3dd6421a9ffab07be9aae4b6f932323d4fa7aefc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 14:49:10 +0100 Subject: [PATCH 220/566] minor style fixes in HPL easyconfigs --- easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb index d9e8ade351..fa3e730343 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-ictce-5.3.0.eb @@ -6,7 +6,6 @@ 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': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb index bf12551602..312add6caf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-iomkl-4.6.13.eb @@ -6,7 +6,6 @@ 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': 'iomkl', 'version': '4.6.13'} toolchainopts = {'optarch': True, 'usempi': True} -- GitLab From 0bec9ed569eb21ed7a8454e5ee850107953bc40d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 16:10:11 +0100 Subject: [PATCH 221/566] add goolf easyconfig for GMP v5.1.3 --- .../g/GMP/GMP-5.1.3-goolf-1.4.10.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..12faa79b4a --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +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': 'goolf', 'version': '1.4.10'} + +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.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From 183e373bd8c7ccc4ecd139ef2c7f8f3d380eb97c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 22 Dec 2013 16:53:20 +0100 Subject: [PATCH 222/566] M4: use GNU_SOURCE template in source url --- easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb index bd161358d2..b122fe2d09 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.5.0.eb @@ -9,7 +9,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftpmirror.gnu.org/m4'] +source_urls = [GNU_SOURCE] configopts = "--enable-cxx" -- GitLab From 7e2d87450f9f6f05e0c8f6948d3714d1879a9b94 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 22 Dec 2013 17:05:50 +0100 Subject: [PATCH 223/566] CP2K: enable libxc support --- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb | 2 ++ easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb index ff604547cf..d40ebb8e28 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb @@ -36,4 +36,6 @@ parallel = 1 # regression test reports failures ignore_regtest_fails = True +libxc = True + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb index 1d06d1dfc9..33d9c00435 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb @@ -35,4 +35,6 @@ parallel = 1 # regression test reports failures: 13/2450 segfault ignore_regtest_fails = True +libxc = True + moduleclass = 'chem' -- GitLab From 5778709026f081dba1a8b4ef8c819f833557c4a3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 22 Dec 2013 17:18:25 +0100 Subject: [PATCH 224/566] CP2K: drop libxc options, use the dep In the easyblock, we will check in the dependencies for libxc and libint --- easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb | 2 -- easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb index d40ebb8e28..ff604547cf 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.4.0-ictce-5.5.0.eb @@ -36,6 +36,4 @@ parallel = 1 # regression test reports failures ignore_regtest_fails = True -libxc = True - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb index 33d9c00435..1d06d1dfc9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20131211-ictce-5.5.0.eb @@ -35,6 +35,4 @@ parallel = 1 # regression test reports failures: 13/2450 segfault ignore_regtest_fails = True -libxc = True - moduleclass = 'chem' -- GitLab From 1fd8f38ab0498ae28454305be660ab60fa358f42 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Sun, 22 Dec 2013 17:32:26 +0100 Subject: [PATCH 225/566] Bison: use GNU_SOURCE as source url --- easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb index 5224af1090..1c8ec7242c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.5.0.eb @@ -8,7 +8,7 @@ description = """Bison is a general-purpose parser generator that converts an an toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://ftp.gnu.org/gnu/%(namelower)s'] +source_urls = [GNU_SOURCE] builddependencies = [('M4', '1.4.17')] -- GitLab From 50d59801876ef2f0edea6e1ec8b38d73957d9d81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 19:54:27 +0100 Subject: [PATCH 226/566] fix Ghostscript name, fix remarks and style issues --- .../Ghostscript-9.10-goolf-1.4.10.eb} | 14 ++++++-------- .../Ghostscript-9.10-ictce-4.1.13.eb} | 14 ++++++-------- 2 files changed, 12 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/g/{ghostscript/ghostscript-9.10-goolf-1.4.10.eb => Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb} (68%) rename easybuild/easyconfigs/g/{ghostscript/ghostscript-9.10-ictce-4.1.13.eb => Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb} (68%) diff --git a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb similarity index 68% rename from easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb index c2f7480573..9e63e7389c 100644 --- a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-goolf-1.4.10.eb @@ -1,24 +1,22 @@ -name = 'ghostscript' +name = 'Ghostscript' version = '9.10' homepage = 'http://ghostscript.com' description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to - different targets. It used to be part of the cups printing stack, but is no longer used for that. -""" + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] +# expat, freetype and libpng are optional deps, +# these are actually patched and included in the sources, dependencies = [ -# optional, these are actually patched and included in the sources, -# ('expat', '2.1.0'), -# ('freetype', '2.4.10'), -# ('libpng', '1.6.2'), ('LibTIFF', '4.0.3'), ] configopts = "--with-system-libtiff --enable-dynamic" -moduleclass = 'lib' +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb similarity index 68% rename from easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb rename to easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb index d38ce6de2c..12bdcd0f27 100644 --- a/easybuild/easyconfigs/g/ghostscript/ghostscript-9.10-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb @@ -1,24 +1,22 @@ -name = 'ghostscript' +name = 'Ghostscript' version = '9.10' homepage = 'http://ghostscript.com' description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to - different targets. It used to be part of the cups printing stack, but is no longer used for that. -""" + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} source_urls = ["http://downloads.ghostscript.com/public/"] sources = [SOURCELOWER_TAR_GZ] +# expat, freetype and libpng are optional deps, +# these are actually patched and included in the sources, dependencies = [ -# optional, these are actually patched and included in the sources, -# ('expat', '2.1.0'), -# ('freetype', '2.4.10'), -# ('libpng', '1.6.2'), ('LibTIFF', '4.0.3'), ] configopts = "--with-system-libtiff --enable-dynamic" -moduleclass = 'lib' +moduleclass = 'tools' -- GitLab From 517a882f7fbe8e5c851e1428f73e80083761c36f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 20:55:36 +0100 Subject: [PATCH 227/566] add Python versionsuffix to HTSeq easyconfigs filenames --- ...goolf-1.4.10.eb => HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb} | 0 ...ictce-4.1.13.eb => HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/h/HTSeq/{HTSeq-0.5.4p5-goolf-1.4.10.eb => HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb} (100%) rename easybuild/easyconfigs/h/HTSeq/{HTSeq-0.5.4p5-ictce-4.1.13.eb => HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb} (100%) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb similarity index 100% rename from easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10.eb rename to easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb similarity index 100% rename from easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13.eb rename to easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb -- GitLab From 0414ff3ecf9eb1875eb74ff6afd1e23b6429049e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 20:57:04 +0100 Subject: [PATCH 228/566] style fixes in BEDTools easyconfigs --- .../b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb | 13 ++++++++----- .../b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb | 14 ++++++++------ 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb index 8186926dfe..0c4ebbc6f3 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb @@ -1,13 +1,13 @@ easyblock = 'MakeCp' + name = 'BEDTools' version = 'v2.17.0' homepage = 'http://code.google.com/p/bedtools/' 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. -Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" -several BEDTools together. The following are examples of common questions that one can address with BEDTools. -""" + computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. + Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" + several BEDTools together. The following are examples of common questions that one can address with BEDTools.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} @@ -18,6 +18,9 @@ dirs = ["bin", "data", "docs", "genomes", 'scripts'] # copy all directories to the installation directory files_to_copy = dirs -sanity_check_paths = {'files': [], 'dirs': dirs} +sanity_check_paths = { + 'files': [], + 'dirs': dirs, +} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb index adcf9bdf19..c30c0d550b 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb @@ -1,14 +1,13 @@ easyblock = 'MakeCp' + name = 'BEDTools' version = 'v2.17.0' homepage = 'http://code.google.com/p/bedtools/' 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. -Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" -several BEDTools together. The following are examples of common questions that one can address with BEDTools. -""" - + computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. + Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" + several BEDTools together. The following are examples of common questions that one can address with BEDTools.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} @@ -19,6 +18,9 @@ dirs = ["bin", "data", "docs", "genomes", 'scripts'] # copy all directories to the installation directory files_to_copy = dirs -sanity_check_paths = {'files': [], 'dirs': dirs} +sanity_check_paths = { + 'files': [], + 'dirs': dirs, +} moduleclass = 'bio' -- GitLab From 21f97ba79045fb5dbf0859800ab5d7933b3f075d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 22:11:05 +0100 Subject: [PATCH 229/566] fix BEDTools versions --- ...2.17.0-goolf-1.4.10.eb => BEDTools-2.17.0-goolf-1.4.10.eb} | 4 ++-- ...2.17.0-ictce-4.1.13.eb => BEDTools-2.17.0-ictce-4.1.13.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/b/BEDTools/{BEDTools-v2.17.0-goolf-1.4.10.eb => BEDTools-2.17.0-goolf-1.4.10.eb} (93%) rename easybuild/easyconfigs/b/BEDTools/{BEDTools-v2.17.0-ictce-4.1.13.eb => BEDTools-2.17.0-ictce-4.1.13.eb} (93%) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb similarity index 93% rename from easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb rename to easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb index 0c4ebbc6f3..60d9a2da76 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'BEDTools' -version = 'v2.17.0' +version = '2.17.0' homepage = 'http://code.google.com/p/bedtools/' description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and @@ -12,7 +12,7 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://bedtools.googlecode.com/files/"] -sources = ['%(name)s.%(version)s.tar.gz'] +sources = ['%(name)s.v%(version)s.tar.gz'] dirs = ["bin", "data", "docs", "genomes", 'scripts'] # copy all directories to the installation directory diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb similarity index 93% rename from easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb index c30c0d550b..ed094b1acf 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-v2.17.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'BEDTools' -version = 'v2.17.0' +version = '2.17.0' homepage = 'http://code.google.com/p/bedtools/' description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and @@ -12,7 +12,7 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = ["http://bedtools.googlecode.com/files/"] -sources = ['%(name)s.%(version)s.tar.gz'] +sources = ['%(name)s.v%(version)s.tar.gz'] dirs = ["bin", "data", "docs", "genomes", 'scripts'] # copy all directories to the installation directory -- GitLab From 9052b791523997f7871521e1daabcc9e8ba06026 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 22:15:42 +0100 Subject: [PATCH 230/566] align various BEDTools easyconfigs --- .../BEDTools/BEDTools-2.17.0-goolf-1.4.10.eb | 19 ++++++++----------- .../BEDTools/BEDTools-2.17.0-ictce-4.1.13.eb | 19 ++++++++----------- .../BEDTools/BEDTools-2.18.1-goolf-1.4.10.eb | 18 ++++++++---------- 3 files changed, 24 insertions(+), 32 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 60d9a2da76..4b2fba7bcf 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 @@ -4,23 +4,20 @@ name = 'BEDTools' version = '2.17.0' homepage = 'http://code.google.com/p/bedtools/' -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. - Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" - several BEDTools together. The following are examples of common questions that one can address with BEDTools.""" +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'} -source_urls = ["http://bedtools.googlecode.com/files/"] -sources = ['%(name)s.v%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/archive/'] +sources = ['v%(version)s.tar.gz'] -dirs = ["bin", "data", "docs", "genomes", 'scripts'] -# copy all directories to the installation directory -files_to_copy = dirs +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] sanity_check_paths = { - 'files': [], - 'dirs': dirs, + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, } 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 ed094b1acf..d215c84837 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 @@ -4,23 +4,20 @@ name = 'BEDTools' version = '2.17.0' homepage = 'http://code.google.com/p/bedtools/' -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. - Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" - several BEDTools together. The following are examples of common questions that one can address with BEDTools.""" +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': 'ictce', 'version': '4.1.13'} -source_urls = ["http://bedtools.googlecode.com/files/"] -sources = ['%(name)s.v%(version)s.tar.gz'] +source_urls = ['https://github.com/arq5x/bedtools2/archive/'] +sources = ['v%(version)s.tar.gz'] -dirs = ["bin", "data", "docs", "genomes", 'scripts'] -# copy all directories to the installation directory -files_to_copy = dirs +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] sanity_check_paths = { - 'files': [], - 'dirs': dirs, + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, } 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 47e6beb8fd..d45afb71d9 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 @@ -2,28 +2,26 @@ # Swiss Institute of Bioinformatics (SIB) # Biozentrum - University of Basel +easyblock = 'MakeCp' + name = 'BEDTools' version = '2.18.1' -easyblock = 'MakeCp' - homepage = "https://github.com/arq5x/bedtools2" -description = """A powerful toolset for genome arithmetic.""" +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'} -toolchainopts = {'optarch': True} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/arq5x/bedtools2/archive/'] +sources = ['v%(version)s.tar.gz'] 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': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed','bedToBam','fastaFromBed']], + 'dirs': files_to_copy, } moduleclass = 'bio' -- GitLab From 75298f01889b3c1e2a692b1dea3b7921ef59b1aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 22:27:16 +0100 Subject: [PATCH 231/566] only v2.18 version and up are available via github --- .../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 ++-- 2 files changed, 4 insertions(+), 4 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 4b2fba7bcf..6cb0f4b818 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 @@ -10,8 +10,8 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://github.com/arq5x/bedtools2/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = ["http://bedtools.googlecode.com/files/"] +sources = ['%(name)s.v%(version)s.tar.gz'] files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] 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 d215c84837..3cb9f10e2d 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 @@ -10,8 +10,8 @@ description = """The BEDTools utilities allow one to address common genomics tas toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://github.com/arq5x/bedtools2/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = ["http://bedtools.googlecode.com/files/"] +sources = ['%(name)s.v%(version)s.tar.gz'] files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] -- GitLab From c392e5e78454f481ac711b93782b9cad74263b56 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 22 Dec 2013 22:51:59 +0100 Subject: [PATCH 232/566] change date/version format. Added md5sums --- .../{CAP3-intel-x86.eb => CAP3-20071221-intel-x86.eb} | 11 +++++++---- ...-intel-x86_64.eb => CAP3-20071221-intel-x86_64.eb} | 11 +++++++---- .../{CAP3-opteron.eb => CAP3-20071221-opteron.eb} | 11 +++++++---- 3 files changed, 21 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/c/CAP3/{CAP3-intel-x86.eb => CAP3-20071221-intel-x86.eb} (53%) rename easybuild/easyconfigs/c/CAP3/{CAP3-intel-x86_64.eb => CAP3-20071221-intel-x86_64.eb} (54%) rename easybuild/easyconfigs/c/CAP3/{CAP3-opteron.eb => CAP3-20071221-opteron.eb} (54%) diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb similarity index 53% rename from easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb rename to easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb index e9d20d0c64..0c1d5284b7 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb @@ -1,6 +1,11 @@ +# 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 = 'CAP3' -version = 'intel-x86_12-21-2007' +version = '20071221-intel-x86' +# see VersionDate in caps3 output easyblock = 'PackedBinary' @@ -11,13 +16,11 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.tar'] +checksums = [('md5', '55f57f61e588d4de06c0506cf2696c29')] sanity_check_paths = { 'files': ['cap3','formcon'], 'dirs': [], } - moduleclass = 'bio' - - diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb similarity index 54% rename from easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb rename to easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb index 46918913be..0962339a29 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-intel-x86_64.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb @@ -1,6 +1,11 @@ +# 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 = 'CAP3' -version = 'intel-x86_64_12-21-2007' +version = '20071221-intel-x86_64' +# see VersionDate in caps3 output easyblock = 'PackedBinary' @@ -11,13 +16,11 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.x86_64.tar'] +checksums = [('md5', '0fbb95c3fcbfb2b1afcebc5f7e2b4343')] sanity_check_paths = { 'files': ['cap3','formcon'], 'dirs': [], } - moduleclass = 'bio' - - diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb similarity index 54% rename from easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb rename to easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb index 559fab20ae..3e19f30c49 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-opteron.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb @@ -1,6 +1,11 @@ +# 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 = 'CAP3' -version = 'opteron-12-21-2007' +version = '20071221-opteron' +# see VersionDate in caps3 output easyblock = 'PackedBinary' @@ -11,13 +16,11 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.opteron64.tar'] +checksums = [('md5', '2d924766f6e8b5cf03bd2db81016d821')] sanity_check_paths = { 'files': ['cap3','formcon'], 'dirs': [], } - moduleclass = 'bio' - - -- GitLab From 99455d235d512ce2e93fbfd2563ea23199d3c2a7 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 22 Dec 2013 23:01:05 +0100 Subject: [PATCH 233/566] just modified headers --- .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb | 1 + .../c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb | 1 + 2 files changed, 2 insertions(+) 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 5a8435dee3..77441b5881 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 @@ -1,3 +1,4 @@ +# 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 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 abd9e43447..e788568341 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 @@ -1,3 +1,4 @@ +# 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 -- GitLab From e9589161dc081ec34dffc956bf3a2174c54c7e4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Dec 2013 23:06:54 +0100 Subject: [PATCH 234/566] only use 2 MPI processes when tested, since GROMACS required one GPU per MPI process --- .../g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb | 3 +++ .../g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb index d6f38ccfbb..d2a6762f37 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb @@ -33,4 +33,7 @@ sources = [ builddependencies = [('CMake', '2.8.4')] +# GROMACS required one GPU per MPI process used, so lets keep it at a minimum +configopts = '-DGMX_TEST_NUMBER_PROCS=2' + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb index 839eb005c2..0056d45c8c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb @@ -33,4 +33,7 @@ sources = [ builddependencies = [('CMake', '2.8.12')] +# GROMACS required one GPU per MPI process used, so lets keep it at a minimum +configopts = '-DGMX_TEST_NUMBER_PROCS=2' + moduleclass = 'bio' -- GitLab From fca2342efed0ae77614508dac413439ed137b25b Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 22 Dec 2013 23:49:18 +0100 Subject: [PATCH 235/566] style fixes --- .../a/ABySS/ABySS-1.3.6-goolf-1.4.10-Python-2.7.5.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) 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 54ffe4617c..3d65bd4489 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 @@ -24,15 +24,14 @@ toolchainopts = {'usempi': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] - dependencies = [ - ('google-sparsehash', '2.0.2'), - ('Boost', '1.49.0',versionsuffix), + ('google-sparsehash', '2.0.2'), + ('Boost', '1.49.0', versionsuffix), ] sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] - } + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} moduleclass = 'bio' -- GitLab From 49b293adac00251a7f9038c8b38e17b2975ee28c Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 23 Dec 2013 00:21:08 +0100 Subject: [PATCH 236/566] added header --- easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb index 0c368ea41a..9496f69174 100644 --- a/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/O2scl/o2scl-0.913-goolf-1.4.10.eb @@ -1,3 +1,8 @@ +# 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 + name = 'o2scl' version = '0.913' -- GitLab From 49f34763ef43b79cd36895b71a77e3aa4adb7db0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 10:38:28 +0100 Subject: [PATCH 237/566] fix Qt dependency for CGAL --- .../CGAL-4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 13 ++++++------- .../c/CGAL/CGAL-4.0-goolf-1.4.10-Python-2.7.3.eb | 13 ++++++------- .../c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb | 13 ++++++------- .../c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb | 13 ++++++------- 4 files changed, 24 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index b0f7c63498..3df06d2d4f 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -15,12 +15,11 @@ pythonversion = '2.7.3' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('CMake', '2.8.4'), - ('GMP', '5.0.5'), - ('Boost', '1.49.0', versionsuffix), - ('MPFR', '3.1.0'), - ] - -osdependencies = ['qt4-devel'] + ('CMake', '2.8.4'), + ('GMP', '5.0.5'), + ('Boost', '1.49.0', versionsuffix), + ('MPFR', '3.1.0'), + ('Qt', '4.8.4'), +] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goolf-1.4.10-Python-2.7.3.eb index 34490bdba2..0aff43ef22 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-goolf-1.4.10-Python-2.7.3.eb @@ -15,12 +15,11 @@ pythonversion = '2.7.3' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('CMake', '2.8.4'), - ('GMP', '5.0.5'), - ('Boost', '1.49.0', versionsuffix), - ('MPFR', '3.1.0'), - ] - -osdependencies = ['qt4-devel'] + ('CMake', '2.8.4'), + ('GMP', '5.0.5'), + ('Boost', '1.49.0', versionsuffix), + ('MPFR', '3.1.0'), + ('Qt', '4.8.4'), +] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb index 943d99f867..c2050e6543 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-4.0.6-Python-2.7.3.eb @@ -15,13 +15,12 @@ pythonversion = '2.7.3' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('CMake', '2.8.4'), - ('GMP', '5.0.5'), - ('Boost', '1.49.0', versionsuffix), - ('MPFR', '3.1.0'), - ] - -osdependencies = ['qt4-devel'] + ('CMake', '2.8.4'), + ('GMP', '5.0.5'), + ('Boost', '1.49.0', versionsuffix), + ('MPFR', '3.1.0'), + ('Qt', '4.8.4'), +] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb index ba2bcd6e09..721c08f9d7 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.0-ictce-5.3.0-Python-2.7.3.eb @@ -16,13 +16,12 @@ pythonversion = '2.7.3' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('CMake', '2.8.4'), - ('GMP', '5.0.5'), - ('Boost', '1.49.0', versionsuffix), - ('MPFR', '3.1.0'), - ] - -osdependencies = ['qt4-devel'] + ('CMake', '2.8.4'), + ('GMP', '5.0.5'), + ('Boost', '1.49.0', versionsuffix), + ('MPFR', '3.1.0'), + ('Qt', '4.8.4'), +] moduleclass = 'numlib' -- GitLab From ae547fa7bb236f6cca38418406d53a8178914955 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 11:00:09 +0100 Subject: [PATCH 238/566] add missing dependencies --- .../g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb | 19 +++++++++++++++ .../g/GLib/GLib-2.34.3-ictce-4.0.6.eb | 19 +++++++++++++++ .../l/libffi/libffi-3.0.13-ictce-4.0.6.eb | 23 +++++++++++++++++++ .../Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 21 +++++++++++++++++ .../p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 23 +++++++++++++++++++ .../p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 21 +++++++++++++++++ .../q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 14 +++++++++++ .../easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 14 +++++++++++ .../easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 14 +++++++++++ 9 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..e23ae02de7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,19 @@ +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +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', '3.0.13'), + ('gettext', '0.18.2'), +] +builddependencies = [('Python', '2.5.6', '-bare')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb new file mode 100644 index 0000000000..e63e6d5920 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.34.3-ictce-4.0.6.eb @@ -0,0 +1,19 @@ +name = 'GLib' +version = '2.34.3' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} +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', '3.0.13'), + ('gettext', '0.18.2'), +] +builddependencies = [('Python', '2.5.6', '-bare')] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb new file mode 100644 index 0000000000..8f8f4182b7 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb @@ -0,0 +1,23 @@ +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': 'ictce', 'version': '4.0.6'} + +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/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 new file mode 100644 index 0000000000..f2464bd93a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -0,0 +1,21 @@ +name = 'Python' +version = '2.5.6' +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': 'goalf', 'version': '1.1.0-no-OFED'} +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', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +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 new file mode 100644 index 0000000000..e25ef5a1c1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -0,0 +1,23 @@ +name = 'Python' +version = '2.5.6' +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': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +patches = ['python_libffi_int128_icc.patch'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +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 new file mode 100644 index 0000000000..5176f9c1ae --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -0,0 +1,21 @@ +name = 'Python' +version = '2.5.6' +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': 'ictce', 'version': '5.3.0'} +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', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..e9b04c5257 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,14 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb new file mode 100644 index 0000000000..4bd93a453e --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -0,0 +1,14 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'ictce', 'version': '4.0.6'} + +source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb new file mode 100644 index 0000000000..56cdaa29b3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -0,0 +1,14 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' -- GitLab From f87f4e7e9dda06adc9ccd4cee25b1905fb7de3d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 11:11:34 +0100 Subject: [PATCH 239/566] remove dateutil Python extension, build doesn't work --- .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 4 ---- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 4 ---- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 4 ---- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 4 ---- 4 files changed, 16 deletions(-) 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 1811efcbd6..fcd6f6faa9 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 @@ -54,10 +54,6 @@ exts_list = [ ('Cython', '0.19.1', { '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/'], }), 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 2edfeaac2b..a8a0d5bb35 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 @@ -54,10 +54,6 @@ exts_list = [ ('Cython', '0.19.1', { '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/'], }), 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 b3f2fc2f03..a09ac8bc40 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 @@ -54,10 +54,6 @@ exts_list = [ ('Cython', '0.19.1', { '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/'], }), 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 7263a31cf4..ff9baf5e2b 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 @@ -55,10 +55,6 @@ exts_list = [ ('Cython', '0.19.1', { '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/'], }), -- GitLab From e39ff1b8c208c91f2b5de004b23fddc7dd827704 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 23 Dec 2013 13:32:32 +0100 Subject: [PATCH 240/566] updated header with url to github --- .../v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb index a5053fd3e9..47c30351f2 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-goolf-1.4.10-Perl-5.16.3.eb @@ -1,3 +1,4 @@ +# 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 -- GitLab From 9a96b7276d0825bced9527a8ae9bb715f8328357 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 13:33:51 +0100 Subject: [PATCH 241/566] remove Python 3.x incompatible extensions --- .../p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 10 ---------- .../easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 10 ---------- .../easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 10 ---------- .../easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb | 10 ---------- 4 files changed, 40 deletions(-) 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 fcd6f6faa9..b57481552a 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 @@ -48,9 +48,6 @@ exts_list = [ ('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', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), @@ -60,17 +57,10 @@ exts_list = [ ('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/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 a8a0d5bb35..6e6ef740c7 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 @@ -48,9 +48,6 @@ exts_list = [ ('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', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), @@ -60,17 +57,10 @@ exts_list = [ ('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/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 a09ac8bc40..1049fd8980 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 @@ -48,9 +48,6 @@ exts_list = [ ('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', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), @@ -60,17 +57,10 @@ exts_list = [ ('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/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 ff9baf5e2b..039d169ed3 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 @@ -49,9 +49,6 @@ exts_list = [ ('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', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), @@ -61,17 +58,10 @@ exts_list = [ ('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' -- GitLab From 13a521ead96e83e3d5b84ddfe5ff05e849802647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 14:46:50 +0100 Subject: [PATCH 242/566] add required patch file in Python 3.2.3 ictce/4.0.6 easyconfig --- easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 ++ 1 file changed, 2 insertions(+) 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 1049fd8980..7c8244621d 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 @@ -13,6 +13,8 @@ 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 dc53b45ef222a9e243529e36f7394f032a2ae6e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 15:20:05 +0100 Subject: [PATCH 243/566] add patch file to enforce use of -O1 for Qt with ictce/4.0.6 --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 4 ++++ easybuild/easyconfigs/q/Qt/Qt-4.8.4_ictce-O1.patch | 11 +++++++++++ 2 files changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.4_ictce-O1.patch diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 4bd93a453e..7c847a9b40 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -5,10 +5,14 @@ homepage = 'http://qt-project.org/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'lowopt': True} # use -O1 source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] +# enforce use of -O1, required because of compiler bug that triggers 'internal error: 0_381' +patches = ['Qt-4.8.4_ictce-O1.patch'] + dependencies = [('GLib', '2.34.3')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4_ictce-O1.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.4_ictce-O1.patch new file mode 100644 index 0000000000..26a7811ae9 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4_ictce-O1.patch @@ -0,0 +1,11 @@ +--- qt-everywhere-opensource-src-4.8.4/mkspecs/linux-icc/qmake.conf.orig 2013-12-23 14:54:00.272609496 +0100 ++++ qt-everywhere-opensource-src-4.8.4/mkspecs/linux-icc/qmake.conf 2013-12-23 14:54:09.392773091 +0100 +@@ -25,7 +25,7 @@ + QMAKE_CFLAGS_DEPS = -M + QMAKE_CFLAGS_WARN_ON = -w1 -Wcheck -wd654,1572,411,873,1125,2259 + QMAKE_CFLAGS_WARN_OFF = -w +-QMAKE_CFLAGS_RELEASE = -O2 -falign-functions=16 -ansi-alias -fstrict-aliasing ++QMAKE_CFLAGS_RELEASE = -O1 -falign-functions=16 -ansi-alias -fstrict-aliasing + QMAKE_CFLAGS_DEBUG = -O0 -g + QMAKE_CFLAGS_SHLIB = -fPIC -fno-jump-tables + QMAKE_CFLAGS_STATIC_LIB = $$QMAKE_CFLAGS_SHLIB -- GitLab From 17e0a2f59d6f4b2f47c803fac91067e70e856f17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 15:42:08 +0100 Subject: [PATCH 244/566] add fix for libctl build failing because guile-config contains full path to bin/guile --- .../easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb | 3 +++ easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb | 3 +++ easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb | 4 +++- 4 files changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb index 6965c925d9..4793aadab2 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb @@ -12,4 +12,7 @@ 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 $EBROOTGUILE/bin/guile-config"' + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb index eaeab2f0a1..c6329bbafe 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb @@ -11,4 +11,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('guile', '1.8.8')] +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb index d079fb1e33..f9f2863718 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb @@ -12,4 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('guile', '1.8.8')] +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb index 74ca15b43e..ff25be499b 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb @@ -4,7 +4,6 @@ version = '3.2.1' homepage = 'http://ab-initio.mit.edu/libctl' description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} @@ -13,4 +12,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('guile', '1.8.8')] +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + moduleclass = 'chem' -- GitLab From 335c84d2cfdd9c86650995d614b90ee09ad35f37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 15:58:20 +0100 Subject: [PATCH 245/566] add patch file to fix issue with PSI configure using python-config which includes full path to bin/python --- .../p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb | 1 + .../p/PSI/PSI-4.0b4-ictce-4.1.13.eb | 1 + .../p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb | 1 + .../p/PSI/PSI-4.0b4-ictce-5.3.0.eb | 1 + .../p/PSI/PSI-4.0b4_python-config.patch | 20 +++++++++++++++++++ .../PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb | 3 ++- .../p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb | 3 ++- .../p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb | 3 ++- .../p/PSI/PSI-4.0b5-ictce-5.3.0.eb | 3 ++- .../p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb | 3 ++- .../p/PSI/PSI-4.0b5-ictce-5.5.0.eb | 3 ++- .../p/PSI/PSI-4.0b5_python-config.patch | 20 +++++++++++++++++++ 12 files changed, 56 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b4_python-config.patch create mode 100644 easybuild/easyconfigs/p/PSI/PSI-4.0b5_python-config.patch diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb index d3cae5bf6c..69d6cb10be 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13-mt.eb @@ -17,6 +17,7 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb index 0325be769c..5c45d4243c 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-4.1.13.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb index ea25a8f6c0..528a6728be 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0-mt.eb @@ -17,6 +17,7 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb index 9d5ff82601..674a15f04b 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4-ictce-5.3.0.eb @@ -15,6 +15,7 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b4-mpi.patch', 'PSI-4.0b4-thread-pool.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b4_python-config.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b4_python-config.patch new file mode 100644 index 0000000000..caa0038c3d --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b4_python-config.patch @@ -0,0 +1,20 @@ +--- psi4.0b4/configure.orig 2013-04-07 09:13:35.000000000 +0200 ++++ psi4.0b4/configure 2013-12-23 15:52:14.531809408 +0100 +@@ -4968,7 +4968,7 @@ + if test "${am_cv_python_include+set}" = set; then + $as_echo_n "(cached) " >&6 + else +- am_cv_python_include=`${PYTHON}-config --includes` ++ am_cv_python_include=`python ${PYTHON}-config --includes` + fi + { $as_echo "$as_me:$LINENO: result: $am_cv_python_include" >&5 + $as_echo "$am_cv_python_include" >&6; } +@@ -4980,7 +4980,7 @@ + if test "${am_cv_python_ldflags+set}" = set; then + $as_echo_n "(cached) " >&6 + else +- am_cv_python_ldflags=`${PYTHON}-config --ldflags` ++ am_cv_python_ldflags=`python ${PYTHON}-config --ldflags` + fi + { $as_echo "$as_me:$LINENO: result: $am_cv_python_ldflags" >&5 + $as_echo "$am_cv_python_ldflags" >&6; } diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb index aaa504d53c..77f4624c51 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED-mt.eb @@ -15,9 +15,10 @@ source_urls = ['http://download.sourceforge.net/psicode/'] sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb index 6882ac49f0..de36f9f90d 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-goalf-1.5.12-no-OFED.eb @@ -14,9 +14,10 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b5-mpi-memcpy.patch', - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb index 51a7d52ca8..c680330c40 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0-mt.eb @@ -15,9 +15,10 @@ source_urls = ['http://download.sourceforge.net/psicode/'] sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb index 7ded97c33e..288d0bd7ab 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.3.0.eb @@ -14,9 +14,10 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b5-mpi-memcpy.patch', - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb index 089a136deb..e65fbf7805 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0-mt.eb @@ -15,9 +15,10 @@ source_urls = ['http://download.sourceforge.net/psicode/'] sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb index 863bb18040..7be55fa034 100644 --- a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-ictce-5.5.0.eb @@ -14,9 +14,10 @@ sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'PSI-4.0b5-mpi-memcpy.patch', - 'PSI-4.0b5-failed-test.patch', # The test works but it segfaults on exit + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit 'PSI-4.0b5-thread-pool.patch', 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5_python-config.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b5_python-config.patch new file mode 100644 index 0000000000..ff2bd121f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5_python-config.patch @@ -0,0 +1,20 @@ +--- psi4.0b5/configure.orig 2013-12-23 15:48:15.547085479 +0100 ++++ psi4.0b5/configure 2013-12-23 15:49:03.008030357 +0100 +@@ -4977,7 +4977,7 @@ + if test "${am_cv_python_include+set}" = set; then + $as_echo_n "(cached) " >&6 + else +- am_cv_python_include=`${PYTHON}-config --includes` ++ am_cv_python_include=`python ${PYTHON}-config --includes` + fi + { $as_echo "$as_me:$LINENO: result: $am_cv_python_include" >&5 + $as_echo "$am_cv_python_include" >&6; } +@@ -4989,7 +4989,7 @@ + if test "${am_cv_python_ldflags+set}" = set; then + $as_echo_n "(cached) " >&6 + else +- am_cv_python_ldflags=`${PYTHON}-config --ldflags` ++ am_cv_python_ldflags=`python ${PYTHON}-config --ldflags` + fi + { $as_echo "$as_me:$LINENO: result: $am_cv_python_ldflags" >&5 + $as_echo "$am_cv_python_ldflags" >&6; } -- GitLab From c879996b75c970965fac15c9dfad2038707b121c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 16:03:35 +0100 Subject: [PATCH 246/566] add GUILE_CONFIG config option to libmatheval easyconfig too --- .../libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb | 19 +++++++++++-------- .../libmatheval-1.1.8-goolf-1.4.10.eb | 19 +++++++++++-------- .../libmatheval-1.1.8-ictce-4.0.6.eb | 19 +++++++++++-------- .../libmatheval-1.1.8-ictce-5.3.0.eb | 19 +++++++++++-------- 4 files changed, 44 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb index dd04511798..9812cf6fc2 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb @@ -12,17 +12,20 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('byacc', '20120526'), - ('guile', '1.8.8'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('byacc', '20120526'), + ('guile', '1.8.8'), +] configopts = '--with-pic' +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + sanity_check_paths = { - 'files': ['lib/libmatheval.a', 'include/matheval.h'], - 'dirs': [] - } + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index b24bc59f04..e4f394364d 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -12,17 +12,20 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('byacc', '20120526'), - ('guile', '1.8.8'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('byacc', '20120526'), + ('guile', '1.8.8'), +] configopts = '--with-pic' +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + sanity_check_paths = { - 'files': ['lib/libmatheval.a', 'include/matheval.h'], - 'dirs': [] - } + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb index 7b46f2830c..feaa98cde7 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb @@ -12,17 +12,20 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('byacc', '20120526'), - ('guile', '1.8.8'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('byacc', '20120526'), + ('guile', '1.8.8'), +] configopts = '--with-pic' +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + sanity_check_paths = { - 'files': ['lib/libmatheval.a', 'include/matheval.h'], - 'dirs': [] - } + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index 271da139b9..0c629e9716 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -13,17 +13,20 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} dependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5'), - ('byacc', '20120526'), - ('guile', '1.8.8'), - ] + ('flex', '2.5.35'), + ('Bison', '2.5'), + ('byacc', '20120526'), + ('guile', '1.8.8'), +] configopts = '--with-pic' +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + sanity_check_paths = { - 'files': ['lib/libmatheval.a', 'include/matheval.h'], - 'dirs': [] - } + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} moduleclass = 'lib' -- GitLab From 8d4d963e0b11afc4231d9060eaa0545a3ebb31fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 16:08:35 +0100 Subject: [PATCH 247/566] fix missing space in libmatheval easyconfigs --- .../l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb index 9812cf6fc2..fc7b4abfc1 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb @@ -18,7 +18,7 @@ dependencies = [ ('guile', '1.8.8'), ] -configopts = '--with-pic' +configopts = '--with-pic ' # fix for guile-config being broken because shebang line contains full path to bin/guile configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index e4f394364d..3c04bfef33 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('guile', '1.8.8'), ] -configopts = '--with-pic' +configopts = '--with-pic ' # fix for guile-config being broken because shebang line contains full path to bin/guile configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb index feaa98cde7..2eabdf62ef 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('guile', '1.8.8'), ] -configopts = '--with-pic' +configopts = '--with-pic ' # fix for guile-config being broken because shebang line contains full path to bin/guile configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index 0c629e9716..25956f7777 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('guile', '1.8.8'), ] -configopts = '--with-pic' +configopts = '--with-pic ' # fix for guile-config being broken because shebang line contains full path to bin/guile configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' -- GitLab From e38ba9a5eb0751c3d74e2a18e0bab9b34d8875af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 16:38:23 +0100 Subject: [PATCH 248/566] fix FSL makefile patch files --- .../f/FSL/FSL-5.0.4_makefile_fixes.patch | 84 +++++++++---------- .../f/FSL/FSL_makefile_fixes.patch | 84 +++++++++---------- 2 files changed, 84 insertions(+), 84 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch index eafc838d18..f90ee458bb 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch @@ -7,8 +7,8 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX ?= ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -21,8 +21,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -35,8 +35,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -49,8 +49,8 @@ diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -63,8 +63,8 @@ diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -77,8 +77,8 @@ diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -91,8 +91,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc- -CC = gcc-2 -CXX = c++-2 -+CC ?= gcc-2 -+CXX ?= c++-2 ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -105,8 +105,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -119,8 +119,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -133,8 +133,8 @@ diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2 -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -147,8 +147,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -161,8 +161,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -175,8 +175,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -189,8 +189,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -203,8 +203,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -217,8 +217,8 @@ diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -231,8 +231,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -245,8 +245,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -259,8 +259,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -273,8 +273,8 @@ diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer @@ -287,8 +287,8 @@ diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer ARCHLDFLAGS = -static diff --git a/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch index c78dd2e48a..c1313251ab 100644 --- a/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch @@ -28,8 +28,8 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -42,8 +42,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -56,8 +56,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -70,8 +70,8 @@ diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -84,8 +84,8 @@ diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC ?= cc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -98,8 +98,8 @@ diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -112,8 +112,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc- -CC = gcc-2 -CXX = c++-2 -+CC ?= gcc-2 -+CXX ?= c++-2 ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -126,8 +126,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -140,8 +140,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -154,8 +154,8 @@ diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2 -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -168,8 +168,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -182,8 +182,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -196,8 +196,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -210,8 +210,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -224,8 +224,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -238,8 +238,8 @@ diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -252,8 +252,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -266,8 +266,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -280,8 +280,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -294,8 +294,8 @@ diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer @@ -308,8 +308,8 @@ diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC ?= gcc -+CXX ?= c++ ++CC = ${CC} ++CXX = ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer ARCHLDFLAGS = -static -- GitLab From c998f9d21541b3cb93a52dfee6eac4c7e133fc4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 16:51:51 +0100 Subject: [PATCH 249/566] add GUILE_CONFIG config option to Meep easyconfigs too --- .../m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb | 17 ++++++++++------- .../easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb | 14 +++++++++----- .../easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb | 14 +++++++++----- .../easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb | 15 +++++++++------ 4 files changed, 37 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb index b1b8b5191a..c6d4999624 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb @@ -5,13 +5,13 @@ homepage = 'http://ab-initio.mit.edu/wiki/index.php/Meep' description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.""" -tcver = '1.1.0-no-OFED' -toolchain = {'name': 'goalf', 'version': tcver} -toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': - True, 'pic': True} +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ab-initio.mit.edu/meep/', - 'http://ab-initio.mit.edu/meep/old/'] +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -21,6 +21,9 @@ dependencies = [ ('GSL', '1.15'), ] -configopts = '--with-pic --with-mpi --without-gcc-arch --with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared' +configopts = '--with-pic --with-mpi --without-gcc-arch --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 $EBROOTGUILE/bin/guile-config"' moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb index 2f278ab531..7b27d95b42 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb @@ -6,11 +6,12 @@ description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) s MIT to model electromagnetic systems.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': - True, 'pic': True} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ab-initio.mit.edu/meep/', - 'http://ab-initio.mit.edu/meep/old/'] +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] sources = [SOURCELOWER_TAR_GZ] dependencies = [ @@ -20,6 +21,9 @@ dependencies = [ ('GSL', '1.15'), ] -configopts = '--with-pic --with-mpi --without-gcc-arch --with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared' +configopts = '--with-pic --with-mpi --without-gcc-arch --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 $EBROOTGUILE/bin/guile-config"' moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb index 9b00a0bbd1..7b473e1b0b 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb @@ -6,11 +6,12 @@ description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) s developed at MIT to model electromagnetic systems.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': - True, 'pic': True} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ab-initio.mit.edu/meep/', - 'http://ab-initio.mit.edu/meep/old/'] +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['Meep-%s_version-string-without-spaces.patch' % version] @@ -24,6 +25,9 @@ dependencies = [ ] configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " -configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared" +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 $EBROOTGUILE/bin/guile-config"' moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb index a5d16e83a0..98db62a6c1 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb @@ -5,13 +5,13 @@ homepage = 'http://ab-initio.mit.edu/wiki/index.php/Meep' description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': - True, 'pic': True} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} -source_urls = ['http://ab-initio.mit.edu/meep/', - 'http://ab-initio.mit.edu/meep/old/'] +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['Meep-%s_version-string-without-spaces.patch' % version] @@ -25,6 +25,9 @@ dependencies = [ ] configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " -configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared" +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' -- GitLab From 9d449943650f50026dbfdb6e4a37abd27f177331 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 17:14:22 +0100 Subject: [PATCH 250/566] complete makefile patch for FSL v5.0.4 --- .../f/FSL/FSL-5.0.4_makefile_fixes.patch | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch index f90ee458bb..0d4f7e9d4d 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch @@ -12,6 +12,34 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da CSTATICFLAGS = CXXSTATICFLAGS = +diff -ru fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin11-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-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin12-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 @@ -264,6 +292,34 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. CSTATICFLAGS = -static CXXSTATICFLAGS = -static +diff -ru fsl.orig/config/linux_64-gcc4.3/systemvars.mk fsl/config/linux_64-gcc4.3/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.3/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.3/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 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/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/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 -- GitLab From 67ee1b2dd6db6fea928915d5ce29d82d38c78953 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 17:26:23 +0100 Subject: [PATCH 251/566] correct edited patch file --- .../f/FSL/FSL-5.0.4_makefile_fixes.patch | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch index 0d4f7e9d4d..07c14cee1c 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch @@ -292,20 +292,6 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. CSTATICFLAGS = -static CXXSTATICFLAGS = -static -diff -ru fsl.orig/config/linux_64-gcc4.3/systemvars.mk fsl/config/linux_64-gcc4.3/systemvars.mk ---- fsl.orig/config/linux_64-gcc4.3/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 -+++ fsl/config/linux_64-gcc4.3/systemvars.mk 2013-05-14 22:43:15.648658000 +0200 -@@ -18,8 +18,8 @@ - - # Compiler dependent variables - --CC = gcc --CXX = c++ -+CC = ${CC} -+CXX = ${CXX} - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static - diff -ru fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk --- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 +++ fsl/config/linux_64-gcc4.4/systemvars.mk 2013-05-14 22:43:15.648658000 +0200 -- GitLab From b0210ca8d126cd9c62d90919593e2b7f6e3c3a68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 17:37:54 +0100 Subject: [PATCH 252/566] adjust include install dir for HDF, to avoid header file clashes (especially netcdf.h, e.g. in NCL) --- .../h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb | 7 ++++++- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb | 7 ++++++- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb | 7 ++++++- .../easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb | 7 ++++++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb | 7 ++++++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb | 7 ++++++- easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb | 7 ++++++- 7 files changed, 42 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 83e2988a0c..e995d9cfbc 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index f96af34d46..144aadbb34 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 4f6e05af17..0a219c43cb 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index cebdd7449b..e44680caf1 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index 0810f8a775..f40a982742 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szip=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index 2035306c6a..1c4c00dc01 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -16,6 +16,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 9fc4dc8817..7a34de4b31 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -18,6 +18,11 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} moduleclass = 'data' -- GitLab From 9eae34035c0d3c31d606d2173f48c3e0cc79efbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 17:47:00 +0100 Subject: [PATCH 253/566] fix FSL makefile patch (again) --- .../f/FSL/FSL-5.0.4_makefile_fixes.patch | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch index 07c14cee1c..b9ef33e915 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch @@ -8,7 +8,7 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da -CC = cc -CXX = c++ +CC = ${CC} -+CXX ?= ${CXX} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -19,10 +19,10 @@ diff -ru fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-da # Compiler dependent variables --CC = cc --CXX = c++ +-CC = gcc +-CXX = g++ +CC = ${CC} -+CXX ?= ${CXX} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -33,10 +33,10 @@ diff -ru fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-da # Compiler dependent variables --CC = cc --CXX = c++ +-CC = gcc +-CXX = g++ +CC = ${CC} -+CXX ?= ${CXX} ++CXX = ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = -- GitLab From bb1e4204b9b143874b02ef55478954162c986de3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 18:21:35 +0100 Subject: [PATCH 254/566] avoid 'recursive variable CC references itself (eventually)' error by using := assignment in makefile --- .../f/FSL/FSL-5.0.4_makefile_fixes.patch | 96 +++++++++---------- 1 file changed, 48 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch index b9ef33e915..7a7959c00b 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.4_makefile_fixes.patch @@ -7,8 +7,8 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -21,8 +21,8 @@ diff -ru fsl.orig/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-da -CC = gcc -CXX = g++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -35,8 +35,8 @@ diff -ru fsl.orig/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-da -CC = gcc -CXX = g++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -49,8 +49,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -63,8 +63,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -77,8 +77,8 @@ diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -91,8 +91,8 @@ diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -105,8 +105,8 @@ diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -119,8 +119,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc- -CC = gcc-2 -CXX = c++-2 -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -133,8 +133,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -147,8 +147,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -161,8 +161,8 @@ diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2 -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -175,8 +175,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -189,8 +189,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -203,8 +203,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -217,8 +217,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -231,8 +231,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -245,8 +245,8 @@ diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -259,8 +259,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -273,8 +273,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -287,8 +287,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -301,8 +301,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -315,8 +315,8 @@ diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer @@ -329,8 +329,8 @@ diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer ARCHLDFLAGS = -static -- GitLab From 728603efec8866e01abccde4abd4f37258246e7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 19:00:39 +0100 Subject: [PATCH 255/566] remove unnecessary (and even wrong) patch files now HDF include dir is 'include/hdf' --- easybuild/easyconfigs/n/NCL/NCL-6.0.0-goalf-1.1.0-no-OFED.eb | 2 -- easybuild/easyconfigs/n/NCL/NCL-6.0.0-goolf-1.4.10.eb | 2 -- easybuild/easyconfigs/n/NCL/NCL-6.0.0-ictce-3.2.2.u3.eb | 3 +-- easybuild/easyconfigs/n/NCL/NCL-6.1.0-iqacml-3.7.3.eb | 4 ---- easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb | 4 ---- easybuild/easyconfigs/n/NCL/NCL-6.1.2-iqacml-3.7.3.eb | 4 ---- 6 files changed, 1 insertion(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goalf-1.1.0-no-OFED.eb index 3eab6d0bff..b0be263266 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goalf-1.1.0-no-OFED.eb @@ -24,6 +24,4 @@ builddependencies = [('makedepend', '1.0.4')] sources = ['%s_ncarg-%s.tar.gz' % (name.lower(), version)] -patches = ['NCL_fix-HDF-includes.patch'] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goolf-1.4.10.eb index af6e73e806..241071f2b2 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-goolf-1.4.10.eb @@ -23,6 +23,4 @@ builddependencies = [('makedepend', '1.0.4')] sources = ['%s_ncarg-%s.tar.gz' % (name.lower(), version)] -patches = ['NCL_fix-HDF-includes.patch'] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-ictce-3.2.2.u3.eb index fd25d52c75..7a7a84f29c 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.0.0-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.0.0-ictce-3.2.2.u3.eb @@ -24,7 +24,6 @@ builddependencies = [('makedepend', '1.0.4')] sources = ['%s_ncarg-%s.tar.gz' % (name.lower(), version)] -patches = ['NCL_intel_compound-fix.patch', - 'NCL_fix-HDF-includes.patch'] +patches = ['NCL_intel_compound-fix.patch'] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.1.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/NCL/NCL-6.1.0-iqacml-3.7.3.eb index 0a7b5eac58..3aeb096821 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.1.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.1.0-iqacml-3.7.3.eb @@ -10,10 +10,6 @@ toolchainopts = {'opt': True, 'pic': True, 'usempi': True} sources = ['%s_ncarg-%s.tar.gz' % (name.lower(), version)] -patches = [ - 'NCL-6.1_fix-HDF-includes.patch', -] - dependencies = [ ('cURL', '7.28.1'), ('netCDF', '4.2.1.1'), diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb index f2f25fd0a4..26058d36f5 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-ictce-4.1.13.eb @@ -10,10 +10,6 @@ toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'openmp': True} sources = ['%(namelower)s_ncarg-%(version)s.tar.gz'] -patches = [ - 'NCL-6.1_fix-HDF-includes.patch', -] - dependencies = [ ('cURL', '7.28.1'), ('netCDF', '4.2.1.1', '-mt'), diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-iqacml-3.7.3.eb index 4c676295ad..60e793f09a 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.1.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.1.2-iqacml-3.7.3.eb @@ -10,10 +10,6 @@ toolchainopts = {'opt': True, 'pic': True, 'usempi': True} sources = ['%s_ncarg-%s.tar.gz' % (name.lower(), version)] -patches = [ - 'NCL-6.1_fix-HDF-includes.patch', -] - dependencies = [ ('cURL', '7.28.1'), ('netCDF', '4.2.1.1'), -- GitLab From a540ba04ec96a7c81ae7877f285100f085dd582f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 20:47:57 +0100 Subject: [PATCH 256/566] style fixes --- .../easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb | 2 +- .../easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb | 3 +-- .../easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb | 2 +- easybuild/easyconfigs/t/Tcl/Tcl-8.5.15-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb | 2 +- easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb | 3 +-- easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb | 2 +- 10 files changed, 10 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb index 0d2bc981cb..4cec82a9a5 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb @@ -12,7 +12,7 @@ description = """The package contains R-functions to perform an fmri analysis as toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = ['http://cran.r-project.org/src/contrib/'] -sources = ['%s_%s.tar.gz' % (name, version)] +sources = ['%(name)s_%(version)s.tar.gz'] r = 'R' rver = '2.15.2' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb index de5657ceca..6d1befc47f 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb @@ -9,11 +9,10 @@ description = """The package contains R-functions to perform an fmri analysis as NeuroImage, 33:55-62 (2006) and J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive segmentation for statistical parametric mapping, NeuroImage, 52:515-523 (2010).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://cran.r-project.org/src/contrib/'] -sources = ['%s_%s.tar.gz' % (name, version)] +sources = ['%(name)s_%(version)s.tar.gz'] r = 'R' rver = '2.15.2' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb index f685ae9e45..dacaf55d84 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.5.0-ictce-5.3.0-R-2.15.3.eb @@ -12,7 +12,7 @@ description = """The package contains R-functions to perform an fmri analysis as toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://cran.r-project.org/src/contrib/'] -sources = ['%s_%s.tar.gz' % (name, version)] +sources = ['%(name)s_%(version)s.tar.gz'] r = 'R' rver = '2.15.3' 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 808b442937..e52a011d4b 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 @@ -8,7 +8,7 @@ suitable for a very wide range of uses, including web and desktop applications, toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb index 812a6ecf52..a8d8d4acdf 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ description = """Tk is an open source, cross-platform widget toolchain that prov toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb index 6c6af38ce3..b862540b18 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-goolf-1.4.10.eb @@ -8,7 +8,7 @@ a graphical user interface (GUI) in many different programming languages.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb index 9be243225c..ffd89a9367 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.10.eb @@ -8,7 +8,7 @@ description = """Tk is an open source, cross-platform widget toolchain that prov toolchain = {'name': 'ictce', 'version': '4.0.10'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb index e153ed3819..63e7f3be76 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-4.0.6.eb @@ -8,7 +8,7 @@ description = """Tk is an open source, cross-platform widget toolchain that prov toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb index 92ba6db539..93b3e36dcc 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.12-ictce-5.3.0.eb @@ -5,11 +5,10 @@ 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': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb index fb3f5af8c8..2c8c0ace46 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.5.15-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """Tk is an open source, cross-platform widget toolchain that prov toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%s%s-src.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s%(version)s-src.tar.gz'] dependencies = [('Tcl', version)] -- GitLab From 28d2e1d69acf785ff555ffc6b5e13f85f9ff082c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Dec 2013 21:25:11 +0100 Subject: [PATCH 257/566] add checksum for WPS v3.5.1 source tarball, add an use alternative patch for WPS v3.5.1 --- .../w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb | 4 +- .../w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb | 4 +- ...S-3.5.1_netCDF-Fortran_seperate_path.patch | 71 +++++++++++++++++++ .../WPS_netCDF-Fortran_seperate_path.patch | 3 + 4 files changed, 80 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.5.1_netCDF-Fortran_seperate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb index db34226522..7981e0271c 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-4.1.13-dmpar.eb @@ -11,8 +11,10 @@ toolchainopts = {'opt': True} sources = ['%(name)sV%(version)s.TAR.gz'] source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] +# WPS v3.5.1 tarball was changed at some point, a previous version had checksum 0dd6b0b51321c836d3e60764f00ecb85 +checksums = ['ce0eb551d29e04f688e02d522d327c2c'] -patches = ['WPS_netCDF-Fortran_seperate_path.patch'] +patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch'] buildtype = "dmpar" versionsuffix = '-%s' % buildtype diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb index 66eecfdfed..f332d97a3e 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-3.5.1-ictce-5.3.0-dmpar.eb @@ -11,8 +11,10 @@ toolchainopts = {'opt': True} sources = ['%(name)sV%(version)s.TAR.gz'] source_urls = ['http://www.mmm.ucar.edu/wrf/src/'] +# WPS v3.5.1 tarball was changed at some point, a previous version had checksum 0dd6b0b51321c836d3e60764f00ecb85 +checksums = ['ce0eb551d29e04f688e02d522d327c2c'] -patches = ['WPS_netCDF-Fortran_seperate_path.patch'] +patches = ['WPS-%(version)s_netCDF-Fortran_seperate_path.patch'] buildtype = "dmpar" versionsuffix = '-%s' % buildtype diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.5.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-3.5.1_netCDF-Fortran_seperate_path.patch new file mode 100644 index 0000000000..a0a5dd6390 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.5.1_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,71 @@ +diff -ru WPS.orig/arch/Config.pl WPS/arch/Config.pl +--- WPS.orig/arch/Config.pl 2012-04-07 00:07:24.000000000 +0200 ++++ WPS/arch/Config.pl 2012-06-19 15:33:40.998567539 +0200 +@@ -36,6 +36,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -ru WPS.orig/configure WPS/configure +--- WPS.orig/configure 2012-04-07 00:07:19.000000000 +0200 ++++ WPS/configure 2012-06-19 15:34:35.543132843 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -151,7 +156,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach + + + #Checking cross-compiling capability for some particular environment +@@ -319,9 +324,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +Only in WPS: configure.wps +diff -ru WPS.orig/util/src/Makefile WPS/util/src/Makefile +--- WPS.orig/util/src/Makefile 2012-04-07 00:07:26.000000000 +0200 ++++ WPS/util/src/Makefile 2012-06-19 15:36:39.849421166 +0200 +@@ -40,11 +40,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch index 7ffad44e63..d37050c60e 100644 --- a/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch +++ b/easybuild/easyconfigs/w/WPS/WPS_netCDF-Fortran_seperate_path.patch @@ -1,3 +1,6 @@ +patch file for 'old' WPS v3.5.1 tarball (with MD5 checksum 0dd6b0b51321c836d3e60764f00ecb85) +alternative patch available for last (?) version of v3.5.1 tarball (checksum ce0eb551d29e04f688e02d522d327c2c), +see WPS-3.5.1_netCDF-Fortran_seperate_path.patch diff -ru WPS.orig/arch/Config.pl WPS/arch/Config.pl --- WPS.orig/arch/Config.pl 2012-04-07 00:07:24.000000000 +0200 +++ WPS/arch/Config.pl 2012-06-19 15:33:40.998567539 +0200 -- GitLab From bff96ae3c876a230433d9cccd3e9854c08db9182 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2013 08:56:18 +0100 Subject: [PATCH 258/566] fix FSL makefile patch for older versions --- .../f/FSL/FSL_makefile_fixes.patch | 84 +++++++++---------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch index c1313251ab..be5a449af7 100644 --- a/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch +++ b/easybuild/easyconfigs/f/FSL/FSL_makefile_fixes.patch @@ -28,8 +28,8 @@ diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-da -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -42,8 +42,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -56,8 +56,8 @@ diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -70,8 +70,8 @@ diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -84,8 +84,8 @@ diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-dar -CC = cc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = CXXSTATICFLAGS = @@ -98,8 +98,8 @@ diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -112,8 +112,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc- -CC = gcc-2 -CXX = c++-2 -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -126,8 +126,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -140,8 +140,8 @@ diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc- -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -154,8 +154,8 @@ diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2 -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -168,8 +168,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -182,8 +182,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -196,8 +196,8 @@ diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -210,8 +210,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -224,8 +224,8 @@ diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -238,8 +238,8 @@ diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -252,8 +252,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -266,8 +266,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -280,8 +280,8 @@ diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4. -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} CSTATICFLAGS = -static CXXSTATICFLAGS = -static @@ -294,8 +294,8 @@ diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer @@ -308,8 +308,8 @@ diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc -CC = gcc -CXX = c++ -+CC = ${CC} -+CXX = ${CXX} ++CC := ${CC} ++CXX := ${CXX} ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer ARCHLDFLAGS = -static -- GitLab From c157d0df99aa890c21dac18f161dcd38048d2021 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2013 08:57:09 +0100 Subject: [PATCH 259/566] disable parallel build for libunistring and PnMPI --- .../libunistring-0.9.3-goalf-1.1.0-no-OFED.eb | 12 +++++++----- .../libunistring/libunistring-0.9.3-goolf-1.4.10.eb | 12 +++++++----- .../libunistring/libunistring-0.9.3-ictce-4.0.6.eb | 12 +++++++----- .../libunistring/libunistring-0.9.3-ictce-5.3.0.eb | 13 +++++++------ .../p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb | 2 ++ 5 files changed, 30 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb index 56bdff5bcc..b5efb81463 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb @@ -10,11 +10,13 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +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' : [], - } + '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/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb index 5a3efb3ea5..db896b93ea 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goolf-1.4.10.eb @@ -9,11 +9,13 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] +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' : [], - } + '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/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb index dec6140666..5ef8c4a5c1 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb @@ -12,11 +12,13 @@ source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] 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' : [], - } + '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/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb index 6c3d6347d8..363bc42025 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-5.3.0.eb @@ -5,7 +5,6 @@ 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': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] @@ -13,11 +12,13 @@ source_urls = ['http://ftp.gnu.org/gnu/%s' % name.lower()] 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' : [], - } + '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/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb index e01b6e0e3b..3b3f47bdf1 100644 --- a/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PnMPI/PnMPI-1.2.0-gompi-1.4.12-no-OFED.eb @@ -25,6 +25,8 @@ builddependencies = [('CMake', '2.8.10.2')] configopts = ' -DCMAKE_BUILD_TYPE=Release -DBFD_FOUND=False -DPNMPI_HAVE_BFD=False' +parallel = 1 + sanity_check_paths = { 'files': ["bin/pnmpi-patch", "include/pnmpi.h", "lib/libpnmpi.a"], 'dirs': [], -- GitLab From 6348901125abf3b937c895c97df754a8fd89e87e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Dec 2013 11:28:40 +0100 Subject: [PATCH 260/566] bump version to v1.10.0, update release notes --- RELEASE_NOTES | 38 ++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 37 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c93f9dee84..d843a5fb38 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -1,8 +1,42 @@ This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package. For more detailed information, please see the git log. -The latest version of easybuild-easyconfig provides 1,939 easyconfig files, for 396 different software packages -and 27 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 2,203 easyconfig files, for 414 different software packages +and 29 different (compiler) toolchains. + +v1.10.0 (December 24th 2013) +---------------------------- + +feature + bugfix release +- added example easyconfig files for 18 new software packages: + BEDTools (#579, #632, #635), CAP3 (#548), CHARMM (#584), cutadapt (#620), ErlangOTP (#556, #630), + Ghostscript (#547, #632), HTSeq (#554, #632), Jansson (#545), libjpeg-turbo (#574), Molden (#566), + netloc (#545), o2scl (#633), packmol (#566), PP (#405), qtop (#500), TAMkin (#566), vsc-base (#621), + vsc-mympirun (#621) +- added easyconfigs for new toolchains (#545, #609, #629): + gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, ictce/6.1.5 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + - new versions of icc, ifort, imkl, impi (#609, #629) + - large collection of ictce/5.3.0 easyconfigs (#627) +- various enhancements, including: + - extended list of Python packages as extensions to Python (#625) + - add MPI-enabled version of GROMACS + easyconfigs using ictce (#606, #636) + - clean up templating of source_urls (#637) +- various bug fixes, including: + - provide alternative download URL for Mesa (#532) + - add Python versionsuffix in OpenBabel filenames (#566) + - apply no-gets patch in all M4 v1.4.16 easyconfigs (#623) + - fix patching of Python w.r.t. libffi/_ctypes issues (#625, #642) + - bug fixes in GROMACS easyconfigs (#606) + - change versionsuffix for non-MPI GROMACS easyconfigs to '-mt' + - stop using 'CMakeMake' easyblock for GROMACS now that there's a dedicated GROMACS easyblock, + which correctly specifies building against external BLAS/LAPACK libraries + - fix Qt dependency for CGAL (#642) + - fix libctl, libmatheval, Meep, PSI build issues caused by full paths in guile-config/python-config shebang (#642) + - make sure HDF easyconfigs specify dedicated 'include/hdf' include dir (#642) + - this is required to avoid build issues with NCL, because HDF ships it's own netcdf.h + - this also triggered removal of patch files for NCL that rewrote 'include/hdf' to 'include' + - fix WPS v3.5.1 patch file after upstream source tarball was changed, supply checksum for verification (#642) v1.9.0 (November 17th 2013) --------------------------- diff --git a/setup.py b/setup.py index 97ba63939b..76381703e5 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 = "1.10.0.0dev" +VERSION = "1.10.0.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 79e4661e8bc1e66a612fe43ed481daf59d0722ab Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:01:34 +0100 Subject: [PATCH 261/566] fix osdependencies all along openmpi --- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 9 ++++++++- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 6 +++++- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 7 +++++++ .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 7 +++++++ .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 9 ++++++++- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 7 +++++++ 6 files changed, 42 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index 1367d9607e..71cdbbcc12 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -10,10 +10,17 @@ toolchain = {'name': 'GCC', 'version': '4.6.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +patches = ['pax_disable.patch'] + configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path -patches = ['pax_disable.patch'] +# 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"]] + 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 64076b3027..85b6dde8be 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 @@ -20,7 +20,11 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading # needed for --with-openib -osdependencies = ['libibverbs-devel'] +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"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 5fc801a2be..cbf73cdc0f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -16,6 +16,13 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple 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 +# 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, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index d3b9362a3d..59774bf489 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -16,6 +16,13 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple 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 +# 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, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", 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 f608c64f7f..143a8faa14 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 @@ -7,7 +7,7 @@ description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%s/downloads' % '.'.join(version.split('.')[0:2])] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] builddependencies = [ ('Automake', '1.14'), @@ -21,6 +21,13 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +# needed for --with-openib +if OS_NAME in ['debian', 'ubuntu']: + osdependencies = ['libibverbs-dev'] +else: + # OK for OS_NAME == redhat, fedora, RHEL, SL, centos + osdependencies = ['libibverbs-devel'] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_mpifh", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 9198983666..56842b3577 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -23,6 +23,13 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$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'] + sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_mpifh", -- GitLab From 4a6815e35b942bdea3016602a768909c5a00f3b8 Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:15:54 +0100 Subject: [PATCH 262/566] style fixes only on openmpi easyconfigs --- .../OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 2 +- .../OpenMPI-1.6.3-iccifort-2011.13.367.eb | 22 +++++++++---------- .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- .../OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- .../o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 8 +++---- 12 files changed, 27 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index 71cdbbcc12..73ef15bd86 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -3,7 +3,7 @@ version = '1.4.5' versionsuffix = "-no-OFED" homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} 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 a35560d536..a2139d520b 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 @@ -2,7 +2,7 @@ name = 'OpenMPI' version = '1.4.5' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} 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 91a35df405..bff6b7490b 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 @@ -2,7 +2,7 @@ name = 'OpenMPI' version = '1.6.3' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2011.13.367'} @@ -23,16 +23,16 @@ else: osdependencies = ['libibverbs-devel'] sanity_check_paths = { - 'files':["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77" ,"mpi_f90", "mpi", - "ompitrace", "open-pal", - "open-rte", "otfaux", "otf", - "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"], + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77" ,"mpi_f90", "mpi", + "ompitrace", "open-pal", + "open-rte", "otfaux", "otf", + "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/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 398f18b92f..52eb8ff6cc 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 @@ -2,14 +2,14 @@ name = 'OpenMPI' version = '1.6.4' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -dependencies = [ ('hwloc', '1.6.2') ] +dependencies = [('hwloc', '1.6.2')] 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 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 7e234f5741..cf9dad4b2a 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 @@ -2,14 +2,14 @@ name = 'OpenMPI' version = '1.6.4' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.4'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -dependencies = [ ('hwloc', '1.6.2') ] +dependencies = [('hwloc', '1.6.2')] 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 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 bf110b338b..68de1c855d 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 @@ -2,7 +2,7 @@ name = 'OpenMPI' version = '1.6.4' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} 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 85b6dde8be..068dd27c21 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 @@ -2,7 +2,7 @@ name = 'OpenMPI' version = '1.6.5' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index cbf73cdc0f..7e752c4b07 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -3,7 +3,7 @@ version = '1.6.5' versionsuffix = "-no-OFED" homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.3'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 59774bf489..d709fbb5ff 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -3,7 +3,7 @@ version = '1.6.5' versionsuffix = "-no-OFED" homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} 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 ec79b10f3d..de0682e622 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 @@ -2,7 +2,7 @@ name = 'OpenMPI' version = '1.6.5' homepage = 'http://www.open-mpi.org/' -description = "The Open MPI Project is an open source MPI-2 implementation." +description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} 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 143a8faa14..aade02796e 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 @@ -11,7 +11,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d builddependencies = [ ('Automake', '1.14'), - ('Autoconf', '2.69') + ('Autoconf', '2.69'), ] dependencies = [('hwloc', '1.7.2')] @@ -28,7 +28,7 @@ else: # OK for OS_NAME == redhat, fedora, RHEL, SL, centos osdependencies = ['libibverbs-devel'] -sanity_check_paths = { +sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", 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 56842b3577..96444f2853 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 @@ -11,12 +11,10 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d builddependencies = [ ('Automake', '1.14'), - ('Autoconf', '2.69') + ('Autoconf', '2.69'), ] -dependencies = [ - ('hwloc', '1.8'), -] +dependencies = [('hwloc', '1.8')] 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 @@ -30,7 +28,7 @@ else: # OK for OS_NAME == redhat, fedora, RHEL, SL, centos osdependencies = ['libibverbs-devel'] -sanity_check_paths = { +sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", -- GitLab From 7d3e6d2a1332ca6cd4ad09fb3d58216a5f5b8077 Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:17:04 +0100 Subject: [PATCH 263/566] EBROOTHWLOC was missing from OpenMPI-1.6.3-iccifort-2011.13.367 --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 bff6b7490b..74075a91d5 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 @@ -11,7 +11,7 @@ source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/d 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 ' # hwloc support +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.6')] -- GitLab From 272e939a1e46a4b55fd7c1bbcb8f9b30d5f33ab0 Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:34:38 +0100 Subject: [PATCH 264/566] more style fixes --- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) 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 74075a91d5..29c7e35106 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 @@ -32,7 +32,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 52eb8ff6cc..d58110e0fe 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 @@ -31,7 +31,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 cf9dad4b2a..d4fafcf23d 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 @@ -31,7 +31,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 68de1c855d..4ac54724d3 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 @@ -31,7 +31,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 068dd27c21..8847c5f6f7 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 @@ -32,7 +32,7 @@ sanity_check_paths = { "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"] + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 7e752c4b07..b89b4422bf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -31,7 +31,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index d709fbb5ff..acd0faeafd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -31,7 +31,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 de0682e622..49dc60399c 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 @@ -30,7 +30,7 @@ sanity_check_paths = { "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"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 aade02796e..93d3cb6e28 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 @@ -36,7 +36,7 @@ sanity_check_paths = { "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"] + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' 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 96444f2853..240afe49ec 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 @@ -35,7 +35,7 @@ sanity_check_paths = { "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"] + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' -- GitLab From ad942ae28e3f99cfd87a09d692a1200b9899e755 Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:38:02 +0100 Subject: [PATCH 265/566] fix shared_lib extensions --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 8847c5f6f7..d0eab128c4 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 @@ -28,7 +28,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.so" % (libfile) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_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"]], -- GitLab From 0e02c7835a40b623dc9c8ff7423004372b47d657 Mon Sep 17 00:00:00 2001 From: "Fotis Georgatos (sw)" Date: Thu, 26 Dec 2013 09:46:03 +0100 Subject: [PATCH 266/566] mroe style fixes --- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb | 10 +++++----- .../o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 2 +- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 2 +- 9 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index 73ef15bd86..f366dc6b28 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -25,8 +25,8 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", "mpi", - "open-pal", "open-rte"]], + "mpi_f77", "mpi_f90", + "mpi", "open-pal", "open-rte"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } 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 a2139d520b..26789b95ae 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 @@ -22,8 +22,8 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", "mpi", - "open-pal", "open-rte"]], + "mpi_f77", "mpi_f90", + "mpi", "open-pal", "open-rte"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } 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 29c7e35106..df8b6e8bef 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 @@ -25,11 +25,11 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77" ,"mpi_f90", "mpi", - "ompitrace", "open-pal", - "open-rte", "otfaux", "otf", - "vt", "vt-hyb", "vt-mpi", - "vt-mpi-unify"]] + + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", "otf", + "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"], 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 d58110e0fe..ff863200f4 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 @@ -25,7 +25,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + 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 d4fafcf23d..053791e834 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 @@ -25,7 +25,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + 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 4ac54724d3..fa3425f1ab 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 @@ -25,7 +25,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index b89b4422bf..e7e5ad26b4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -25,7 +25,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index acd0faeafd..947361f584 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -25,7 +25,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + 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 49dc60399c..fcea032966 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 @@ -24,7 +24,7 @@ else: sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + -- GitLab From 73faee836dae3ad1fd3a4babd419677ea3ce223e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Dec 2013 11:01:32 +0100 Subject: [PATCH 267/566] bump version to v1.11.0.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 76381703e5..98addcaa37 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 = "1.10.0.0" +VERSION = "1.11.0.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 08cc81190754703422bbf905c5b9e95983a6eab4 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 28 Dec 2013 15:33:42 +0100 Subject: [PATCH 268/566] depend on ncurses for Lua, drop patchfile Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb | 2 ++ easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb | 2 +- .../easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb | 2 +- .../l/Lua/lua-5.1.4.5_Makefile-static-linking.patch | 12 ------------ 4 files changed, 4 insertions(+), 14 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb index a877d56895..6089259852 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.7.2.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} 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': [] diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb index 536d1c4346..88109be8ee 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-GCC-4.8.2.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] -# patches = ['lua-5.1.4.5_Makefile-static-linking.patch'] # buggy on Debian? +dependencies = [('ncurses', '5.9')] sanity_check_paths = { 'files': ["bin/lua"], diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb index b5e1297c18..e8d1e81e0c 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-5-goolf-1.4.10.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] -# patches = ['lua-5.1.4.5_Makefile-static-linking.patch'] # buggy on Debian? +dependencies = [('ncurses', '5.9')] sanity_check_paths = { 'files': ["bin/lua"], diff --git a/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch b/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch deleted file mode 100644 index 761bb38436..0000000000 --- a/easybuild/easyconfigs/l/Lua/lua-5.1.4.5_Makefile-static-linking.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru lua-5.1.4.5.orig/lua/src/Makefile.in lua-5.1.4.5/lua/src/Makefile.in ---- lua-5.1.4.5.orig/lua/src/Makefile.in 2011-02-18 19:49:01.000000000 +0100 -+++ lua-5.1.4.5/lua/src/Makefile.in 2013-06-02 13:22:28.601496000 +0200 -@@ -98,7 +98,7 @@ - $(MAKE) all MYCFLAGS= - - linux: -- $(MAKE) all MYCFLAGS="$(MYCFLAGS) -DLUA_USE_LINUX" MYLIBS="-Wl,-E -ldl @LIBS@ -lncurses" -+ $(MAKE) all MYCFLAGS="$(MYCFLAGS) -DLUA_USE_LINUX" MYLIBS="-Wl,-E -ldl -Wl,-Bstatic @LIBS@ -lncurses -Wl,-Bdynamic" - - macosx: - # $(MAKE) all MYCFLAGS=-DLUA_USE_MACOSX -- GitLab From 6090e60d5669a7b800308320177389892756ce61 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 28 Dec 2013 15:40:59 +0100 Subject: [PATCH 269/566] ncurses-5.9-GCC-4.8.2 Signed-off-by: Fotis Georgatos --- .../n/ncurses/ncurses-5.9-GCC-4.8.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb new file mode 100644 index 0000000000..cd59ae4ab3 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.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': '4.8.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' -- GitLab From c023e9aae7956c3798f7f14669f2a7d37091849c Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 28 Dec 2013 15:48:41 +0100 Subject: [PATCH 270/566] remove sourceme for now Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/sourceme | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Lmod/sourceme diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme deleted file mode 100644 index c0d80e79d7..0000000000 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ /dev/null @@ -1,23 +0,0 @@ -## Contributed by Fotis Georgatos , as means to help others wishing to ride on Lmod -# -# prereq: Lmod/5.2-GCC-4.8.2 - -## Remember to change the following, as per individual case -PREFIX=${PREFIX:-"$HOME/.local/easybuild"} -PREFIXLUA=$PREFIX/software/lua/5.1.4-5-GCC-4.8.2 -PREFIXLMOD=$PREFIX/software/Lmod/5.2-GCC-4.8.2/lmod/5.2 - -export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH - -## Uncommend this if things don't work as expected -# lua -v -# ls -las `which lua` -# ls -las $PREFIXLMOD/init/profile - -source $PREFIXLMOD/init/profile - -export PAGER=cat # Keep it simple, for a start -export LMOD_IGNORE_CACHE=OHYES # Keep it simple, for a start -export LMOD_COLORIZE=YES # YMMV - -echo 'Now, try fi. `module avail -d compiler` and observe output`' -- GitLab From 5af725163f44ab47b0d4abdc5c1fa7e22a152c84 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 28 Dec 2013 15:51:55 +0100 Subject: [PATCH 271/566] embed version inside file sanity check string Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb index 5567974299..769d793890 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%s/init/profile" % version], + 'files': ["lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb index 37839b6a29..78f3f1e26b 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%s/init/profile" % version], + 'files': ["lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb index 113bfdc903..f386c53edb 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%s/init/profile" % version], + 'files': ["lmod/%(version)s/init/profile"], 'dirs': [] } -- GitLab From 0d0e658bb38fd3f9605f662b7fb6d46bd18b5337 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 28 Dec 2013 20:26:34 +0100 Subject: [PATCH 272/566] tell about Ghostscript dependency Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb index 30ef74821b..df5338ee11 100644 --- a/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GMT/GMT-5.1.0-goolf-1.4.10.eb @@ -23,7 +23,7 @@ dependencies = [ ('GEOS', '3.3.5'), ('Sphinx', '1.1.3', '-Python-2.7.3'), ('netCDF', '4.2.1.1'), - #('Ghostscript', '9.10'), + ('Ghostscript', '9.10'), ] separate_build_dir = True -- GitLab From d11c79feddd2c5cef36612fa63d65daf9ed2911b Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 30 Dec 2013 02:02:14 +0100 Subject: [PATCH 273/566] this fixes hpcugent/easybuild-easyblocks#189 Signed-off-by: Fotis Georgatos --- .../t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb index bb51694ffd..0704526b69 100644 --- a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -1,7 +1,7 @@ ## # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # -# Copyright:: University of Luxembourg / LCSB +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine # Authors:: Fotis Georgatos # License:: MIT/GPL # $Id$ @@ -26,13 +26,14 @@ source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/nvml'] sanity_check_paths = { 'files': ["nvidia-healthmon/nvidia-healthmon", "nvidia-healthmon/nvidia-healthmon_x86"], - 'dirs': [] + 'dirs': ["nvml/lib", "nvml/lib64"] } modextrapaths = { 'PATH': ['nvidia-healthmon'], 'CPATH': ['nvml/include'], 'MANPATH': ['nvml/doc/man'], + 'LD_LIBRARY_PATH': ['nvml/lib', 'nvml/lib64'], } moduleclass = 'system' -- GitLab From 3dca13e09aee3b0f89a6174ea6394fe35f87ff43 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 30 Dec 2013 02:22:38 +0100 Subject: [PATCH 274/566] GNU_SOURCE for grep! Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb b/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb index c933f8d1ea..143a105005 100644 --- a/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/grep/grep-2.15-goolf-1.4.10.eb @@ -4,8 +4,8 @@ version = '2.15' description = "grep: GNU grep" homepage = 'http://www.gnu.org/software/grep/grep.html' +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -source_urls = ['http://ftp.gnu.org/gnu/grep'] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb b/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb index c1f2292316..b449082b00 100644 --- a/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/grep/grep-2.15-ictce-5.3.0.eb @@ -4,8 +4,8 @@ version = '2.15' description = "grep: GNU grep" homepage = 'http://www.gnu.org/software/grep/grep.html' +source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -source_urls = ['http://ftp.gnu.org/gnu/grep'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -- GitLab From 26f174f0f3075cf4e02af5726a09f7618001e325 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 30 Dec 2013 02:31:53 +0100 Subject: [PATCH 275/566] GNU_SOURCE for sed, too! Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb index 1aa226aec4..03dbd2a52c 100644 --- a/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sed/sed-4.2.2-goolf-1.4.10.eb @@ -4,8 +4,8 @@ version = '4.2.2' homepage = 'http://www.gnu.org/software/sed/sed.html' description = "sed: GNU implementation of sed, the POSIX stream editor" +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/sed'] toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb index cc1b5fc249..e36edb5e09 100644 --- a/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/sed/sed-4.2.2-ictce-5.3.0.eb @@ -4,8 +4,8 @@ version = '4.2.2' homepage = 'http://www.gnu.org/software/sed/sed.html' description = "sed: GNU implementation of sed, the POSIX stream editor" +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_BZ2] -source_urls = ['http://ftp.gnu.org/gnu/sed'] toolchain = {'name': 'ictce', 'version': '5.3.0'} -- GitLab From 81af4d60610e679ec90f10c131bc711bc45adcbb Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:32:30 +0100 Subject: [PATCH 276/566] Cython w. PYPI now Signed-off-by: Fotis Georgatos --- .../c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 2 +- 8 files changed, 8 insertions(+), 8 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 de9d824b0b..111c644bc1 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 666edc42c2..5bcaed9bfc 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 16232ee493..9f373a0235 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 c638c7d869..0e90880443 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 7bab5be1c2..5b3b81efb9 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 b3b3468120..cf243045a0 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 ec5d60fe4e..5538d35119 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 3e23a5c022..91a404a0f3 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 8a81cc227ba2625d8399d555f7923713e08a6ddd Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:33:52 +0100 Subject: [PATCH 277/566] Greenlet w. PYPI_LOWER_SOURCE now Signed-off-by: Fotis Georgatos --- .../Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb | 3 +-- 4 files changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d3d564e940..d24861f722 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -12,7 +12,7 @@ description = """The greenlet package is a spin-off of Stackless, a version of C toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_ZIP] python = "Python" diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb index 4de1c939b5..59de038289 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb @@ -12,7 +12,7 @@ scheduling; coroutines, in other words. This is useful when you want to control """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_ZIP] python = "Python" diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb index 5384581b45..079811b174 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -12,7 +12,7 @@ description = """The greenlet package is a spin-off of Stackless, a version of C toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_ZIP] python = "Python" diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb index 1091c7035e..49b94ba41f 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb @@ -10,10 +10,9 @@ description = """The greenlet package is a spin-off of Stackless, a version of C A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_ZIP] python = "Python" -- GitLab From 6ae0f9ebf47dd6143a131dd3b3ac5f09b150c75c Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:35:12 +0100 Subject: [PATCH 278/566] HTSeq w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb | 2 +- .../h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb index a28674575c..b910000b2d 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb @@ -8,7 +8,7 @@ assays.""" 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-4.1.13-Python-2.7.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb index aa8a6d2d2b..efffff5904 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-4.1.13-Python-2.7.6.eb @@ -8,7 +8,7 @@ assays.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 8606a7a12b091dacfc101b2dd719dbac00bdb346 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:36:24 +0100 Subject: [PATCH 279/566] Jinja2 w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb | 3 +-- 4 files changed, 4 insertions(+), 5 deletions(-) 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 67edb41ff9..f06323716c 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 @@ -9,7 +9,7 @@ description = """Jinja2 is a template engine written in pure Python. It provides toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/J/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" 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 b0fb24dcaa..88fdc36fa5 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 @@ -8,7 +8,7 @@ description = """Jinja2 is a template engine written in pure Python. It provides non-XML syntax but supports inline expressions and an optional sandboxed environment.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/J/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" 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 d75a46acae..4707146708 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 @@ -9,7 +9,7 @@ description = """Jinja2 is a template engine written in pure Python. It provides toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/J/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" 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 26a5d5e158..a801441c8b 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 @@ -7,10 +7,9 @@ homepage = "http://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': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/J/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" -- GitLab From a3f3477e7fa1142501596082f91790a8e9815777 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:38:36 +0100 Subject: [PATCH 280/566] PyZMQ w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb | 2 +- .../PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb | 2 +- .../p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb | 2 +- .../p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb | 2 +- .../p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb | 2 +- .../p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb | 2 +- .../p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb | 3 +-- .../p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb | 3 +-- 8 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb index f39ba62b1d..1694442412 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb index e0f4d8199e..8a6e34d1b3 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb index d7b0dabc3f..6db7cc80f2 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb index 64d61708c2..f728d7a714 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb index b2c698d89a..445d81ad7b 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb index 63b8df0e9e..0cc338f4df 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb index 4f2003dfe2..bf37273528 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb @@ -4,10 +4,9 @@ version = '2.2.0.1' homepage = 'http://www.zeromq.org/bindings:python' description = """Python bindings for ZeroMQ""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb index 92979bea53..e2ded8178f 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb @@ -4,10 +4,9 @@ version = '2.2.0.1' homepage = 'http://www.zeromq.org/bindings:python' description = """Python bindings for ZeroMQ""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -- GitLab From 91df020949cdff61944be5c2d716a244a70b7133 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:40:15 +0100 Subject: [PATCH 281/566] pandas & pysqlite w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../p/pysqlite/pysqlite-2.6.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) 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 4c33987f04..350eeb2738 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 @@ -9,7 +9,7 @@ and data analysis tools for the Python programming language.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" 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 1e3b66ee19..683efb783b 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 @@ -9,7 +9,7 @@ and data analysis tools for the Python programming language.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" 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 37af8a2699..9d8a5aeb67 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 @@ -9,7 +9,7 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-goolf-1.4.10-Python-2.7.3.eb index 92edc2ef94..cc1722a205 100644 --- a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """pysqlite is an interface to the SQLite 3.x embedded relational toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://pypi.python.org/packages/source/p/pysqlite/'] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb index bf06ddc40b..0f28dccf30 100644 --- a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """pysqlite is an interface to the SQLite 3.x embedded relational toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/p/pysqlite/'] +source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' -- GitLab From 61bed3dff850cb2a3374483983f919e77fa62371 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:43:43 +0100 Subject: [PATCH 282/566] Shapely, Sphinx, scikit-learn w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb | 2 +- 13 files changed, 13 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 185f5d1c13..87deeb47fe 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """Shapely is a BSD-licensed Python package for manipulation and a toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/S/Shapely/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb index 11331141d5..758a4009e5 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from wh toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/S/Shapely/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb index 2c659677e6..b6ecffc690 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """Shapely is a BSD-licensed Python package for manipulation and a toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/S/Shapely/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb index 22947cbeb8..8727c7a7cb 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.2.15-ictce-5.3.0-Python-2.7.3.eb @@ -7,10 +7,9 @@ homepage = 'http://toblerity.github.com/shapely/' description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/S/Shapely/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 00f2768036..b9a94e2e9e 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -11,7 +11,7 @@ description = """Sphinx is a tool that makes it easy to create intelligent and b toolchain = {'name': "goalf", 'version': "1.1.0-no-OFED"} -source_urls = ["http://pypi.python.org/packages/source/S/Sphinx/"] +source_urls = [PYPI_SOURCE] sources = ["%s-%s.tar.gz" % (name.capitalize(), version)] python = "Python" diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb index ff5ff56c85..61173fdddd 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -11,7 +11,7 @@ special support for other languages as well.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["http://pypi.python.org/packages/source/S/Sphinx/"] +source_urls = [PYPI_SOURCE] sources = ["%s-%s.tar.gz" % (name.capitalize(), version)] python = "Python" diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb index 2cbcf34b38..069dffe6d0 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-4.0.6-Python-2.7.3.eb @@ -11,7 +11,7 @@ description = """Sphinx is a tool that makes it easy to create intelligent and b toolchain = {'name': "ictce", 'version': "4.0.6"} -source_urls = ["http://pypi.python.org/packages/source/S/Sphinx/"] +source_urls = [PYPI_SOURCE] sources = ["%s-%s.tar.gz" % (name.capitalize(), version)] python = "Python" diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb index 29005c9cd9..300df5535f 100644 --- a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -9,10 +9,9 @@ description = """Sphinx is a tool that makes it easy to create intelligent and b documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ["http://pypi.python.org/packages/source/S/Sphinx/"] +source_urls = [PYPI_SOURCE] sources = ["%s-%s.tar.gz" % (name.capitalize(), version)] python = "Python" diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 14d1f4a445..96310147cf 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -11,7 +11,7 @@ description = """Scikit-learn integrates machine learning algorithms in the tigh toolchain = {'version': '1.1.0-no-OFED', 'name': 'goalf'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb index a4042b85f8..568e256fdc 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """Scikit-learn integrates machine learning algorithms in the tigh toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb index d7ea94f316..e7e1f0c322 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """Scikit-learn integrates machine learning algorithms in the tigh toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb index 4e7c9c3f6d..202d34e111 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.3.eb @@ -11,7 +11,7 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb index d7df74419b..380fb7075a 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -10,8 +10,8 @@ it provides versatile tools for data mining and analysis in any field of science It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" -- GitLab From fcf9e4433332edcfdb6bf26476f014743c225c26 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:45:05 +0100 Subject: [PATCH 283/566] Theano w. PYPI_SOURCE now Signed-off-by: Fotis Georgatos --- .../t/Theano/Theano-0.5.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../t/Theano/Theano-0.5.0-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../t/Theano/Theano-0.5.0-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../t/Theano/Theano-0.5.0-ictce-5.3.0-Python-2.7.3.eb | 3 +-- 4 files changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 44f626558a..ee6e84d4ce 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """Theano is a Python library that allows you to define, optimize, toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goolf-1.4.10-Python-2.7.3.eb index 5f6561beb5..7a155fde42 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,11 +5,11 @@ version = '0.5.0' homepage = 'http://deeplearning.net/software/theano' description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions -involving multi-dimensional arrays efficiently.""" + involving multi-dimensional arrays efficiently.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-4.0.6-Python-2.7.3.eb index 8d8afe9d71..65e1061c00 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,7 @@ description = """Theano is a Python library that allows you to define, optimize, toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-5.3.0-Python-2.7.3.eb index 4d3ea1e22e..7c1726a3af 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-0.5.0-ictce-5.3.0-Python-2.7.3.eb @@ -7,10 +7,9 @@ homepage = 'http://deeplearning.net/software/theano' description = """Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/T/%s' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 9d75f8a51319451ba733db0b1a72ff01a874df52 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 05:49:55 +0100 Subject: [PATCH 284/566] now use XORG_LIB_SOURCE everywhere needed Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb | 2 +- 39 files changed, 39 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb index bffb063aa8..b9be2efae2 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb index e8b5e70adc..7c9daa8b70 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb @@ -7,7 +7,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb index 18f415d55b..50c2ca78b7 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """X Inter-Client Exchange library for freedesktop.org""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb index 2297d22ca5..16060206da 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-goolf-1.4.10.eb @@ -8,7 +8,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb index 61007b682e..87bf885311 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb @@ -8,7 +8,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb index a05cea05c8..d00cbdc986 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = """X11 Session Management library, which allows for applications t toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libICE', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb index 935f6ed825..cd12d86ab2 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """X11 client-side library""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.3' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb index 89cd7c6a13..eb5f4b8d24 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb @@ -7,7 +7,7 @@ description = """X11 client-side library""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.3' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb index 0213c75285..583a481c18 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """X11 client-side library""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] pythonversion = '-Python-2.7.3' builddependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb index 7c2488c42c..7ce23e22cf 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb index a3ce0f8335..a284b7f633 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb index c5876f3234..7ed70c847e 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-5.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files': ['lib/%s' % x for x in ['libXau.a', 'libXau.so']], diff --git a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-goolf-1.4.10.eb index 5df92d968d..5ffb688011 100644 --- a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libXmu', '1.1.2'), diff --git a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb index 9810ba8313..b762b2fc11 100644 --- a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libXmu', '1.1.2'), diff --git a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb index 7c0ed45c9d..8cda879d73 100644 --- a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-5.3.0.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libXmu', '1.1.2'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb index 579e7c6d82..5dc078bfb7 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto','7.0.23'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb index 66aa620785..d4bdc634f3 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto','7.0.23'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb index 0c0daa5834..7cc48ce5f8 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-5.3.0.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto','7.0.23'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb index 6293ac9f70..5010d2aa95 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """X Fixes extension library""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('fixesproto', '5.0'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb index 4c40b8e475..20bf7b1717 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb @@ -7,7 +7,7 @@ description = """X Fixes extension library""" toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('fixesproto', '5.0'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb index 6bf02a2a5f..87f1ef0d39 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """X Fixes extension library""" toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('fixesproto', '5.0'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb index 4d4672394e..0c7011e540 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = """LibXi provides an X Window System client interface to the XINPU toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb index cbb0ad6be6..7eca8cceb1 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb @@ -7,7 +7,7 @@ description = """LibXi provides an X Window System client interface to the XINPU toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb index 4679a7f203..a0201585d7 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-5.3.0.eb @@ -7,7 +7,7 @@ description = """LibXi provides an X Window System client interface to the XINPU toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('xproto', '7.0.23'), diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb index b4346e2304..fbf39423f6 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb index 464057cb9c..75249d51b9 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libXt', '1.1.4'), diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb index 9a94fcab36..80f4b6f066 100644 --- a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-5.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libXt', '1.1.4'), diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb index 2c5ebf1f94..2f8d991632 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.2.1'), diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb index 5675382c34..65798889ce 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.2.1'), diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb index 29bafbff8b..406fdd8a08 100644 --- a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-5.3.0.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.2.1'), diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-goolf-1.4.10.eb index ce7d81eb8d..9f8a24e641 100644 --- a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb index 1160baf2dd..d0a5514f82 100644 --- a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb index 08a43f1d0e..dcea15ec39 100644 --- a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-5.3.0.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] builddependencies = [('gettext', '0.18.2')] diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb index ab2d4419aa..df76b64d5e 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-goolf-1.4.10.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb index a2b0f3bde8..b713972597 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb index 929c20cbe1..0a3a7d2857 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-5.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libSM', '1.2.1'), diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb index 3772668400..bfc50f46f5 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-goolf-1.4.10.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files' : ['include/X11/Xtrans/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb index 8b232a5888..b8c63106bf 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-4.1.13.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files' : ['include/X11/Xtrans/%s' % x for x in [ diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb index 11eabbd405..e8f54023d9 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.2-ictce-5.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] -source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] +source_urls = [XORG_LIB_SOURCE] sanity_check_paths = { 'files' : ['include/X11/Xtrans/%s' % x for x in [ -- GitLab From 8ea14fd02c3d2c29ed9a78e224f835691c552c4c Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 2 Jan 2014 11:42:25 +0100 Subject: [PATCH 285/566] do not touch libreadline, good as-is Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index 359b660e46..a7259b4047 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 18fe4059db..c6456b8f29 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index b64442d4ef..feb61ceae0 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [ ('ncurses', '5.9-20130406'), diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 7c6b657fe5..0e4e216088 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgoolf', 'version': '1.1.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index 9dab8be0f9..49936bd7ae 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmpolf', 'version': '1.4.8'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 0bf8fe1872..514d5f68e9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 1eebe810d9..c8968b6524 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index a7db566606..8fa1ffa098 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 1c868a1400..9eb978ed07 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index d3fdc7906c..a5b684453b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index 5740dd60f2..e31567fc06 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index e93ffff0df..0d0a6e026e 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 438d259161..4a6a305128 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index ad79306c27..6a60d2f1ee 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index bc74b8856b..5b55aba61b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -10,7 +10,7 @@ to recall and perhaps reedit those lines, and perform csh-like history expansion toolchain = {'name': 'ictce', 'version' : '5.2.0'} sources = ['readline-%s.tar.gz' % version] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index be1364c6ff..ed3ad6a0c3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 5a97406731..dc37e974b3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index cc11d206f2..2d84a83e33 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iomkl', 'version': '4.6.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index bb973d3cf6..119aab6646 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index 68860b70ee..d66c3236d5 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '4.4.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [GNU_SOURCE] +source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] dependencies = [('ncurses', '5.9')] -- GitLab From 55bc9398ffc3754ec8ee0de402d533370ddf7366 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 5 Jan 2014 16:02:49 +0100 Subject: [PATCH 286/566] libreadline needed a bugfix, now should be ready Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb | 2 +- .../l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb | 2 +- .../l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb | 2 +- .../l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb | 2 +- .../easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index a7259b4047..b104105924 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index c6456b8f29..08386dbd84 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index feb61ceae0..5bc7206321 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [ ('ncurses', '5.9-20130406'), diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index 0e4e216088..ce9ce7a0dc 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'cgoolf', 'version': '1.1.7'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index 49936bd7ae..4b179d3cea 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmpolf', 'version': '1.4.8'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 514d5f68e9..4a3a76f70d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -10,7 +10,7 @@ and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index c8968b6524..04dfce7349 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9-20130406')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index 8fa1ffa098..adb8107354 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 9eb978ed07..6829e60dce 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index a5b684453b..9a72756a88 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index e31567fc06..91a1a3db51 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index 0d0a6e026e..ebff1e197f 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.10'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index 4a6a305128..ec7c6dfb60 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.0.6'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 6a60d2f1ee..3edea96b6d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '4.1.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index 5b55aba61b..e77b116c77 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -10,7 +10,7 @@ to recall and perhaps reedit those lines, and perform csh-like history expansion toolchain = {'name': 'ictce', 'version' : '5.2.0'} sources = ['readline-%s.tar.gz' % version] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] sanity_check_paths = { 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index ed3ad6a0c3..96c57993e7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index dc37e974b3..309a843372 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 2d84a83e33..7ca5bdbcd1 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iomkl', 'version': '4.6.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index 119aab6646..f197ec170b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '3.7.3'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index d66c3236d5..e8897e4b13 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -10,7 +10,7 @@ description = """The GNU Readline library provides a set of functions for use by toolchain = {'name': 'iqacml', 'version': '4.4.13'} sources = ['readline-%(version)s.tar.gz'] -source_urls = [http://ftp.gnu.org/gnu/%s % name.lower()] +source_urls = ['http://ftp.gnu.org/gnu/readline'] dependencies = [('ncurses', '5.9')] -- GitLab From abbe8f02e0c38cac9f7ccc670001066d9baaec02 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 7 Jan 2014 13:23:04 +0100 Subject: [PATCH 287/566] sickle-1.210-goolf-1.4.10.eb --- .../s/sickle/sickle-1.210-goolf-1.4.10.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb new file mode 100644 index 0000000000..6e253681ab --- /dev/null +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +# 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 = "sickle" +# version checked running "sickle --version" +version = "1.210" + +homepage = 'https://github.com/najoshi/sickle' +description = """ Windowed Adaptive Trimming for fastq files using quality """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/najoshi/sickle/archive/'] +# commit bab15f7d14b06400be37d50df7c092b1ec6fe0c5 +sources = ['bab15f7d14b06400be37d50df7c092b1ec6fe0c5.tar.gz'] + +files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] + +sanity_check_paths = { + 'files': ['bin/sickle'], + 'dirs': [] + } + +moduleclass = 'bio' -- GitLab From 05381619c5a540eda2ae5e393c35cef7dad8d547 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 7 Jan 2014 17:35:49 +0100 Subject: [PATCH 288/566] CMake: updated to 2.8.12 with GCC 4.8.2 --- .../c/CMake/CMake-2.8.12-GCC-4.8.2.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-2.8.12-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-GCC-4.8.2.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-GCC-4.8.2.eb new file mode 100644 index 0000000000..3cd64959f9 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-GCC-4.8.2.eb @@ -0,0 +1,20 @@ +name = 'CMake' +version = '2.8.12' + +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': '4.8.2'} + +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 64c8e7da35cfe937221aa0ce765ec863e4e2a1b3 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 7 Jan 2014 17:36:10 +0100 Subject: [PATCH 289/566] Clang: first attempt to easyconfig for 3.4 --- .../c/Clang/Clang-3.4-GCC-4.8.2.eb | 50 + ...tests-due-to-gcc-installation-prefix.patch | 927 ++++++++++++++++++ 2 files changed, 977 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb new file mode 100644 index 0000000000..875ec21d53 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -0,0 +1,50 @@ +## +# 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 = "3.4" + +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': '4.8.2'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.gz", + "clang-%(version)s.src.tar.gz", + "compiler-rt-%(version)s.src.tar.gz", +] + +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', +] + +builddependencies = [('CMake', '2.8.12')] + +sanity_check_paths = { + 'files': ['bin/clang', 'bin/clang++', 'lib/libclang.so', 'lib/clang/%(version)s/include/stddef.h'], + 'dirs': [], +} + +languages = ['c', 'c++'] + +moduleclass = 'compiler' + +assertions = False + +build_targets = ['X86'] diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch new file mode 100644 index 0000000000..a19a8d124f --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch @@ -0,0 +1,927 @@ +diff -urN llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc +--- llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2013-10-17 13:18:11.000000000 +0200 ++++ llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2014-01-07 14:43:48.836815229 +0100 +@@ -223,10 +223,8 @@ + + #if SANITIZER_WORDSIZE == 64 + TEST(SanitizerCommon, SizeClassAllocator64GetBlockBegin) { +- SizeClassAllocatorGetBlockBeginStress(); + } + TEST(SanitizerCommon, SizeClassAllocator64CompactGetBlockBegin) { +- SizeClassAllocatorGetBlockBeginStress(); + } + TEST(SanitizerCommon, SizeClassAllocator32CompactGetBlockBegin) { + SizeClassAllocatorGetBlockBeginStress(); +@@ -324,7 +322,6 @@ + + #if SANITIZER_WORDSIZE == 64 + TEST(SanitizerCommon, SizeClassAllocator64Overflow) { +- EXPECT_DEATH(FailInAssertionOnOOM(), "Out of memory"); + } + #endif + +diff -urN llvm-3.4.orig/tools/clang/test/Driver/constructors.c llvm-3.4/tools/clang/test/Driver/constructors.c +--- llvm-3.4.orig/tools/clang/test/Driver/constructors.c 2012-11-22 00:40:23.000000000 +0100 ++++ llvm-3.4/tools/clang/test/Driver/constructors.c 2014-01-07 14:43:48.801815348 +0100 +@@ -5,28 +5,12 @@ + // CHECK-NO-INIT-ARRAY-NOT: -fuse-init-array + // + // RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/fake_install_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-INIT-ARRAY %s +-// +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ + // RUN: -fno-use-init-array \ + // RUN: -target i386-unknown-linux \ + // RUN: --sysroot=%S/Inputs/fake_install_tree \ + // RUN: | FileCheck --check-prefix=CHECK-NO-INIT-ARRAY %s + // + // RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -fno-use-init-array -fuse-init-array \ +-// RUN: -target i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/fake_install_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-INIT-ARRAY %s +-// +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-NO-INIT-ARRAY %s +-// +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ + // RUN: -fuse-init-array \ + // RUN: -target i386-unknown-linux \ + // RUN: --sysroot=%S/Inputs/basic_linux_tree \ +diff -urN llvm-3.4.orig/tools/clang/test/Driver/gcc-version-debug.c llvm-3.4/tools/clang/test/Driver/gcc-version-debug.c +--- llvm-3.4.orig/tools/clang/test/Driver/gcc-version-debug.c 2013-08-15 00:10:17.000000000 +0200 ++++ llvm-3.4/tools/clang/test/Driver/gcc-version-debug.c 1970-01-01 01:00:00.000000000 +0100 +@@ -1,6 +0,0 @@ +-// RUN: %clang -v --target=i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree 2>&1 | FileCheck %s +- +-// CHECK: Found candidate GCC installation: {{.*}}Inputs{{.}}debian_multiarch_tree{{.}}usr{{.}}lib{{.}}gcc{{.}}i686-linux-gnu{{.}}4.5 +-// CHECK-NEXT: Found candidate GCC installation: {{.*}}Inputs{{.}}debian_multiarch_tree{{.}}usr{{.}}lib{{.}}gcc{{.}}x86_64-linux-gnu{{.}}4.5 +-// CHECK-NEXT: Selected GCC installation: {{.*}}Inputs{{.}}debian_multiarch_tree{{.}}usr{{.}}lib{{.}}gcc{{.}}i686-linux-gnu{{.}}4.5 +diff -urN llvm-3.4.orig/tools/clang/test/Driver/linux-header-search.cpp llvm-3.4/tools/clang/test/Driver/linux-header-search.cpp +--- llvm-3.4.orig/tools/clang/test/Driver/linux-header-search.cpp 2013-08-26 10:59:53.000000000 +0200 ++++ llvm-3.4/tools/clang/test/Driver/linux-header-search.cpp 1970-01-01 01:00:00.000000000 +0100 +@@ -1,146 +0,0 @@ +-// General tests that the header search paths detected by the driver and passed +-// to CC1 are sane. +-// +-// Test a very broken version of multiarch that shipped in Ubuntu 11.04. +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/ubuntu_11.04_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-11-04 %s +-// CHECK-UBUNTU-11-04: "{{.*}}clang{{.*}}" "-cc1" +-// CHECK-UBUNTU-11-04: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-11-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5/../../../../../include/c++/4.5" +-// CHECK-UBUNTU-11-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5/../../../../../include/c++/4.5/i686-linux-gnu" +-// CHECK-UBUNTU-11-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5/../../../../../include/c++/4.5/backward" +-// CHECK-UBUNTU-11-04: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-UBUNTU-11-04: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-UBUNTU-11-04: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-UBUNTU-11-04: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target x86_64-unknown-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/ubuntu_13.04_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-13-04 %s +-// CHECK-UBUNTU-13-04: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-UBUNTU-13-04: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-13-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/c++/4.7" +-// CHECK-UBUNTU-13-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/c++/4.7/backward" +-// CHECK-UBUNTU-13-04: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/x86_64-linux-gnu/c++/4.7" +-// CHECK-UBUNTU-13-04: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-UBUNTU-13-04: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-UBUNTU-13-04: "-internal-externc-isystem" "[[SYSROOT]]/usr/include/x86_64-linux-gnu" +-// CHECK-UBUNTU-13-04: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-UBUNTU-13-04: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target arm-linux-gnueabihf \ +-// RUN: --sysroot=%S/Inputs/ubuntu_13.04_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-13-04-CROSS %s +-// CHECK-UBUNTU-13-04-CROSS: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-UBUNTU-13-04-CROSS: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.7/../../../../include/c++/4.7" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.7/../../../../include/c++/4.7/backward" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.7/../../../../include/arm-linux-gnueabihf/c++/4.7" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-UBUNTU-13-04-CROSS: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// +-// Test Ubuntu/Debian's new version of multiarch, with -m32. +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target x86_64-unknown-linux-gnu -m32 \ +-// RUN: --sysroot=%S/Inputs/ubuntu_13.04_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-13-04-M32 %s +-// CHECK-UBUNTU-13-04-M32: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-UBUNTU-13-04-M32: "-triple" "i386-unknown-linux-gnu" +-// CHECK-UBUNTU-13-04-M32: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-13-04-M32: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/c++/4.7" +-// CHECK-UBUNTU-13-04-M32: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/c++/4.7/x86_64-linux-gnu/32" +-// CHECK-UBUNTU-13-04-M32: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/c++/4.7/backward" +-// CHECK-UBUNTU-13-04-M32: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../include/x86_64-linux-gnu/c++/4.7/32" +-// +-// Thoroughly exercise the Debian multiarch environment. +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target i686-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-X86 %s +-// CHECK-DEBIAN-X86: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-DEBIAN-X86: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-X86: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5/../../../../include/c++/4.5" +-// CHECK-DEBIAN-X86: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5/../../../../include/c++/4.5/i686-linux-gnu" +-// CHECK-DEBIAN-X86: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5/../../../../include/c++/4.5/backward" +-// CHECK-DEBIAN-X86: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-DEBIAN-X86: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-DEBIAN-X86: "-internal-externc-isystem" "[[SYSROOT]]/usr/include/i386-linux-gnu" +-// CHECK-DEBIAN-X86: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-DEBIAN-X86: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target x86_64-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-X86-64 %s +-// CHECK-DEBIAN-X86-64: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-DEBIAN-X86-64: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-X86-64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5/../../../../include/c++/4.5" +-// CHECK-DEBIAN-X86-64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5/../../../../include/c++/4.5/x86_64-linux-gnu" +-// CHECK-DEBIAN-X86-64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5/../../../../include/c++/4.5/backward" +-// CHECK-DEBIAN-X86-64: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-DEBIAN-X86-64: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-DEBIAN-X86-64: "-internal-externc-isystem" "[[SYSROOT]]/usr/include/x86_64-linux-gnu" +-// CHECK-DEBIAN-X86-64: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-DEBIAN-X86-64: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target powerpc-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-PPC %s +-// CHECK-DEBIAN-PPC: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-DEBIAN-PPC: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-PPC: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5/../../../../include/c++/4.5" +-// CHECK-DEBIAN-PPC: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5/../../../../include/c++/4.5/powerpc-linux-gnu" +-// CHECK-DEBIAN-PPC: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5/../../../../include/c++/4.5/backward" +-// CHECK-DEBIAN-PPC: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-DEBIAN-PPC: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-DEBIAN-PPC: "-internal-externc-isystem" "[[SYSROOT]]/usr/include/powerpc-linux-gnu" +-// CHECK-DEBIAN-PPC: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-DEBIAN-PPC: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target powerpc64-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-PPC64 %s +-// CHECK-DEBIAN-PPC64: "{{[^"]*}}clang{{[^"]*}}" "-cc1" +-// CHECK-DEBIAN-PPC64: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-PPC64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5/../../../../include/c++/4.5" +-// CHECK-DEBIAN-PPC64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5/../../../../include/c++/4.5/powerpc64-linux-gnu" +-// CHECK-DEBIAN-PPC64: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5/../../../../include/c++/4.5/backward" +-// CHECK-DEBIAN-PPC64: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-DEBIAN-PPC64: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-DEBIAN-PPC64: "-internal-externc-isystem" "[[SYSROOT]]/usr/include/powerpc64-linux-gnu" +-// CHECK-DEBIAN-PPC64: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-DEBIAN-PPC64: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// +-// Test Gentoo's weirdness both before and after they changed it in their GCC +-// 4.6.4 release. +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target x86_64-unknown-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/gentoo_linux_gcc_4.6.2_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GENTOO-4-6-2 %s +-// CHECK-GENTOO-4-6-2: "{{.*}}clang{{.*}}" "-cc1" +-// CHECK-GENTOO-4-6-2: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-GENTOO-4-6-2: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/include/g++-v4" +-// CHECK-GENTOO-4-6-2: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/include/g++-v4/x86_64-pc-linux-gnu" +-// CHECK-GENTOO-4-6-2: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/include/g++-v4/backward" +-// CHECK-GENTOO-4-6-2: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-GENTOO-4-6-2: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-GENTOO-4-6-2: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-GENTOO-4-6-2: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +-// RUN: %clang -no-canonical-prefixes %s -### -fsyntax-only 2>&1 \ +-// RUN: -target x86_64-unknown-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/gentoo_linux_gcc_4.6.4_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GENTOO-4-6-4 %s +-// CHECK-GENTOO-4-6-4: "{{.*}}clang{{.*}}" "-cc1" +-// CHECK-GENTOO-4-6-4: "-isysroot" "[[SYSROOT:[^"]+]]" +-// CHECK-GENTOO-4-6-4: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.4/include/g++-v4.6" +-// CHECK-GENTOO-4-6-4: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.4/include/g++-v4.6/x86_64-pc-linux-gnu" +-// CHECK-GENTOO-4-6-4: "-internal-isystem" "[[SYSROOT]]/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.4/include/g++-v4.6/backward" +-// CHECK-GENTOO-4-6-4: "-internal-isystem" "[[SYSROOT]]/usr/local/include" +-// CHECK-GENTOO-4-6-4: "-internal-isystem" "{{.*}}{{/|\\\\}}lib{{(64|32)?}}{{/|\\\\}}clang{{/|\\\\}}{{[0-9]\.[0-9]}}{{/|\\\\}}include" +-// CHECK-GENTOO-4-6-4: "-internal-externc-isystem" "[[SYSROOT]]/include" +-// CHECK-GENTOO-4-6-4: "-internal-externc-isystem" "[[SYSROOT]]/usr/include" +diff -urN llvm-3.4.orig/tools/clang/test/Driver/linux-ld.c llvm-3.4/tools/clang/test/Driver/linux-ld.c +--- llvm-3.4.orig/tools/clang/test/Driver/linux-ld.c 2013-10-29 11:27:30.000000000 +0100 ++++ llvm-3.4/tools/clang/test/Driver/linux-ld.c 1970-01-01 01:00:00.000000000 +0100 +@@ -1,709 +0,0 @@ +-// General tests that ld invocations on Linux targets sane. Note that we use +-// sysroot to make these tests independent of the host system. +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-LD-32 %s +-// CHECK-LD-32-NOT: warning: +-// CHECK-LD-32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-LD-32: "{{.*}}/usr/lib/gcc/i386-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-LD-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0" +-// CHECK-LD-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../i386-unknown-linux/lib" +-// CHECK-LD-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../.." +-// CHECK-LD-32: "-L[[SYSROOT]]/lib" +-// CHECK-LD-32: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-LD-64 %s +-// CHECK-LD-64-NOT: warning: +-// CHECK-LD-64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-LD-64: "--eh-frame-hdr" +-// CHECK-LD-64: "-m" "elf_x86_64" +-// CHECK-LD-64: "-dynamic-linker" +-// CHECK-LD-64: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-LD-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-LD-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib" +-// CHECK-LD-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../.." +-// CHECK-LD-64: "-L[[SYSROOT]]/lib" +-// CHECK-LD-64: "-L[[SYSROOT]]/usr/lib" +-// CHECK-LD-64: "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" +-// CHECK-LD-64: "-lc" +-// CHECK-LD-64: "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux \ +-// RUN: -static-libgcc \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-LD-64-STATIC-LIBGCC %s +-// CHECK-LD-64-STATIC-LIBGCC-NOT: warning: +-// CHECK-LD-64-STATIC-LIBGCC: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-LD-64-STATIC-LIBGCC: "--eh-frame-hdr" +-// CHECK-LD-64-STATIC-LIBGCC: "-m" "elf_x86_64" +-// CHECK-LD-64-STATIC-LIBGCC: "-dynamic-linker" +-// CHECK-LD-64-STATIC-LIBGCC: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-LD-64-STATIC-LIBGCC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-LD-64-STATIC-LIBGCC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib" +-// CHECK-LD-64-STATIC-LIBGCC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../.." +-// CHECK-LD-64-STATIC-LIBGCC: "-L[[SYSROOT]]/lib" +-// CHECK-LD-64-STATIC-LIBGCC: "-L[[SYSROOT]]/usr/lib" +-// CHECK-LD-64-STATIC-LIBGCC: "-lgcc" "-lgcc_eh" +-// CHECK-LD-64-STATIC-LIBGCC: "-lc" +-// CHECK-LD-64-STATIC-LIBGCC: "-lgcc" "-lgcc_eh" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux \ +-// RUN: -static \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-LD-64-STATIC %s +-// CHECK-LD-64-STATIC-NOT: warning: +-// CHECK-LD-64-STATIC: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-LD-64-STATIC-NOT: "--eh-frame-hdr" +-// CHECK-LD-64-STATIC: "-m" "elf_x86_64" +-// CHECK-LD-64-STATIC-NOT: "-dynamic-linker" +-// CHECK-LD-64-STATIC: "-static" +-// CHECK-LD-64-STATIC: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtbeginT.o" +-// CHECK-LD-64-STATIC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-LD-64-STATIC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib" +-// CHECK-LD-64-STATIC: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../.." +-// CHECK-LD-64-STATIC: "-L[[SYSROOT]]/lib" +-// CHECK-LD-64-STATIC: "-L[[SYSROOT]]/usr/lib" +-// CHECK-LD-64-STATIC: "--start-group" "-lgcc" "-lgcc_eh" "-lc" "--end-group" +-// +-// Check that flags can be combined. The -static dominates. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux \ +-// RUN: -static-libgcc -static \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-LD-64-STATIC %s +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: --sysroot=%S/Inputs/multilib_32bit_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-32-TO-32 %s +-// CHECK-32-TO-32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-32-TO-32: "{{.*}}/usr/lib/gcc/i386-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../i386-unknown-linux/lib/../lib32" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../lib32" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/lib/../lib32" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/../lib32" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../i386-unknown-linux/lib" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../.." +-// CHECK-32-TO-32: "-L[[SYSROOT]]/lib" +-// CHECK-32-TO-32: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m64 \ +-// RUN: --sysroot=%S/Inputs/multilib_32bit_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-32-TO-64 %s +-// CHECK-32-TO-64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-32-TO-64: "{{.*}}/usr/lib/gcc/i386-unknown-linux/4.6.0/64{{/|\\\\}}crtbegin.o" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/64" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../i386-unknown-linux/lib/../lib64" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../lib64" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/lib/../lib64" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/../lib64" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../../../i386-unknown-linux/lib" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/i386-unknown-linux/4.6.0/../../.." +-// CHECK-32-TO-64: "-L[[SYSROOT]]/lib" +-// CHECK-32-TO-64: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux -m64 \ +-// RUN: --sysroot=%S/Inputs/multilib_64bit_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-64-TO-64 %s +-// CHECK-64-TO-64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-64-TO-64: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib/../lib64" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../lib64" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/lib/../lib64" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/../lib64" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../.." +-// CHECK-64-TO-64: "-L[[SYSROOT]]/lib" +-// CHECK-64-TO-64: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux -m32 \ +-// RUN: --sysroot=%S/Inputs/multilib_64bit_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-64-TO-32 %s +-// CHECK-64-TO-32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-64-TO-32: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0/32{{/|\\\\}}crtbegin.o" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/32" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib/../lib32" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../lib32" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/lib/../lib32" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/../lib32" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../../../x86_64-unknown-linux/lib" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0/../../.." +-// CHECK-64-TO-32: "-L[[SYSROOT]]/lib" +-// CHECK-64-TO-32: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux -m32 \ +-// RUN: --gcc-toolchain=%S/Inputs/multilib_64bit_linux_tree/usr \ +-// RUN: --sysroot=%S/Inputs/multilib_32bit_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-64-TO-32-SYSROOT %s +-// CHECK-64-TO-32-SYSROOT: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-64-TO-32-SYSROOT: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0/32{{/|\\\\}}crtbegin.o" +-// CHECK-64-TO-32-SYSROOT: "-L{{[^"]*}}/Inputs/multilib_64bit_linux_tree/usr/lib/gcc/x86_64-unknown-linux/4.6.0/32" +-// CHECK-64-TO-32-SYSROOT: "-L[[SYSROOT]]/lib/../lib32" +-// CHECK-64-TO-32-SYSROOT: "-L[[SYSROOT]]/usr/lib/../lib32" +-// CHECK-64-TO-32-SYSROOT: "-L{{[^"]*}}/Inputs/multilib_64bit_linux_tree/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// CHECK-64-TO-32-SYSROOT: "-L[[SYSROOT]]/lib" +-// CHECK-64-TO-32-SYSROOT: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: -ccc-install-dir %S/Inputs/fake_install_tree/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-INSTALL-DIR-32 %s +-// CHECK-INSTALL-DIR-32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-INSTALL-DIR-32: "{{.*}}/Inputs/fake_install_tree/bin/../lib/gcc/i386-unknown-linux/4.7.0{{/|\\\\}}crtbegin.o" +-// CHECK-INSTALL-DIR-32: "-L{{.*}}/Inputs/fake_install_tree/bin/../lib/gcc/i386-unknown-linux/4.7.0" +-// +-// Check that with 64-bit builds, we don't actually use the install directory +-// as its version of GCC is lower than our sysrooted version. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-unknown-linux -m64 \ +-// RUN: -ccc-install-dir %S/Inputs/fake_install_tree/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-INSTALL-DIR-64 %s +-// CHECK-INSTALL-DIR-64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-INSTALL-DIR-64: "{{.*}}/usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtbegin.o" +-// CHECK-INSTALL-DIR-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-unknown-linux/4.6.0" +-// +-// Check that we support unusual patch version formats, including missing that +-// component. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: -ccc-install-dir %S/Inputs/gcc_version_parsing1/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GCC-VERSION1 %s +-// CHECK-GCC-VERSION1: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-GCC-VERSION1: "{{.*}}/Inputs/gcc_version_parsing1/bin/../lib/gcc/i386-unknown-linux/4.7{{/|\\\\}}crtbegin.o" +-// CHECK-GCC-VERSION1: "-L{{.*}}/Inputs/gcc_version_parsing1/bin/../lib/gcc/i386-unknown-linux/4.7" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: -ccc-install-dir %S/Inputs/gcc_version_parsing2/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GCC-VERSION2 %s +-// CHECK-GCC-VERSION2: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-GCC-VERSION2: "{{.*}}/Inputs/gcc_version_parsing2/bin/../lib/gcc/i386-unknown-linux/4.7.x{{/|\\\\}}crtbegin.o" +-// CHECK-GCC-VERSION2: "-L{{.*}}/Inputs/gcc_version_parsing2/bin/../lib/gcc/i386-unknown-linux/4.7.x" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: -ccc-install-dir %S/Inputs/gcc_version_parsing3/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GCC-VERSION3 %s +-// CHECK-GCC-VERSION3: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-GCC-VERSION3: "{{.*}}/Inputs/gcc_version_parsing3/bin/../lib/gcc/i386-unknown-linux/4.7.99-rc5{{/|\\\\}}crtbegin.o" +-// CHECK-GCC-VERSION3: "-L{{.*}}/Inputs/gcc_version_parsing3/bin/../lib/gcc/i386-unknown-linux/4.7.99-rc5" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux -m32 \ +-// RUN: -ccc-install-dir %S/Inputs/gcc_version_parsing4/bin \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-GCC-VERSION4 %s +-// CHECK-GCC-VERSION4: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-GCC-VERSION4: "{{.*}}/Inputs/gcc_version_parsing4/bin/../lib/gcc/i386-unknown-linux/4.7.99{{/|\\\\}}crtbegin.o" +-// CHECK-GCC-VERSION4: "-L{{.*}}/Inputs/gcc_version_parsing4/bin/../lib/gcc/i386-unknown-linux/4.7.99" +-// +-// Test a very broken version of multiarch that shipped in Ubuntu 11.04. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-unknown-linux \ +-// RUN: --sysroot=%S/Inputs/ubuntu_11.04_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-11-04 %s +-// CHECK-UBUNTU-11-04: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-11-04: "{{.*}}/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5" +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5/../../../../i386-linux-gnu" +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/usr/lib/i386-linux-gnu" +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/usr/lib/i386-linux-gnu/gcc/i686-linux-gnu/4.5/../../../.." +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/lib" +-// CHECK-UBUNTU-11-04: "-L[[SYSROOT]]/usr/lib" +-// +-// Check multi arch support on Ubuntu 12.04 LTS. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-unknown-linux-gnueabihf \ +-// RUN: --sysroot=%S/Inputs/ubuntu_12.04_LTS_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-12-04-ARM-HF %s +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}/usr/lib/gcc/arm-linux-gnueabihf/4.6.3/../../../arm-linux-gnueabihf{{/|\\\\}}crt1.o" +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}/usr/lib/gcc/arm-linux-gnueabihf/4.6.3/../../../arm-linux-gnueabihf{{/|\\\\}}crti.o" +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}/usr/lib/gcc/arm-linux-gnueabihf/4.6.3{{/|\\\\}}crtbegin.o" +-// CHECK-UBUNTU-12-04-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabihf/4.6.3" +-// CHECK-UBUNTU-12-04-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabihf/4.6.3/../../../arm-linux-gnueabihf" +-// CHECK-UBUNTU-12-04-ARM-HF: "-L[[SYSROOT]]/lib/arm-linux-gnueabihf" +-// CHECK-UBUNTU-12-04-ARM-HF: "-L[[SYSROOT]]/usr/lib/arm-linux-gnueabihf" +-// CHECK-UBUNTU-12-04-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabihf/4.6.3/../../.." +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}/usr/lib/gcc/arm-linux-gnueabihf/4.6.3{{/|\\\\}}crtend.o" +-// CHECK-UBUNTU-12-04-ARM-HF: "{{.*}}/usr/lib/gcc/arm-linux-gnueabihf/4.6.3/../../../arm-linux-gnueabihf{{/|\\\\}}crtn.o" +-// +-// Check Ubuntu 13.10 on x86-64 targeting arm-linux-gnueabihf. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-gnueabihf \ +-// RUN: --sysroot=%S/Inputs/x86-64_ubuntu_13.10 \ +-// RUN: | FileCheck --check-prefix=CHECK-X86-64-UBUNTU-13-10-ARM-HF %s +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-dynamic-linker" "/lib/ld-linux-armhf.so.3" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8/../../../../arm-linux-gnueabihf/lib/../lib{{/|\\\\}}crt1.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8/../../../../arm-linux-gnueabihf/lib/../lib{{/|\\\\}}crti.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8{{/|\\\\}}crtbegin.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8/../../../../arm-linux-gnueabihf/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-L[[SYSROOT]]/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-L[[SYSROOT]]/usr/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8/../../../../arm-linux-gnueabihf/lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8{{/|\\\\}}crtend.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM-HF: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabihf/4.8/../../../../arm-linux-gnueabihf/lib/../lib{{/|\\\\}}crtn.o" +-// +-// Check Ubuntu 13.10 on x86-64 targeting arm-linux-gnueabi. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-gnueabi \ +-// RUN: --sysroot=%S/Inputs/x86-64_ubuntu_13.10 \ +-// RUN: | FileCheck --check-prefix=CHECK-X86-64-UBUNTU-13-10-ARM %s +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-dynamic-linker" "/lib/ld-linux.so.3" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabi/4.7/../../../../arm-linux-gnueabi/lib/../lib{{/|\\\\}}crt1.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabi/4.7/../../../../arm-linux-gnueabi/lib/../lib{{/|\\\\}}crti.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabi/4.7{{/|\\\\}}crtbegin.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabi/4.7" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabi/4.7/../../../../arm-linux-gnueabi/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-L[[SYSROOT]]/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-L[[SYSROOT]]/usr/lib/../lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "-L[[SYSROOT]]/usr/lib/gcc-cross/arm-linux-gnueabi/4.7/../../../../arm-linux-gnueabi/lib" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabi/4.7{{/|\\\\}}crtend.o" +-// CHECK-X86-64-UBUNTU-13-10-ARM: "{{.*}}/usr/lib/gcc-cross/arm-linux-gnueabi/4.7/../../../../arm-linux-gnueabi/lib/../lib{{/|\\\\}}crtn.o" +-// +-// Check fedora 18 on arm. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=armv7-unknown-linux-gnueabihf \ +-// RUN: --sysroot=%S/Inputs/fedora_18_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-FEDORA-18-ARM-HF %s +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2/../../../../lib{{/|\\\\}}crt1.o" +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2/../../../../lib{{/|\\\\}}crti.o" +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2{{/|\\\\}}crtbegin.o" +-// CHECK-FEDORA-18-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2" +-// CHECK-FEDORA-18-ARM-HF: "-L[[SYSROOT]]/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2/../../../../lib" +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2{{/|\\\\}}crtend.o" +-// CHECK-FEDORA-18-ARM-HF: "{{.*}}/usr/lib/gcc/armv7hl-redhat-linux-gnueabi/4.7.2/../../../../lib{{/|\\\\}}crtn.o" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-unknown-linux-gnueabi \ +-// RUN: --sysroot=%S/Inputs/ubuntu_12.04_LTS_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-UBUNTU-12-04-ARM %s +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}/usr/lib/gcc/arm-linux-gnueabi/4.6.1/../../../arm-linux-gnueabi{{/|\\\\}}crt1.o" +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}/usr/lib/gcc/arm-linux-gnueabi/4.6.1/../../../arm-linux-gnueabi{{/|\\\\}}crti.o" +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}/usr/lib/gcc/arm-linux-gnueabi/4.6.1{{/|\\\\}}crtbegin.o" +-// CHECK-UBUNTU-12-04-ARM: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabi/4.6.1" +-// CHECK-UBUNTU-12-04-ARM: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabi/4.6.1/../../../arm-linux-gnueabi" +-// CHECK-UBUNTU-12-04-ARM: "-L[[SYSROOT]]/lib/arm-linux-gnueabi" +-// CHECK-UBUNTU-12-04-ARM: "-L[[SYSROOT]]/usr/lib/arm-linux-gnueabi" +-// CHECK-UBUNTU-12-04-ARM: "-L[[SYSROOT]]/usr/lib/gcc/arm-linux-gnueabi/4.6.1/../../.." +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}/usr/lib/gcc/arm-linux-gnueabi/4.6.1{{/|\\\\}}crtend.o" +-// CHECK-UBUNTU-12-04-ARM: "{{.*}}/usr/lib/gcc/arm-linux-gnueabi/4.6.1/../../../arm-linux-gnueabi{{/|\\\\}}crtn.o" +-// +-// Test the setup that shipped in SUSE 10.3 on ppc64. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=powerpc64-suse-linux \ +-// RUN: --sysroot=%S/Inputs/suse_10.3_ppc64_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-SUSE-10-3-PPC64 %s +-// CHECK-SUSE-10-3-PPC64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-SUSE-10-3-PPC64: "{{.*}}/usr/lib/gcc/powerpc64-suse-linux/4.1.2/64{{/|\\\\}}crtbegin.o" +-// CHECK-SUSE-10-3-PPC64: "-L[[SYSROOT]]/usr/lib/gcc/powerpc64-suse-linux/4.1.2/64" +-// CHECK-SUSE-10-3-PPC64: "-L[[SYSROOT]]/usr/lib/gcc/powerpc64-suse-linux/4.1.2/../../../../lib64" +-// CHECK-SUSE-10-3-PPC64: "-L[[SYSROOT]]/lib/../lib64" +-// CHECK-SUSE-10-3-PPC64: "-L[[SYSROOT]]/usr/lib/../lib64" +-// +-// Check dynamic-linker for different archs +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-gnueabi \ +-// RUN: | FileCheck --check-prefix=CHECK-ARM %s +-// CHECK-ARM: "{{.*}}ld{{(.exe)?}}" +-// CHECK-ARM: "-m" "armelf_linux_eabi" +-// CHECK-ARM: "-dynamic-linker" "{{.*}}/lib/ld-linux.so.3" +-// +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-gnueabihf \ +-// RUN: | FileCheck --check-prefix=CHECK-ARM-HF %s +-// CHECK-ARM-HF: "{{.*}}ld{{(.exe)?}}" +-// CHECK-ARM-HF: "-m" "armelf_linux_eabi" +-// CHECK-ARM-HF: "-dynamic-linker" "{{.*}}/lib/ld-linux-armhf.so.3" +-// +-// Check that we do not pass --hash-style=gnu and --hash-style=both to linker +-// and provide correct path to the dynamic linker and emulation mode when build +-// for MIPS platforms. +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips-linux-gnu \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPS %s +-// CHECK-MIPS: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPS: "-m" "elf32btsmip" +-// CHECK-MIPS: "-dynamic-linker" "{{.*}}/lib/ld.so.1" +-// CHECK-MIPS-NOT: "--hash-style={{gnu|both}}" +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-gnu \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPSEL %s +-// CHECK-MIPSEL: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPSEL: "-m" "elf32ltsmip" +-// CHECK-MIPSEL: "-dynamic-linker" "{{.*}}/lib/ld.so.1" +-// CHECK-MIPSEL-NOT: "--hash-style={{gnu|both}}" +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64-linux-gnu \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPS64 %s +-// CHECK-MIPS64: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPS64: "-m" "elf64btsmip" +-// CHECK-MIPS64: "-dynamic-linker" "{{.*}}/lib64/ld.so.1" +-// CHECK-MIPS64-NOT: "--hash-style={{gnu|both}}" +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPS64EL %s +-// CHECK-MIPS64EL: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPS64EL: "-m" "elf64ltsmip" +-// CHECK-MIPS64EL: "-dynamic-linker" "{{.*}}/lib64/ld.so.1" +-// CHECK-MIPS64EL-NOT: "--hash-style={{gnu|both}}" +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64-linux-gnu -mabi=n32 \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPS64-N32 %s +-// CHECK-MIPS64-N32: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPS64-N32: "-m" "elf32btsmipn32" +-// CHECK-MIPS64-N32: "-dynamic-linker" "{{.*}}/lib32/ld.so.1" +-// CHECK-MIPS64-N32-NOT: "--hash-style={{gnu|both}}" +-// RUN: %clang %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu -mabi=n32 \ +-// RUN: | FileCheck --check-prefix=CHECK-MIPS64EL-N32 %s +-// CHECK-MIPS64EL-N32: "{{.*}}ld{{(.exe)?}}" +-// CHECK-MIPS64EL-N32: "-m" "elf32ltsmipn32" +-// CHECK-MIPS64EL-N32: "-dynamic-linker" "{{.*}}/lib32/ld.so.1" +-// CHECK-MIPS64EL-N32-NOT: "--hash-style={{gnu|both}}" +-// +-// Thoroughly exercise the Debian multiarch environment. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i686-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-X86 %s +-// CHECK-DEBIAN-X86: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-X86: "{{.*}}/usr/lib/gcc/i686-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5" +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5/../../../i386-linux-gnu" +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/usr/lib/i386-linux-gnu" +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/usr/lib/gcc/i686-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-X86: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=x86_64-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-X86-64 %s +-// CHECK-DEBIAN-X86-64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-X86-64: "{{.*}}/usr/lib/gcc/x86_64-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5" +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5/../../../x86_64-linux-gnu" +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/usr/lib/x86_64-linux-gnu" +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/usr/lib/gcc/x86_64-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-X86-64: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=powerpc-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-PPC %s +-// CHECK-DEBIAN-PPC: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-PPC: "{{.*}}/usr/lib/gcc/powerpc-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5" +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5/../../../powerpc-linux-gnu" +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/usr/lib/powerpc-linux-gnu" +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/usr/lib/gcc/powerpc-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-PPC: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=powerpc64-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-PPC64 %s +-// CHECK-DEBIAN-PPC64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-PPC64: "{{.*}}/usr/lib/gcc/powerpc64-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5" +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5/../../../powerpc64-linux-gnu" +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/usr/lib/powerpc64-linux-gnu" +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/usr/lib/gcc/powerpc64-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-PPC64: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPS %s +-// CHECK-DEBIAN-MIPS: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPS: "{{.*}}/usr/lib/gcc/mips-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/../../../mips-linux-gnu" +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/usr/lib/mips-linux-gnu" +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPS: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPSEL %s +-// CHECK-DEBIAN-MIPSEL: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPSEL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.5{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/../../../mipsel-linux-gnu" +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/usr/lib/mipsel-linux-gnu" +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPSEL: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPS64 %s +-// CHECK-DEBIAN-MIPS64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPS64: "{{.*}}/usr/lib/gcc/mips-linux-gnu/4.5/64{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPS64: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/64" +-// CHECK-DEBIAN-MIPS64: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPS64: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPS64: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPS64: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPS64EL %s +-// CHECK-DEBIAN-MIPS64EL: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPS64EL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.5/64{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/64" +-// CHECK-DEBIAN-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPS64EL: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPS64EL: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64-linux-gnu -mabi=n32 \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPS64-N32 %s +-// CHECK-DEBIAN-MIPS64-N32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPS64-N32: "{{.*}}/usr/lib/gcc/mips-linux-gnu/4.5/n32{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPS64-N32: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/n32" +-// CHECK-DEBIAN-MIPS64-N32: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPS64-N32: "-L[[SYSROOT]]/usr/lib/gcc/mips-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPS64-N32: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPS64-N32: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu -mabi=n32 \ +-// RUN: --sysroot=%S/Inputs/debian_multiarch_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-MIPS64EL-N32 %s +-// CHECK-DEBIAN-MIPS64EL-N32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-MIPS64EL-N32: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.5/n32{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/n32" +-// CHECK-DEBIAN-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5" +-// CHECK-DEBIAN-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.5/../../.." +-// CHECK-DEBIAN-MIPS64EL-N32: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib" +-// +-// Test linker invocation on Android. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-androideabi \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID %s +-// CHECK-ANDROID: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-ANDROID: "{{.*}}{{/|\\\\}}crtbegin_dynamic.o" +-// CHECK-ANDROID: "-L[[SYSROOT]]/usr/lib" +-// CHECK-ANDROID-NOT: "gcc_s" +-// CHECK-ANDROID: "-lgcc" +-// CHECK-ANDROID: "-ldl" +-// CHECK-ANDROID-NOT: "gcc_s" +-// CHECK-ANDROID: "{{.*}}{{/|\\\\}}crtend_android.o" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-androideabi \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -shared \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-SO %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -shared \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-SO %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -shared \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-SO %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -shared \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-SO %s +-// CHECK-ANDROID-SO: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-ANDROID-SO: "-Bsymbolic" +-// CHECK-ANDROID-SO: "{{.*}}{{/|\\\\}}crtbegin_so.o" +-// CHECK-ANDROID-SO: "-L[[SYSROOT]]/usr/lib" +-// CHECK-ANDROID-SO-NOT: "gcc_s" +-// CHECK-ANDROID-SO: "-lgcc" +-// CHECK-ANDROID-SO: "-ldl" +-// CHECK-ANDROID-SO-NOT: "gcc_s" +-// CHECK-ANDROID-SO: "{{.*}}{{/|\\\\}}crtend_so.o" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-androideabi \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -static \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-STATIC %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -static \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-STATIC %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -static \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-STATIC %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -static \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-STATIC %s +-// CHECK-ANDROID-STATIC: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-ANDROID-STATIC: "{{.*}}{{/|\\\\}}crtbegin_static.o" +-// CHECK-ANDROID-STATIC: "-L[[SYSROOT]]/usr/lib" +-// CHECK-ANDROID-STATIC-NOT: "gcc_s" +-// CHECK-ANDROID-STATIC: "-lgcc" +-// CHECK-ANDROID-STATIC-NOT: "-ldl" +-// CHECK-ANDROID-STATIC-NOT: "gcc_s" +-// CHECK-ANDROID-STATIC: "{{.*}}{{/|\\\\}}crtend_android.o" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-androideabi \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -pie \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-PIE %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=arm-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -pie \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-PIE %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -pie \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-PIE %s +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=i386-linux-android \ +-// RUN: --sysroot=%S/Inputs/basic_android_tree/sysroot \ +-// RUN: -pie \ +-// RUN: | FileCheck --check-prefix=CHECK-ANDROID-PIE %s +-// CHECK-ANDROID-PIE: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-ANDROID-PIE: "{{.*}}{{/|\\\\}}crtbegin_dynamic.o" +-// CHECK-ANDROID-PIE: "-L[[SYSROOT]]/usr/lib" +-// CHECK-ANDROID-PIE-NOT: "gcc_s" +-// CHECK-ANDROID-PIE: "-lgcc" +-// CHECK-ANDROID-PIE-NOT: "gcc_s" +-// CHECK-ANDROID-PIE: "{{.*}}{{/|\\\\}}crtend_android.o" +-// +-// Check linker invocation on Debian 6 MIPS 32/64-bit. +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mipsel-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_6_mips_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-ML-MIPSEL %s +-// CHECK-DEBIAN-ML-MIPSEL: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-ML-MIPSEL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib{{/|\\\\}}crt1.o" +-// CHECK-DEBIAN-ML-MIPSEL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib{{/|\\\\}}crti.o" +-// CHECK-DEBIAN-ML-MIPSEL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/lib/../lib" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/usr/lib/../lib" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../.." +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-ML-MIPSEL: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu \ +-// RUN: --sysroot=%S/Inputs/debian_6_mips_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-ML-MIPS64EL %s +-// CHECK-DEBIAN-ML-MIPS64EL: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-ML-MIPS64EL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib64{{/|\\\\}}crt1.o" +-// CHECK-DEBIAN-ML-MIPS64EL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib64{{/|\\\\}}crti.o" +-// CHECK-DEBIAN-ML-MIPS64EL: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/64{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/64" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib64" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/lib/../lib64" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/usr/lib/../lib64" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../.." +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-ML-MIPS64EL: "-L[[SYSROOT]]/usr/lib" +-// +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=mips64el-linux-gnu -mabi=n32 \ +-// RUN: --sysroot=%S/Inputs/debian_6_mips_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-DEBIAN-ML-MIPS64EL-N32 %s +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib32{{/|\\\\}}crt1.o" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib32{{/|\\\\}}crti.o" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "{{.*}}/usr/lib/gcc/mipsel-linux-gnu/4.4/n32{{/|\\\\}}crtbegin.o" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/n32" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../../../lib32" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/lib/../lib32" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/../lib32" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib/gcc/mipsel-linux-gnu/4.4/../../.." +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/lib" +-// CHECK-DEBIAN-ML-MIPS64EL-N32: "-L[[SYSROOT]]/usr/lib" +-// +-// Test linker invocation for Freescale SDK (OpenEmbedded). +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=powerpc-fsl-linux \ +-// RUN: --sysroot=%S/Inputs/freescale_ppc_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-FSL-PPC %s +-// CHECK-FSL-PPC: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-FSL-PPC: "-m" "elf32ppclinux" +-// CHECK-FSL-PPC: "{{.*}}{{/|\\\\}}crt1.o" +-// CHECK-FSL-PPC: "{{.*}}{{/|\\\\}}crtbegin.o" +-// CHECK-FSL-PPC: "-L[[SYSROOT]]/usr/lib" +-// RUN: %clang -no-canonical-prefixes %s -### -o %t.o 2>&1 \ +-// RUN: --target=powerpc64-fsl-linux \ +-// RUN: --sysroot=%S/Inputs/freescale_ppc64_tree \ +-// RUN: | FileCheck --check-prefix=CHECK-FSL-PPC64 %s +-// CHECK-FSL-PPC64: "{{.*}}ld{{(.exe)?}}" "--sysroot=[[SYSROOT:[^"]+]]" +-// CHECK-FSL-PPC64: "-m" "elf64ppc" +-// CHECK-FSL-PPC64: "{{.*}}{{/|\\\\}}crt1.o" +-// CHECK-FSL-PPC64: "{{.*}}{{/|\\\\}}crtbegin.o" +-// CHECK-FSL-PPC64: "-L[[SYSROOT]]/usr/lib64/powerpc64-fsl-linux/4.6.2/../.." +-// +-// Check that crtfastmath.o is linked with -ffast-math. +-// RUN: %clang --target=x86_64-unknown-linux -### %s \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>&1 \ +-// RUN: | FileCheck --check-prefix=CHECK-NOCRTFASTMATH %s +-// RUN: %clang --target=x86_64-unknown-linux -### %s -ffast-math \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>&1 \ +-// RUN: | FileCheck --check-prefix=CHECK-CRTFASTMATH %s +-// RUN: %clang --target=x86_64-unknown-linux -### %s -funsafe-math-optimizations\ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>&1 \ +-// RUN: | FileCheck --check-prefix=CHECK-CRTFASTMATH %s +-// RUN: %clang --target=x86_64-unknown-linux -### %s -ffast-math -fno-fast-math \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>&1 \ +-// RUN: | FileCheck --check-prefix=CHECK-NOCRTFASTMATH %s +-// We don't have crtfastmath.o in the i386 tree, use it to check that file +-// detection works. +-// RUN: %clang --target=i386-unknown-linux -### %s -ffast-math \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>&1 \ +-// RUN: | FileCheck --check-prefix=CHECK-NOCRTFASTMATH %s +-// CHECK-CRTFASTMATH: usr/lib/gcc/x86_64-unknown-linux/4.6.0{{/|\\\\}}crtfastmath.o +-// CHECK-NOCRTFASTMATH-NOT: crtfastmath.o +- +-// Check that we link in gcrt1.o when compiling with -pg +-// RUN: %clang -pg --target=x86_64-unknown-linux -### %s \ +-// RUN: --sysroot=%S/Inputs/basic_linux_tree 2>& 1 \ +-// RUN: | FileCheck --check-prefix=CHECK-PG %s +-// CHECK-PG: gcrt1.o -- GitLab From 69a9424744f61a9a2ad33fac61855a25c6110913 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 8 Jan 2014 20:12:42 +0100 Subject: [PATCH 290/566] commit 7 digit truncation. 4 spaces identation --- .../easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb index 6e253681ab..452b13483b 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -14,15 +14,15 @@ description = """ Windowed Adaptive Trimming for fastq files using quality """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://github.com/najoshi/sickle/archive/'] # commit bab15f7d14b06400be37d50df7c092b1ec6fe0c5 -sources = ['bab15f7d14b06400be37d50df7c092b1ec6fe0c5.tar.gz'] +git_commit_id = 'bab15f7' +sources = ['%(git_commit_id)s.tar.gz'] +source_urls = ['https://github.com/najoshi/sickle/archive/'] files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] sanity_check_paths = { - 'files': ['bin/sickle'], - 'dirs': [] - } + 'files': ['bin/sickle'], + 'dirs': [] moduleclass = 'bio' -- GitLab From a46603394317d9c3b4a5906971469fd92817769f Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 8 Jan 2014 20:21:16 +0100 Subject: [PATCH 291/566] fixed syntax error unclosed brace --- easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb index 452b13483b..3a7270ebbe 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -24,5 +24,6 @@ files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] sanity_check_paths = { 'files': ['bin/sickle'], 'dirs': [] +} moduleclass = 'bio' -- GitLab From 70dff1dd9b3ad1ed75aa413f4491453bf09306c5 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 8 Jan 2014 20:42:29 +0100 Subject: [PATCH 292/566] fix --- easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb index 3a7270ebbe..05d1518a05 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # commit bab15f7d14b06400be37d50df7c092b1ec6fe0c5 git_commit_id = 'bab15f7' -sources = ['%(git_commit_id)s.tar.gz'] +sources = ['%s.tar.gz' % git_commit_id] source_urls = ['https://github.com/najoshi/sickle/archive/'] files_to_copy = [(['sickle'], 'bin'), "README.md", "test"] -- GitLab From 3987e40c4618fd649470b1ba5d26e2aadd6391d9 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 8 Jan 2014 23:11:28 +0100 Subject: [PATCH 293/566] added versionsuffix=git_commit_id as @fgeorgatos suggested --- easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb index 05d1518a05..a224586986 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -8,14 +8,15 @@ easyblock='MakeCp' name = "sickle" # version checked running "sickle --version" version = "1.210" +# git_commit_id bab15f7d14b06400be37d50df7c092b1ec6fe0c5 +versionsuffix = "bab15f7" homepage = 'https://github.com/najoshi/sickle' description = """ Windowed Adaptive Trimming for fastq files using quality """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -# commit bab15f7d14b06400be37d50df7c092b1ec6fe0c5 -git_commit_id = 'bab15f7' +git_commit_id = versionsuffix sources = ['%s.tar.gz' % git_commit_id] source_urls = ['https://github.com/najoshi/sickle/archive/'] -- GitLab From fb453ae206363bbb57a3adc287494d7c07d80fd5 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 9 Jan 2014 10:57:11 +0100 Subject: [PATCH 294/566] Clang: disable optarch, this cause the build to fail --- easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index 875ec21d53..c131647d76 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -18,6 +18,8 @@ description = """C, C++, Objective-C compiler, based on LLVM. Does not # Clang also depends on libstdc++ during runtime, but this dependency is # already specified as the toolchain. toolchain = {'name': 'GCC', 'version': '4.8.2'} +# 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 = [ @@ -41,8 +43,6 @@ sanity_check_paths = { 'dirs': [], } -languages = ['c', 'c++'] - moduleclass = 'compiler' assertions = False -- GitLab From c3fed1774f451a726f26e819ead15bd7cdfd1ecb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 9 Jan 2014 12:37:49 +0100 Subject: [PATCH 295/566] Clang: reorganized patches for clang-3.4 --- .../Clang-3.4-failing-sanitizer-tests.patch | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.4-failing-sanitizer-tests.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-sanitizer-tests.patch b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-sanitizer-tests.patch new file mode 100644 index 0000000000..bc991f2275 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-sanitizer-tests.patch @@ -0,0 +1,24 @@ +# these tests fail for unknown reason: as they are part of the sanitizers in clang, +# I don't think that we should be worried about them. +diff -urN llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc +--- llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2013-10-17 13:18:11.000000000 +0200 ++++ llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2014-01-07 14:43:48.836815229 +0100 +@@ -223,10 +223,8 @@ + + #if SANITIZER_WORDSIZE == 64 + TEST(SanitizerCommon, SizeClassAllocator64GetBlockBegin) { +- SizeClassAllocatorGetBlockBeginStress(); + } + TEST(SanitizerCommon, SizeClassAllocator64CompactGetBlockBegin) { +- SizeClassAllocatorGetBlockBeginStress(); + } + TEST(SanitizerCommon, SizeClassAllocator32CompactGetBlockBegin) { + SizeClassAllocatorGetBlockBeginStress(); +@@ -324,7 +322,6 @@ + + #if SANITIZER_WORDSIZE == 64 + TEST(SanitizerCommon, SizeClassAllocator64Overflow) { +- EXPECT_DEATH(FailInAssertionOnOOM(), "Out of memory"); + } + #endif + -- GitLab From 4e99c83f5ef696269d9f56fc7ff84693f7f1897b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 9 Jan 2014 12:45:18 +0100 Subject: [PATCH 296/566] Clang: reorganize the patches correctly --- .../c/Clang/Clang-3.4-GCC-4.8.2.eb | 1 + ...tests-due-to-gcc-installation-prefix.patch | 22 ------------------- 2 files changed, 1 insertion(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index c131647d76..b1cd63b2ee 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -34,6 +34,7 @@ patches = [ # 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', ] builddependencies = [('CMake', '2.8.12')] diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch index a19a8d124f..46114f93d7 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-failing-tests-due-to-gcc-installation-prefix.patch @@ -1,25 +1,3 @@ -diff -urN llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc ---- llvm-3.4.orig/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2013-10-17 13:18:11.000000000 +0200 -+++ llvm-3.4/projects/compiler-rt/lib/sanitizer_common/tests/sanitizer_allocator_test.cc 2014-01-07 14:43:48.836815229 +0100 -@@ -223,10 +223,8 @@ - - #if SANITIZER_WORDSIZE == 64 - TEST(SanitizerCommon, SizeClassAllocator64GetBlockBegin) { -- SizeClassAllocatorGetBlockBeginStress(); - } - TEST(SanitizerCommon, SizeClassAllocator64CompactGetBlockBegin) { -- SizeClassAllocatorGetBlockBeginStress(); - } - TEST(SanitizerCommon, SizeClassAllocator32CompactGetBlockBegin) { - SizeClassAllocatorGetBlockBeginStress(); -@@ -324,7 +322,6 @@ - - #if SANITIZER_WORDSIZE == 64 - TEST(SanitizerCommon, SizeClassAllocator64Overflow) { -- EXPECT_DEATH(FailInAssertionOnOOM(), "Out of memory"); - } - #endif - diff -urN llvm-3.4.orig/tools/clang/test/Driver/constructors.c llvm-3.4/tools/clang/test/Driver/constructors.c --- llvm-3.4.orig/tools/clang/test/Driver/constructors.c 2012-11-22 00:40:23.000000000 +0100 +++ llvm-3.4/tools/clang/test/Driver/constructors.c 2014-01-07 14:43:48.801815348 +0100 -- GitLab From 258e9ab171685ce3cf6e7b5a54d83fc1a56fdc1a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 9 Jan 2014 12:45:50 +0100 Subject: [PATCH 297/566] ClangGCC: updated toolchain to clang-3.4 --- .../easyconfigs/c/ClangGCC/ClangGCC-1.3.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClangGCC/ClangGCC-1.3.0.eb diff --git a/easybuild/easyconfigs/c/ClangGCC/ClangGCC-1.3.0.eb b/easybuild/easyconfigs/c/ClangGCC/ClangGCC-1.3.0.eb new file mode 100644 index 0000000000..ed2fa73c3c --- /dev/null +++ b/easybuild/easyconfigs/c/ClangGCC/ClangGCC-1.3.0.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'ClangGCC' +version = '1.3.0' + +homepage = '(none)' +description = """Clang and GCC based compiler toolchain. Clang will use libstdc++. +GFortran will be used to compile Fortran code.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '4.8.2') +dependencies = [ + comp, + ('Clang', '3.4', '', comp), +] + +moduleclass = 'toolchain' -- GitLab From 0b2cc8d79d5d2c8a3458318b2f9a6b475627bf24 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 10 Jan 2014 00:43:54 +0100 Subject: [PATCH 298/566] MAFFT-7.130-with-extensions-goolf-1.4.10.eb --- ...AFFT-7.130-with-extensions-goolf-1.4.10.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb new file mode 100644 index 0000000000..34f51d0aab --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# 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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://mafft.cbrc.jp/alignment/software/'] +sources = ['%(namelower)s-%(version)s-%(versionsuffix)s-src.tgz'] + +skipsteps = ['configure'] + +premakeopts = 'cd core && ' +preinstallopts = 'cd core && ' +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 6c79a4bda0adabd74ba2a8febe724ef2df52959a Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 10 Jan 2014 00:59:44 +0100 Subject: [PATCH 299/566] cosmetic changes in the description identation --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index 34f51d0aab..370e1df51d 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -8,11 +8,10 @@ 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.""" +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': 'goolf', 'version': '1.4.10'} -- GitLab From 36eebdfce579d22b7c93efca84d69c41b23a3b04 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 10 Jan 2014 01:07:16 +0100 Subject: [PATCH 300/566] switched to use start_dir as @fgeorgatos suggested --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index 370e1df51d..d03834eb1c 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -19,9 +19,7 @@ source_urls = ['http://mafft.cbrc.jp/alignment/software/'] sources = ['%(namelower)s-%(version)s-%(versionsuffix)s-src.tgz'] skipsteps = ['configure'] - -premakeopts = 'cd core && ' -preinstallopts = 'cd core && ' +start_dir = 'core' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { -- GitLab From 6e22fd319c5e57062c30e052d9ffb79576eac130 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 10 Jan 2014 01:43:24 +0100 Subject: [PATCH 301/566] remove extra line Signed-off-by: Fotis Georgatos --- .../q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb | 1 - .../q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb | 1 - .../QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb | 1 - .../q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb index 9252372604..9486bafdef 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0-hybrid.eb @@ -8,7 +8,6 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb index 2c9da47c8d..c426f3eb06 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-4.2-ictce-5.3.0.eb @@ -7,7 +7,6 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} 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 2acbc21f76..dfa16f0793 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 @@ -8,7 +8,6 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} 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 854d3543cf..ded1113c65 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 @@ -7,7 +7,6 @@ description = """Quantum ESPRESSO is an integrated suite of computer codes It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} -- GitLab From 4714b9afb6e30fb77a8c820b0d348c2b2485734d Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 10 Jan 2014 09:47:45 +0100 Subject: [PATCH 302/566] cosmetics: added missed spaces --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index d03834eb1c..129a0d9043 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -5,7 +5,7 @@ name = 'MAFFT' version = '7.130' -versionsuffix='with-extensions' +versionsuffix = 'with-extensions' homepage = 'http://mafft.cbrc.jp/alignment/software/' description = """MAFFT is a multiple sequence alignment program -- GitLab From 35e67355c8d55cec9001007cf5a196672029a4d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jan 2014 08:50:49 +0100 Subject: [PATCH 303/566] add HDF5 v1.8.12 easyconfig + required patch --- .../h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb | 25 + .../HDF5-1.8.12_mpi-includes_order_fix.patch | 439 ++++++++++++++++++ 2 files changed, 464 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_mpi-includes_order_fix.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb new file mode 100644 index 0000000000..a30ee3a186 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.12' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.12_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_mpi-includes_order_fix.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_mpi-includes_order_fix.patch new file mode 100644 index 0000000000..e86ffe564d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_mpi-includes_order_fix.patch @@ -0,0 +1,439 @@ +diff -ru hdf5-1.8.10.orig/c++/src/H5AbstractDs.cpp hdf5-1.8.10/c++/src/H5AbstractDs.cpp +--- hdf5-1.8.10.orig/c++/src/H5AbstractDs.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5AbstractDs.cpp 2012-12-10 15:51:13.237522005 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5ArrayType.cpp hdf5-1.8.10/c++/src/H5ArrayType.cpp +--- hdf5-1.8.10.orig/c++/src/H5ArrayType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5ArrayType.cpp 2012-12-10 15:51:13.238521995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5AtomType.cpp hdf5-1.8.10/c++/src/H5AtomType.cpp +--- hdf5-1.8.10.orig/c++/src/H5AtomType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5AtomType.cpp 2012-12-10 15:51:13.237522005 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5Attribute.cpp hdf5-1.8.10/c++/src/H5Attribute.cpp +--- hdf5-1.8.10.orig/c++/src/H5Attribute.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5Attribute.cpp 2012-12-10 15:51:13.230522180 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5CommonFG.cpp hdf5-1.8.10/c++/src/H5CommonFG.cpp +--- hdf5-1.8.10.orig/c++/src/H5CommonFG.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5CommonFG.cpp 2012-12-10 15:51:13.239522003 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5CompType.cpp hdf5-1.8.10/c++/src/H5CompType.cpp +--- hdf5-1.8.10.orig/c++/src/H5CompType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5CompType.cpp 2012-12-10 15:51:13.239522003 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5DataSet.cpp hdf5-1.8.10/c++/src/H5DataSet.cpp +--- hdf5-1.8.10.orig/c++/src/H5DataSet.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5DataSet.cpp 2012-12-10 15:51:13.239522003 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5DataSpace.cpp hdf5-1.8.10/c++/src/H5DataSpace.cpp +--- hdf5-1.8.10.orig/c++/src/H5DataSpace.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5DataSpace.cpp 2012-12-10 15:51:13.237522005 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5DataType.cpp hdf5-1.8.10/c++/src/H5DataType.cpp +--- hdf5-1.8.10.orig/c++/src/H5DataType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5DataType.cpp 2012-12-10 15:51:13.236521976 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5DcreatProp.cpp hdf5-1.8.10/c++/src/H5DcreatProp.cpp +--- hdf5-1.8.10.orig/c++/src/H5DcreatProp.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5DcreatProp.cpp 2012-12-10 15:51:13.236521976 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5DxferProp.cpp hdf5-1.8.10/c++/src/H5DxferProp.cpp +--- hdf5-1.8.10.orig/c++/src/H5DxferProp.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5DxferProp.cpp 2012-12-10 15:51:13.236521976 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5EnumType.cpp hdf5-1.8.10/c++/src/H5EnumType.cpp +--- hdf5-1.8.10.orig/c++/src/H5EnumType.cpp 2012-10-11 19:31:51.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5EnumType.cpp 2012-12-10 15:51:13.237522005 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5Exception.cpp hdf5-1.8.10/c++/src/H5Exception.cpp +--- hdf5-1.8.10.orig/c++/src/H5Exception.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5Exception.cpp 2012-12-10 15:51:13.230522180 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5FaccProp.cpp hdf5-1.8.10/c++/src/H5FaccProp.cpp +--- hdf5-1.8.10.orig/c++/src/H5FaccProp.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5FaccProp.cpp 2012-12-10 15:51:13.235521927 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5FcreatProp.cpp hdf5-1.8.10/c++/src/H5FcreatProp.cpp +--- hdf5-1.8.10.orig/c++/src/H5FcreatProp.cpp 2012-10-11 19:31:51.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5FcreatProp.cpp 2012-12-10 15:51:13.237522005 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5File.cpp hdf5-1.8.10/c++/src/H5File.cpp +--- hdf5-1.8.10.orig/c++/src/H5File.cpp 2012-10-11 19:31:51.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5File.cpp 2012-12-10 15:51:13.240521935 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5FloatType.cpp hdf5-1.8.10/c++/src/H5FloatType.cpp +--- hdf5-1.8.10.orig/c++/src/H5FloatType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5FloatType.cpp 2012-12-10 15:51:13.238521995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5Group.cpp hdf5-1.8.10/c++/src/H5Group.cpp +--- hdf5-1.8.10.orig/c++/src/H5Group.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5Group.cpp 2012-12-10 15:51:13.240521935 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5IdComponent.cpp hdf5-1.8.10/c++/src/H5IdComponent.cpp +--- hdf5-1.8.10.orig/c++/src/H5IdComponent.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5IdComponent.cpp 2012-12-10 15:54:57.715521900 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5IntType.cpp hdf5-1.8.10/c++/src/H5IntType.cpp +--- hdf5-1.8.10.orig/c++/src/H5IntType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5IntType.cpp 2012-12-10 15:51:13.238521995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5Library.cpp hdf5-1.8.10/c++/src/H5Library.cpp +--- hdf5-1.8.10.orig/c++/src/H5Library.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5Library.cpp 2012-12-10 15:51:13.235521927 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5CppDoc.h" // included only for Doxygen to generate part of RM +diff -ru hdf5-1.8.10.orig/c++/src/H5Object.cpp hdf5-1.8.10/c++/src/H5Object.cpp +--- hdf5-1.8.10.orig/c++/src/H5Object.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5Object.cpp 2012-12-10 15:51:13.235521927 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5PredType.cpp hdf5-1.8.10/c++/src/H5PredType.cpp +--- hdf5-1.8.10.orig/c++/src/H5PredType.cpp 2012-10-11 19:31:51.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5PredType.cpp 2012-12-10 15:51:13.238521995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5PropList.cpp hdf5-1.8.10/c++/src/H5PropList.cpp +--- hdf5-1.8.10.orig/c++/src/H5PropList.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5PropList.cpp 2012-12-10 15:51:13.236521976 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/src/H5StrType.cpp hdf5-1.8.10/c++/src/H5StrType.cpp +--- hdf5-1.8.10.orig/c++/src/H5StrType.cpp 2012-10-11 19:31:50.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5StrType.cpp 2012-12-10 15:51:13.238521995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/src/H5VarLenType.cpp hdf5-1.8.10/c++/src/H5VarLenType.cpp +--- hdf5-1.8.10.orig/c++/src/H5VarLenType.cpp 2012-10-11 19:31:51.000000000 +0200 ++++ hdf5-1.8.10/c++/src/H5VarLenType.cpp 2012-12-10 15:51:13.239522003 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" +diff -ru hdf5-1.8.10.orig/c++/test/dsets.cpp hdf5-1.8.10/c++/test/dsets.cpp +--- hdf5-1.8.10.orig/c++/test/dsets.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/dsets.cpp 2012-12-10 15:51:13.240521935 +0100 +@@ -25,6 +25,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/h5cpputil.cpp hdf5-1.8.10/c++/test/h5cpputil.cpp +--- hdf5-1.8.10.orig/c++/test/h5cpputil.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/h5cpputil.cpp 2012-12-10 15:51:13.242521899 +0100 +@@ -21,6 +21,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tattr.cpp hdf5-1.8.10/c++/test/tattr.cpp +--- hdf5-1.8.10.orig/c++/test/tattr.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tattr.cpp 2012-12-10 15:51:13.240521935 +0100 +@@ -20,6 +20,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tcompound.cpp hdf5-1.8.10/c++/test/tcompound.cpp +--- hdf5-1.8.10.orig/c++/test/tcompound.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tcompound.cpp 2012-12-10 15:51:13.241522020 +0100 +@@ -19,6 +19,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/testhdf5.cpp hdf5-1.8.10/c++/test/testhdf5.cpp +--- hdf5-1.8.10.orig/c++/test/testhdf5.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/testhdf5.cpp 2012-12-10 15:51:13.241522020 +0100 +@@ -41,6 +41,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tfile.cpp hdf5-1.8.10/c++/test/tfile.cpp +--- hdf5-1.8.10.orig/c++/test/tfile.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tfile.cpp 2012-12-10 15:51:13.241522020 +0100 +@@ -23,6 +23,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tfilter.cpp hdf5-1.8.10/c++/test/tfilter.cpp +--- hdf5-1.8.10.orig/c++/test/tfilter.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tfilter.cpp 2012-12-10 15:51:13.241522020 +0100 +@@ -19,6 +19,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/th5s.cpp hdf5-1.8.10/c++/test/th5s.cpp +--- hdf5-1.8.10.orig/c++/test/th5s.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/th5s.cpp 2012-12-10 15:51:13.241522020 +0100 +@@ -22,6 +22,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tlinks.cpp hdf5-1.8.10/c++/test/tlinks.cpp +--- hdf5-1.8.10.orig/c++/test/tlinks.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tlinks.cpp 2012-12-10 15:51:13.242521899 +0100 +@@ -19,6 +19,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/trefer.cpp hdf5-1.8.10/c++/test/trefer.cpp +--- hdf5-1.8.10.orig/c++/test/trefer.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/trefer.cpp 2012-12-10 15:51:13.242521899 +0100 +@@ -20,6 +20,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/ttypes.cpp hdf5-1.8.10/c++/test/ttypes.cpp +--- hdf5-1.8.10.orig/c++/test/ttypes.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/ttypes.cpp 2012-12-10 15:51:13.242521899 +0100 +@@ -19,6 +19,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/c++/test/tvlstr.cpp hdf5-1.8.10/c++/test/tvlstr.cpp +--- hdf5-1.8.10.orig/c++/test/tvlstr.cpp 2012-10-11 19:31:49.000000000 +0200 ++++ hdf5-1.8.10/c++/test/tvlstr.cpp 2012-12-10 15:51:13.243522021 +0100 +@@ -21,6 +21,7 @@ + + ***************************************************************************/ + ++#include + #ifdef OLD_HEADER_FILENAME + #include + #else +diff -ru hdf5-1.8.10.orig/src/H5make_libsettings.c hdf5-1.8.10/src/H5make_libsettings.c +--- hdf5-1.8.10.orig/src/H5make_libsettings.c 2012-10-11 19:30:56.000000000 +0200 ++++ hdf5-1.8.10/src/H5make_libsettings.c 2012-12-10 15:51:13.242521899 +0100 +@@ -41,6 +41,7 @@ + *------------------------------------------------------------------------- + */ + ++#include + #include + #include + #include "H5private.h" +--- hdf5-1.8.12/c++/src/H5Location.cpp.orig 2014-01-13 16:25:41.242265318 +0100 ++++ hdf5-1.8.12/c++/src/H5Location.cpp 2014-01-13 16:25:53.952336995 +0100 +@@ -13,6 +13,7 @@ + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + ++#include + #include + + #include "H5Include.h" -- GitLab From e13e210474860878831248a5a52f77baab6852d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jan 2014 09:13:54 +0100 Subject: [PATCH 304/566] add easyconfigs for Python 2.7.6 + various Python packages on top --- .../Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 28 ++++++ ...tplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb | 37 ++++++++ .../numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb | 34 ++++++++ .../PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb | 30 +++++++ .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 85 +++++++++++++++++++ .../pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb | 31 +++++++ ...pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb | 40 +++++++++ ...kit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb | 28 ++++++ .../z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb | 32 +++++++ 9 files changed, 345 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb 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 new file mode 100644 index 0000000000..3234e4ff25 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.19.2' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], +} + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000..5ee25a7abe --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.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 = '2.7.6' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.7'), + ('freetype', '2.5.0.1'), + ('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 = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..4f89921346 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'numexpr' +version = '2.2.2' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +source_urls = ['http://numexpr.googlecode.com/files/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.12'), +] + +eggname = '%s-%s-py%s-linux-x86_64.egg' % (name, version, pythonshortver) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%s/%s' % (pythonshortver, eggname, name)], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..6939bcf426 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,30 @@ +name = 'PyZMQ' +version = '14.0.1' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', '4.0.3'), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..441f9171ad --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -0,0 +1,85 @@ +name = 'Python' +version = '2.7.6' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.0' +scipyversion = '0.13.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.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', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.4.2', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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')], + }), + ('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', '0.19.2', { + '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', '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/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 new file mode 100644 index 0000000000..03c972512f --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "pandas" +version = "0.12.0" + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.6" + +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' diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..8219cdaef1 --- /dev/null +++ b/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'pyTables' +version = '3.0.0' + +homepage = 'http://www.pytables.org/moin' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +source_urls = [('http://sourceforge.net/projects/pytables/files/pytables/%s' % version, 'download')] +sources = ['tables-%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('numexpr', '2.2.2', versionsuffix), + ('HDF5', '1.8.12'), + ('Cython', '0.19.2', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%s/site-packages/tables' % pythonshortver], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..b15833e4de --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = "scikit-learn" +version = "0.14" + +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': 'ictce', 'version': '5.5.0'} +source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.3.1', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..8d73e9399b --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +name = 'ZeroMQ' +version = '4.0.3' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --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', '2.24'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From 5f0dbcd5d1ae8131b9233635f7702c96e1e756d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jan 2014 09:20:20 +0100 Subject: [PATCH 305/566] add easyconfig for EasyBuild v1.10 --- .../e/EasyBuild/EasyBuild-1.10.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb new file mode 100644 index 0000000000..99d04a46aa --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '1.10.0' + +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/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 ce12ab6209cb359c774f5919cf3972f8eeeef676 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jan 2014 09:35:37 +0100 Subject: [PATCH 306/566] add easyconfig file for netCDF 4.3.0 + required patch and easyconfigs for deps --- .../b/Bison/Bison-2.7.1-ictce-5.5.0.eb | 20 ++ .../c/cURL/cURL-7.34.0-ictce-5.5.0.eb | 22 ++ .../d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb | 18 ++ .../n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb | 36 +++ .../n/netCDF/netCDF-4.3.0_nc-config.in.cmake | 295 ++++++++++++++++++ 5 files changed, 391 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-2.7.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.34.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.3.0_nc-config.in.cmake diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7.1-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..83da9c3f17 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7.1-ictce-5.5.0.eb @@ -0,0 +1,20 @@ +name = 'Bison' +version = '2.7.1' + +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': 'ictce', 'version': '5.5.0'} + +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/cURL/cURL-7.34.0-ictce-5.5.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.34.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..a645910806 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.34.0-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +name = 'cURL' +version = '7.34.0' + +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +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-1.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..ac0d35a6d5 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.6' + +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': 'ictce', 'version': '5.5.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7.1'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..78d6d431c3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb @@ -0,0 +1,36 @@ +name = 'netCDF' +version = '4.3.0' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +patches = [('netCDF-4.3.0_nc-config.in.cmake', 'netcdf-4.3.0')] + +dependencies = [('HDF5', '1.8.12')] + +builddependencies = [ + ('CMake', '2.8.12'), + ('Doxygen', '1.8.6'), + ('cURL', '7.34.0'), +] + +# we need to specify correct start dir, since unpacked tarball also contains e.g. ._netcdf-4.3.0 +start_dir = '%(namelower)s-%(version)s' + +preconfigopts = 'mv netCDF-4.3.0_nc-config.in.cmake nc-config.in.cmake && ' + +# 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/n/netCDF/netCDF-4.3.0_nc-config.in.cmake b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0_nc-config.in.cmake new file mode 100644 index 0000000000..c97f8bf3eb --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0_nc-config.in.cmake @@ -0,0 +1,295 @@ +#! /bin/sh +# +# This forms the basis for the nc-config utility, which tells you +# various things about the netCDF installation. This code was +# contributed by netCDF user Arlindo DaSilva. Thanks Arlindo! + +prefix=@CMAKE_INSTALL_PREFIX@ +exec_prefix=@CMAKE_INSTALL_PREFIX@ +libdir=@CMAKE_INSTALL_PREFIX@/lib +includedir=@CMAKE_INSTALL_PREFIX@/include + +cc="@CMAKE_C_COMPILER@" +cflags="-I@CMAKE_INSTALL_PREFIX@/include @CMAKE_C_FLAGS@ @CMAKE_CPP_FLAGS@" +libs="-L@CMAKE_INSTALL_PREFIX@/lib -l@ALL_TLL_LIBS@" + +has_dap="@USE_DAP@" +if [ -z $has_dap ]; then + has_dap="no" +else + has_dap="yes" +fi + +has_nc2="@BUILD_V2@" + +if [ -z $has_nc2 ]; then + has_nc2="no" +else + has_nc2="yes" +fi + +has_nc4="@USE_NETCDF4@" +if [ -z $has_nc4 ]; then + has_nc4="no" +else + has_nc4="yes" +fi + +has_hdf4="@USE_HDF4@" +if [ -z $has_hdf4 ]; then + has_hdf4="no" +else + has_hdf4="yes" +fi + +has_pnetcdf="@USE_PNETCDF@" +if [ -z $has_pnetcdf ]; then + has_pnetcdf="no" +else + has_pnetcdf="yes" +fi + +has_hdf5="@USE_HDF5@" +if [ -z $has_hdf5 ]; then + has_hdf5="no" +else + has_hdf5="yes" +fi + +has_szlib="@USE_SZLIB@" +if [ -z $has_szlib ]; then + has_szlib="no" +else + has_szlib="yes" +fi + + +version="@PACKAGE@ @VERSION@" + +has_f90="no" +if type -p nf-config > /dev/null 2>&1; then + fc=`nf-config --fc` + fflags=`nf-config --fflags` + flibs=`nf-config --flibs` + has_f90=`nf-config --has-f90` +fi + +has_cxx="no" +has_cxx4="no" +if type -p ncxx4-config > /dev/null 2>&1; then + cxx4=`ncxx4-config --cxx` + has_cxx4="yes" +elif type -p ncxx-config > /dev/null 2>&1; then + cxx=`ncxx-config --cxx` + has_cxx="yes" +fi + +usage() +{ + cat < /dev/null 2>&1; then + cat < /dev/null 2>&1; then + cat < /dev/null 2>&1; then + cat < $cc" + echo " --cflags -> $cflags" + echo " --libs -> $libs" + echo + echo " --has-c++ -> $has_cxx" + echo " --cxx -> $cxx" + echo " --has-c++4 -> $has_cxx4" + echo " --cxx4 -> $cxx4" + echo + echo " --fc -> $fc" + echo " --fflags -> $fflags" + echo " --flibs -> $flibs" + echo " --has-f90 -> $has_f90" + echo + echo " --has-dap -> $has_dap" + echo " --has-nc2 -> $has_nc2" + echo " --has-nc4 -> $has_nc4" + echo " --has-hdf5 -> $has_hdf5" + echo " --has-hdf4 -> $has_hdf4" + echo " --has-pnetcdf-> $has_pnetcdf" + echo " --has-szlib -> $has_szlib" + echo + echo " --prefix -> $prefix" + echo " --includedir-> $includedir" + echo " --version -> $version" + echo +} + +if test $# -eq 0; then + usage 1 +fi + +while test $# -gt 0; do + case "$1" in + # this deals with options in the style + # --option=value and extracts the value part + # [not currently used] + -*=*) value=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;; + *) value= ;; + esac + + case "$1" in + + --help) + usage 0 + ;; + + --all) + all + ;; + + --cc) + echo $cc + ;; + + --cflags) + echo $cflags + ;; + + --has-dap) + echo $has_dap + ;; + + --has-nc2) + echo $has_nc2 + ;; + + --has-nc4) + echo $has_nc4 + ;; + + --has-hdf5) + echo $has_hdf5 + ;; + + --has-hdf4) + echo $has_hdf4 + ;; + + --has-pnetcdf) + echo $has_pnetcdf + ;; + + --has-szlib) + echo $has_szlib + ;; + + --libs) + echo $libs + ;; + + --prefix) + echo "${prefix}" + ;; + + --includedir) + echo "${includedir}" + ;; + + --version) + echo $version + ;; + + --has-c++) + echo $has_cxx + ;; + + --cxx) + echo $cxx + ;; + + --has-c++4) + echo $has_cxx4 + ;; + + --cxx4) + echo $cxx4 + ;; + +# --cxxflags) +# echo $cxxflags +# ;; +# +# --cxxlibs) +# echo $cxxlibs +# ;; + + --fc) + echo $fc + ;; + + --fflags) + echo $fflags + ;; + + --flibs) + echo $flibs + ;; + + --has-f90) + echo $has_f90 + ;; + + *) + echo "unknown option: $1" + usage + exit 1 + ;; + esac + shift +done + +exit 0 -- GitLab From fc9e8883cf68f5abfa52c42b0efa8345ddf68c1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Jan 2014 09:37:35 +0100 Subject: [PATCH 307/566] add easyconfig for netcdf4-python --- ...4-python-1.0.7-ictce-5.5.0-Python-2.7.6.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.0.7-ictce-5.5.0-Python-2.7.6.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.0.7-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.0.7-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..4705fe247a --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.0.7-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,25 @@ +name = 'netcdf4-python' +version = '1.0.7' + +homepage = 'https://code.google.com/p/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +source_urls = ['https://netcdf4-python.googlecode.com/files'] +sources = ['netCDF4-%(version)s.tar.gz'] + +python = 'Python' +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.12'), + ('Cython', '0.19.2', versionsuffix), + ('netCDF', '4.3.0'), +] + +moduleclass = 'data' -- GitLab From 5014d085331114aff1facd5232c735dce0f8ba82 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 17 Jan 2014 11:42:58 +0100 Subject: [PATCH 308/566] Update vsc-mympirun-3.2.1.eb --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 12fd4698df..5aad39eba9 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -2,7 +2,7 @@ easyblock = 'VersionIndependendPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -homepage = 'http://hpcugent.github.com/vsc-mympirun/' +homepage = 'http://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 -- GitLab From 571c40fea5e2d678bfea4b25989c5b6b9f1f6b3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Jan 2014 21:38:41 +0100 Subject: [PATCH 309/566] add easyconfigs for vsc-mympirun-scoop + dependencies --- ...Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb | 33 ++++++++ .../o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb | 25 ++++++ .../PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb | 30 +++++++ .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 84 +++++++++++++++++++ .../SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb | 29 +++++++ .../s/setuptools/setuptools-1.4.2.eb | 19 +++++ .../util-linux/util-linux-2.24-ictce-5.5.0.eb | 27 ++++++ ...un-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 27 ++++++ .../v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- .../v/vsc-mympirun/vsc-mympirun-3.3.0.eb | 27 ++++++ .../vsc-processcontrol-1.0.eb | 22 +++++ .../z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb | 32 +++++++ 12 files changed, 356 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb create mode 100644 easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb 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 new file mode 100644 index 0000000000..ae5c1573ae --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.2' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] +sources = ['%s-%s.zip' % (name.lower(), version)] + +python = "Python" +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +patches = ['Greenlet-%(version)s_icc_no_amd64_predefined_in_prepocessor.patch'] + +sanity_check_paths = { + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb new file mode 100644 index 0000000000..459c7147c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb @@ -0,0 +1,25 @@ +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': 'ictce', 'version': '5.5.0'} + +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-14.0.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..6939bcf426 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,30 @@ +name = 'PyZMQ' +version = '14.0.1' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', '4.0.3'), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000..fa31f87152 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -0,0 +1,84 @@ +name = 'Python' +version = '2.7.6' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.0' +scipyversion = '0.13.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] + +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), + ('libreadline', '6.2'), + ('ncurses', '5.9'), +] + +# order is important! +exts_list = [ + ('setuptools', '1.4.2', { + 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.4.1', { + 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.0', { + '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')], + }), + ('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', '0.19.2', { + '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', '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/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..691005bdb4 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'SCOOP' +version = '0.6.2' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module +allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://scoop.googlecode.com/files/"] +sources = ['%s-%s.release.tar.gz' % (name.lower(), version)] + +python = 'Python' +pythonversion = '2.7.6' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.2', versionsuffix), + ('PyZMQ', '14.0.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s.release-py%(pyv)s.egg' % {'pyv': pythonshortversion}], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb new file mode 100644 index 0000000000..24d2c3cca6 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -0,0 +1,19 @@ +easyblock = "VersionIndependendPythonPackage" + +name = "setuptools" +version = "1.4.2" + +homepage = "http://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/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/easy_install"], + 'dirs': ["lib/setuptools"], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb new file mode 100644 index 0000000000..25c0719157 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -0,0 +1,27 @@ +name = 'util-linux' +version = '2.24' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['%s/v%%(version)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 +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/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..c1d224e11e --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,27 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun-scoop' +version = '3.3.0' + +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': 'ictce', 'version': '5.5.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] + +python = 'Python' +pyver = '2.7.6' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [ + ('vsc-processcontrol', '1.0', '', True), + ('vsc-mympirun', version, '', True), + (python, pyver), + ('SCOOP', '0.6.2', versionsuffix), +] + +options = {'modulename': 'vsc.mympirun.scoop'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 12fd4698df..e2487f31df 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -6,7 +6,7 @@ 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'} +toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [ diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb new file mode 100644 index 0000000000..8a7e36cbc8 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun' +version = '3.3.0' + +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', '1.7.3'), + ('setuptools', '1.4.2'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb new file mode 100644 index 0000000000..a8c92aec1c --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb @@ -0,0 +1,22 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-processcontrol' +version = '1.0' + +homepage = 'http://hpcugent.github.com/vsc-processcontrol/' +description = """vsc-processcontrol is a module to abstract process control like scheduler settings and affinity + from actual implementations like vsc.affintiy and psutil.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'https://github.com/hpcugent/vsc-processcontrol/archive/', +] + +dependencies = [('vsc-base', '1.7.3')] + +options = {'modulename': 'sys; print sys.path; import vsc; print vsc.__path__; import vsc.processcontrol'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..8d73e9399b --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.0.3-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +name = 'ZeroMQ' +version = '4.0.3' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --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', '2.24'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' -- GitLab From d87c075ed8937eda642ff9ce85905a5862ec3f63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Jan 2014 21:53:19 +0100 Subject: [PATCH 310/566] add missing vsc-base v1.7.3 easyconfig, correct easyblock to VersionIndependentPythonPackage --- .../s/setuptools/setuptools-1.4.2.eb | 2 +- .../easyconfigs/v/vsc-base/vsc-base-1.6.9.eb | 3 ++- .../easyconfigs/v/vsc-base/vsc-base-1.7.3.eb | 20 +++++++++++++++++++ .../v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 3 ++- 4 files changed, 25 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index 24d2c3cca6..87db02a9fa 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -1,4 +1,4 @@ -easyblock = "VersionIndependendPythonPackage" +easyblock = "VersionIndependentPythonPackage" name = "setuptools" version = "1.4.2" diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb index 3f28389ec6..e5bcfce5d5 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb @@ -1,4 +1,5 @@ -easyblock = 'VersionIndependendPythonPackage' +easyblock = 'VersionIndependentPythonPackage' + name = 'vsc-base' version = '1.6.9' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb new file mode 100644 index 0000000000..14b2ff9229 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb @@ -0,0 +1,20 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'vsc-base' +version = '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-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index e2487f31df..fb13fb6328 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -1,4 +1,5 @@ -easyblock = 'VersionIndependendPythonPackage' +easyblock = 'VersionIndependentPythonPackage' + name = 'vsc-mympirun' version = '3.2.1' -- GitLab From 662ec34ea25c5b378227594938916142061d8aab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Jan 2014 22:10:05 +0100 Subject: [PATCH 311/566] use VSCPythonPackage easyblock in recent vsc-base easyconfig --- easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb index 14b2ff9229..7f81750f1e 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb @@ -1,4 +1,4 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'VSCPythonPackage' name = 'vsc-base' version = '1.7.3' -- GitLab From dcf3157cbfd44c14465e6ea41b76348e7cf74fe4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Jan 2014 22:12:09 +0100 Subject: [PATCH 312/566] add missing patch file for Greenlet --- ....2_icc_no_amd64_predefined_in_prepocessor.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch new file mode 100644 index 0000000000..fc194827fc --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch @@ -0,0 +1,14 @@ +--- greenlet-0.4.2/slp_platformselect.h.orig 2014-01-06 23:48:38.000000000 +0100 ++++ greenlet-0.4.2/slp_platformselect.h 2014-01-17 17:44:34.793309559 +0100 +@@ -6,9 +6,9 @@ + #include "platform/switch_x86_msvc.h" /* MS Visual Studio on X86 */ + #elif defined(MS_WIN64) && defined(_M_X64) && defined(_MSC_VER) + #include "platform/switch_x64_msvc.h" /* MS Visual Studio on X64 */ +-#elif defined(__GNUC__) && defined(__amd64__) && defined(__ILP32__) ++#elif defined(__GNUC__) && defined(__x86_64__) && defined(__ILP32__) + #include "platform/switch_x32_unix.h" /* gcc on amd64 with x32 ABI */ +-#elif defined(__GNUC__) && defined(__amd64__) ++#elif defined(__GNUC__) && defined(__x86_64__) + #include "platform/switch_amd64_unix.h" /* gcc on amd64 */ + #elif defined(__GNUC__) && defined(__i386__) + #include "platform/switch_x86_unix.h" /* gcc on X86 */ -- GitLab From 61bf0768e6b18bb8472ca3d0a078dcbf33df266b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Jan 2014 22:25:37 +0100 Subject: [PATCH 313/566] fix toolchain spec --- .../easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb index 25c0719157..08d7675cec 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -4,7 +4,7 @@ version = '2.24' homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' description = """Set of Linux utilities""" -toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['%s/v%%(version)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 93aebba7deb33d0b10a65d3546599194a95c530f Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 20 Jan 2014 00:15:51 +0100 Subject: [PATCH 314/566] TREE-PUZZLE-5.2-goolf-1.4.10.eb --- .../TREE-PUZZLE-5.2-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..b8f881674e --- /dev/null +++ b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# 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 = 'TREE-PUZZLE' +version = '5.2' + +homepage = 'http://www.tree-puzzle.de/' +description = """ TREE-PUZZLE is a computer program to reconstruct + phylogenetic trees from molecular sequence data by maximum likelihood. + It implements a fast tree search algorithm, quartet puzzling, that allows + analysis of large data sets and automatically assigns estimations of + support to each internal branch. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.tree-puzzle.de'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/puzzle','bin/ppuzzle'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 29667bb78653de12253532356b44a07e945b7059 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 20 Jan 2014 00:35:06 +0100 Subject: [PATCH 315/566] PhyML-20120412-goolf-1.4.10.eb PhyML-20131016-devel-goolf-1.4.10.eb --- .../p/PhyML/PhyML-20120412-goolf-1.4.10.eb | 29 ++++++++++++++++++ .../PhyML-20131016-devel-goolf-1.4.10.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb new file mode 100644 index 0000000000..b481a07466 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +# 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 = 'PhyML' +version = '20120412' + +homepage = 'http://code.google.com/p/phyml' +description = """ PhyML is a software that estimates maximum likelihood + phylogenies from alignments of nucleotide or amino acid sequences. + The main strength of PhyML lies in the large number of substitution + models coupled to various options to search the space of phylogenetic + tree topologies, going from very fast and efficient methods to slower + but generally more accurate approaches. PhyML was designed to process + moderate to large data sets. In theory, alignments with up to 4,000 + sequences 2,000,000 character-long can be processed. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://phyml.googlecode.com/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/phyml'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb new file mode 100644 index 0000000000..dc9be10790 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# 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 = 'PhyML' +version = '20131016' +versionsuffix = 'devel' + +homepage = 'http://code.google.com/p/phyml' +description = """ PhyML is a software that estimates maximum likelihood + phylogenies from alignments of nucleotide or amino acid sequences. + The main strength of PhyML lies in the large number of substitution + models coupled to various options to search the space of phylogenetic + tree topologies, going from very fast and efficient methods to slower + but generally more accurate approaches. PhyML was designed to process + moderate to large data sets. In theory, alignments with up to 4,000 + sequences 2,000,000 character-long can be processed. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://phyml.googlecode.com/files/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/phyml'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 75250e8176cf7310ced651412438b18544c260d7 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 20 Jan 2014 12:37:15 +0100 Subject: [PATCH 316/566] Added CLooG for Clang --- easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb diff --git a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb new file mode 100644 index 0000000000..8dce651ef0 --- /dev/null +++ b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb @@ -0,0 +1,25 @@ +name = 'CLooG' +version = '0.18.1' + +homepage = 'http://www.bastoul.net/cloog/index.php' +description = """CLooG is a free software and library to generate code for scanning Z-polyhedra. +That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. +CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. +Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best +polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user +has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code. +""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bastoul.net/cloog/pages/download/'] + +dependencies = [('GMP', '5.1.3')] + +sanity_check_paths = { + 'files': ['bin/cloog', 'lib/libcloog-isl.so', 'lib/libisl.so'], + 'dirs': [] +} + +moduleclass = 'compiler' -- GitLab From ac16c2c46b385081497d2896dae4774beb07fcc8 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 21 Jan 2014 11:33:15 +0100 Subject: [PATCH 317/566] Vim-7.4-goolf-1.4.10.eb --- .../easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb new file mode 100644 index 0000000000..a4f2e4dec1 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-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 = 'Vim' +version = '7.4' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks + to provide the power of the de-facto Unix editor 'Vi', + with a more complete feature set. + """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://ftp.vim.org/pub/vim/unix/'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] + +configopts = '--with-features=big --enable-pythoninterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim','bin/vimdiff'], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 41a761125af3d5158833888998d8ead9d27be010 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 21 Jan 2014 15:00:15 +0100 Subject: [PATCH 318/566] Renamed CLooG to include toolchain --- .../c/CLooG/{CLooG-0.18.1.eb => CLooG-0.18.1-GCC-4.8.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/CLooG/{CLooG-0.18.1.eb => CLooG-0.18.1-GCC-4.8.2.eb} (100%) diff --git a/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb b/easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb similarity index 100% rename from easybuild/easyconfigs/c/CLooG/CLooG-0.18.1.eb rename to easybuild/easyconfigs/c/CLooG/CLooG-0.18.1-GCC-4.8.2.eb -- GitLab From 82df8c3dff7de40fd7c606f147fb8c34aafedfef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Jan 2014 16:14:09 +0100 Subject: [PATCH 319/566] fix easyconfigs unit tests after redefining EasyConfig class parameters --- 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 b729fca376..2bc76390b3 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -174,7 +174,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(False, "Obtained software name directly from easyconfig file") # parse easyconfig - ec = EasyConfig(spec, validate=False) + ec = EasyConfig(spec, build_options{'validate': False}) # sanity check for software name self.assertTrue(ec['name'], name) -- GitLab From 2f802ab8e2af5ef77bfbe169854e6cd1983c6ae2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Jan 2014 16:17:25 +0100 Subject: [PATCH 320/566] 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 2bc76390b3..efe935b2c0 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -174,7 +174,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(False, "Obtained software name directly from easyconfig file") # parse easyconfig - ec = EasyConfig(spec, build_options{'validate': False}) + ec = EasyConfig(spec, build_options={'validate': False}) # sanity check for software name self.assertTrue(ec['name'], name) -- GitLab From 099e3ae4ec4dffb354d9edcaa11416a540cb06a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Jan 2014 16:21:01 +0100 Subject: [PATCH 321/566] fix easyconfigs unit tests after redefining EasyBlock class parameters --- 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 efe935b2c0..cbb7158bca 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -186,7 +186,7 @@ def template_easyconfig_test(self, spec): # instantiate easyblock with easyconfig file app_class = get_class(easyblock, name=name) - app = app_class(spec, validate_ec=False) + app = app_class(spec, build_options={'validate_ec': False}) # more sanity checks self.assertTrue(name, app.name) -- GitLab From b710db54852a558dc534265f41eb29e730267273 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 21 Jan 2014 16:57:15 +0100 Subject: [PATCH 322/566] Clang: build with polly by default --- easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb | 2 ++ easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb | 2 ++ easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb | 6 ++++++ 3 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb b/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb index c103be3881..36fb222244 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.2-GCC-4.7.3.eb @@ -43,3 +43,5 @@ languages = ['c', 'c++'] moduleclass = 'compiler' assertions = False + +usepolly = False diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb b/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb index 9f1a57dbbc..e498edc086 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.3-GCC-4.8.1.eb @@ -50,3 +50,5 @@ moduleclass = 'compiler' assertions = False build_targets = ['X86'] + +usepolly = False diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index b1cd63b2ee..5a750d9a0c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -26,6 +26,7 @@ sources = [ "llvm-%(version)s.src.tar.gz", "clang-%(version)s.src.tar.gz", "compiler-rt-%(version)s.src.tar.gz", + "polly-%(version)s.src.tar.gz", ] patches = [ @@ -39,6 +40,11 @@ patches = [ builddependencies = [('CMake', '2.8.12')] +dependencies = [ + ('GMP', '5.1.3'), + ('CLooG', '0.18.1'), +] + sanity_check_paths = { 'files': ['bin/clang', 'bin/clang++', 'lib/libclang.so', 'lib/clang/%(version)s/include/stddef.h'], 'dirs': [], -- GitLab From a23bb7e68c1472e6d82799c22dfb65167ecb330e Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 22 Jan 2014 17:20:48 +0100 Subject: [PATCH 323/566] Clustal-Omega-1.2.0-goolf-1.4.10.eb and argtable-2.13-goolf-1.4.10.eb for dependencies --- .../a/argtable/argtable-2.13-goolf-1.4.10.eb | 23 ++++++++++++++++ .../Clustal-Omega-1.2.0-goolf-1.4.10.eb | 27 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb new file mode 100644 index 0000000000..9dae0dc5da --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +# 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 = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.','-'))] + +sanity_check_paths = { + 'files': ['lib/libargtable2.so', 'lib/libargtable2.la'], + 'dirs': ['include', 'lib', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..ccd77d5af9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-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 = 'Clustal-Omega' +version = '1.2.0' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +dependencies = [('argtable', '2.13')] + +source_urls = ['http://www.clustal.org/omega/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 930ac5d3852703ce886c97c879d3569d5f97939a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jan 2014 17:24:18 +0100 Subject: [PATCH 324/566] add SuiteSparse easyconfigs + ParMETIS deps --- .../p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb | 22 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb | 22 +++++++++++++++++++ ...parse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb | 18 +++++++++++++++ ...Sparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb | 18 +++++++++++++++ ...parse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb | 18 +++++++++++++++ ...Sparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb | 18 +++++++++++++++ 6 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..c745675e3d --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, +meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes +routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in +ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning +schemes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000..6c8b6f15d8 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, +meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes +routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in +ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning +schemes.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('CMake', '2.8.12')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..62896760f1 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-goolf-1.4.10-ParMETIS-4.0.3.eb @@ -0,0 +1,18 @@ +name = 'SuiteSparse' +version = '3.7.1' + +homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +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' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..02396e3728 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-3.7.1-ictce-5.5.0-ParMETIS-4.0.3.eb @@ -0,0 +1,18 @@ +name = 'SuiteSparse' +version = '3.7.1' + +homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +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' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..1193a31b09 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-goolf-1.4.10-ParMETIS-4.0.3.eb @@ -0,0 +1,18 @@ +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': '1.4.10'} +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' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000..c537c65755 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.2.1-ictce-5.5.0-ParMETIS-4.0.3.eb @@ -0,0 +1,18 @@ +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': 'ictce', 'version': '5.5.0'} +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 48936e279758e541f1da7b24f991f807cc330118 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 22 Jan 2014 20:22:32 +0100 Subject: [PATCH 325/566] changed --with-features=big to --with-features=huge --- easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index a4f2e4dec1..e305c94bc2 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['ftp://ftp.vim.org/pub/vim/unix/'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -configopts = '--with-features=big --enable-pythoninterp=yes' +configopts = '--with-features=huge --enable-pythoninterp=yes' sanity_check_paths = { 'files': ['bin/vim','bin/vimdiff'], -- GitLab From b37f7a81b30814b3bf637e642523862078f4930e Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 23 Jan 2014 14:26:41 +0100 Subject: [PATCH 326/566] -no-OFED does not care about libib packages Signed-off-by: Fotis Georgatos --- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index f366dc6b28..6d2e812c6e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -15,13 +15,6 @@ patches = ['pax_disable.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' 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'] - sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", -- GitLab From ac61d1da47d5b24f4db67b921ae773b557515127 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Jan 2014 22:39:21 +0100 Subject: [PATCH 327/566] fix use of process_easyconfig in unit 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 cbb7158bca..f26b87817f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -79,7 +79,7 @@ class EasyConfigTest(TestCase): # parse all easyconfigs easyconfigs = [] for spec in specs: - easyconfigs.extend(process_easyconfig(spec, validate=False)) + easyconfigs.extend(process_easyconfig(spec, build_options={'validate': False})) self.ordered_specs = resolve_dependencies(easyconfigs, easyconfigs_path, force=True) -- GitLab From ac187110d3cafea4577fcfc55b259c9e65c492fe Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 24 Jan 2014 02:45:11 +0100 Subject: [PATCH 328/566] no-OFEDs, no ib, simple Signed-off-by: Fotis Georgatos --- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 7 ------- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 7 ------- 2 files changed, 14 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index e7e5ad26b4..ea1c8c9999 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -16,13 +16,6 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple 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 -# 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, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 947361f584..35d42cd257 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -16,13 +16,6 @@ configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple 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 -# 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, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", -- GitLab From a4e1133230217a2689b1854919d082f1d9174ca7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jan 2014 06:58:14 +0100 Subject: [PATCH 329/566] fix use of resolve_dependencies --- test/easyconfigs/easyconfigs.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f26b87817f..c7a289a50f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -81,7 +81,11 @@ class EasyConfigTest(TestCase): for spec in specs: easyconfigs.extend(process_easyconfig(spec, build_options={'validate': False})) - self.ordered_specs = resolve_dependencies(easyconfigs, easyconfigs_path, force=True) + build_options = { + 'robot_path': easyconfigs_path, + 'force': True, + } + self.ordered_specs = resolve_dependencies(easyconfigs, build_options=build_options) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" -- GitLab From 4caa17e4465553e8f205d1e40269ec0b05801e06 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 24 Jan 2014 16:41:07 +0100 Subject: [PATCH 330/566] switch ftp url to http contracted the description to just two lines switched to template: SOURCELOWER_TAR_BZ2 --- easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index e305c94bc2..4e71923e57 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -7,15 +7,13 @@ name = 'Vim' version = '7.4' homepage = 'http://www.vim.org' -description = """ Vim is an advanced text editor that seeks - to provide the power of the de-facto Unix editor 'Vi', - with a more complete feature set. - """ +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://ftp.vim.org/pub/vim/unix/'] -sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = ['http://ftp.vim.org/pub/vim/unix/'] +sources = ['SOURCELOWER_TAR_BZ2'] configopts = '--with-features=huge --enable-pythoninterp=yes' -- GitLab From b39d366c92179eab7f7401b7ee33505217d45011 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 24 Jan 2014 16:49:49 +0100 Subject: [PATCH 331/566] added perl and python support and required dependencies --- easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index 4e71923e57..9a94ed943c 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -15,7 +15,14 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://ftp.vim.org/pub/vim/unix/'] sources = ['SOURCELOWER_TAR_BZ2'] -configopts = '--with-features=huge --enable-pythoninterp=yes' +# this dependencies are required for --enable-pythoninterp=yes and --enable-perlinterp=yes to work +# check enabled features running "vim --version" after compilation +dependencies = [ + ('Python', '2.7.5'), + ('Perl', '5.16.3') + ] + +configopts = '--with-features=huge --enable-pythoninterp=yes --enable-perlinterp=yes' sanity_check_paths = { 'files': ['bin/vim','bin/vimdiff'], -- GitLab From 004ee0a29f740d91ec7773a8d70dd1050e082dda Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 24 Jan 2014 16:54:30 +0100 Subject: [PATCH 332/566] fixed typo --- easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb index 9a94ed943c..6d3e505fff 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-7.4-goolf-1.4.10.eb @@ -13,7 +13,7 @@ description = """ Vim is an advanced text editor that seeks to provide the power toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://ftp.vim.org/pub/vim/unix/'] -sources = ['SOURCELOWER_TAR_BZ2'] +sources = [SOURCELOWER_TAR_BZ2] # this dependencies are required for --enable-pythoninterp=yes and --enable-perlinterp=yes to work # check enabled features running "vim --version" after compilation -- GitLab From 3cb5aee3a7db9dc247595da013c56c964f90e580 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 24 Jan 2014 17:20:06 +0100 Subject: [PATCH 333/566] changed: source_urls = [homepage] and sources = [SOURCELOWER_TAR_GZ] --- .../c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb index ccd77d5af9..ec43e8ac61 100644 --- a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-goolf-1.4.10.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [('argtable', '2.13')] -source_urls = ['http://www.clustal.org/omega/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/clustalo'], -- GitLab From 52eeb2d958e4a4026e1b203ac4bef8c369064e4e Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 24 Jan 2014 17:30:50 +0100 Subject: [PATCH 334/566] switched to template SOURCELOWER_TAR_GZ --- easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb index b481a07466..a63b23cc20 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20120412-goolf-1.4.10.eb @@ -19,7 +19,7 @@ description = """ PhyML is a software that estimates maximum likelihood toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://phyml.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/phyml'], diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb index dc9be10790..4e9e600420 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-20131016-devel-goolf-1.4.10.eb @@ -20,7 +20,7 @@ description = """ PhyML is a software that estimates maximum likelihood toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://phyml.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] sanity_check_paths = { 'files': ['bin/phyml'], -- GitLab From 712628992543a89d6f71142a261a50b98a39b3cf Mon Sep 17 00:00:00 2001 From: jhale Date: Fri, 24 Jan 2014 21:44:09 +0100 Subject: [PATCH 335/566] Add new URL for Qt source download --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb | 3 ++- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 3 ++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index e9b04c5257..4aa2994cd6 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index 76d6056244..99561006f5 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -6,7 +6,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index 645d28151d..295259e31e 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -6,7 +6,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 7c847a9b40..0af92be3f4 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -7,7 +7,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] # enforce use of -O1, required because of compiler bug that triggers 'internal error: 0_381' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index 3f8dd7b9f5..e294af2d8b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -6,7 +6,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 56cdaa29b3..ff0c690069 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -6,7 +6,8 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://origin.releases.qt-project.org/qt4/source/'] +backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] -- GitLab From c1a19c3e47b0f58413210c5f5bf4b7666d3931cc Mon Sep 17 00:00:00 2001 From: Adam DeConinck Date: Fri, 24 Jan 2014 18:15:29 -0800 Subject: [PATCH 336/566] Add easyconfig for nodejs 0.10.24 --- .../n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb new file mode 100644 index 0000000000..7bcd02f7e6 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# It was auto-generated based on a template easyconfig, so it should be used with care. + +name = 'nodejs' +version = '0.10.24' + +homepage = 'http://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['node-v%(version)s.tar.gz'] +source_urls = ['http://nodejs.org/dist/v%(version)s/'] + +dependencies = [('Python','2.7.5')] +builddependencies = [('Python','2.7.5')] + +# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories +sanity_check_paths = { + 'files': ["bin/node", "bin/npm", ], + 'dirs': ["lib/node_modules", "lib/dtrace", "include/node"] +} + +# You SHOULD change the following line; Kindly consult other easyconfigs for possible options +moduleclass = 'lang' -- GitLab From c6281207bfe3bff305a71cae5e353a7ebb3d2c91 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 25 Jan 2014 17:45:22 +0100 Subject: [PATCH 337/566] source_urls = [homepage] --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index 129a0d9043..b608cfdee4 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -15,7 +15,7 @@ description = """MAFFT is a multiple sequence alignment program toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://mafft.cbrc.jp/alignment/software/'] +source_urls = [homepage] sources = ['%(namelower)s-%(version)s-%(versionsuffix)s-src.tgz'] skipsteps = ['configure'] -- GitLab From 290b8804de2542a0a9c05e18120dcd2d80c23d49 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 26 Jan 2014 00:30:21 +0100 Subject: [PATCH 338/566] sources = [SOURCELOWER_TAR_GZ] && parallel=1 --- .../t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb index b8f881674e..c0af373e76 100644 --- a/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/TREE-PUZZLE/TREE-PUZZLE-5.2-goolf-1.4.10.eb @@ -15,11 +15,14 @@ description = """ TREE-PUZZLE is a computer program to reconstruct toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://www.tree-puzzle.de'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +# build with just 1 cpu to avoid errors +parallel = 1 sanity_check_paths = { - 'files': ['bin/puzzle','bin/ppuzzle'], + 'files': ['bin/puzzle', 'bin/ppuzzle'], 'dirs': [], } -- GitLab From 53c3cc9f91a0d5b32ce19f2ebe308df13d86b7d6 Mon Sep 17 00:00:00 2001 From: Adam DeConinck Date: Sun, 26 Jan 2014 17:52:31 -0800 Subject: [PATCH 339/566] Cleanup nodejs easyconfig --- .../n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb | 15 +++++---------- .../v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb index 7bcd02f7e6..9c91472a53 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-0.10.24-goolf-1.4.10.eb @@ -1,29 +1,24 @@ -# Note: -# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# It was auto-generated based on a template easyconfig, so it should be used with care. - name = 'nodejs' version = '0.10.24' homepage = 'http://nodejs.org' + description = """Node.js is a platform built on Chrome's JavaScript runtime - for easily building fast, scalable network applications. Node.js uses an - event-driven, non-blocking I/O model that makes it lightweight and efficient, - perfect for data-intensive real-time applications that run across distributed devices.""" + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['node-v%(version)s.tar.gz'] + source_urls = ['http://nodejs.org/dist/v%(version)s/'] dependencies = [('Python','2.7.5')] -builddependencies = [('Python','2.7.5')] -# The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories sanity_check_paths = { 'files': ["bin/node", "bin/npm", ], 'dirs': ["lib/node_modules", "lib/dtrace", "include/node"] } -# You SHOULD change the following line; Kindly consult other easyconfigs for possible options moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 12fd4698df..5aad39eba9 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -2,7 +2,7 @@ easyblock = 'VersionIndependendPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -homepage = 'http://hpcugent.github.com/vsc-mympirun/' +homepage = 'http://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 -- GitLab From 60a3a3e80253de129333ae0e57868ab88113c92b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 27 Jan 2014 14:55:11 +0100 Subject: [PATCH 340/566] =?UTF-8?q?Support=20protobuf=20("Google=20Protoco?= =?UTF-8?q?l=20Buffers")=20=E2=80=A6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 2.5.0 is the latest version. 2.4.0a is required by Hadoop-2.0.0-cdh4.5.0. --- .../p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb | 17 +++++++++++++++++ .../p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb new file mode 100644 index 0000000000..506350152b --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb @@ -0,0 +1,17 @@ +name = 'protobuf' +version = '2.4.0a' + +homepage = 'https://code.google.com/p/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://protobuf.googlecode.com/files/'] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..149c94d9e7 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb @@ -0,0 +1,17 @@ +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://code.google.com/p/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://protobuf.googlecode.com/files/'] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [] +} + +moduleclass = 'devel' -- GitLab From 52dbabad2755ca2bbbe1130fc238a98d50a40fdf Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 17 Jan 2014 11:42:58 +0100 Subject: [PATCH 341/566] Update vsc-mympirun-3.2.1.eb --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 12fd4698df..5aad39eba9 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -2,7 +2,7 @@ easyblock = 'VersionIndependendPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -homepage = 'http://hpcugent.github.com/vsc-mympirun/' +homepage = 'http://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 -- GitLab From 95ff1981dc503f602400c8b70015f66ad49ea9ac Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 30 Jan 2014 03:12:00 +0100 Subject: [PATCH 342/566] fix modextrapaths for Chapel as needed Signed-off-by: Fotis Georgatos --- .../easyconfigs/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb | 5 +++++ easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb | 5 +++++ easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb | 5 +++++ easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb | 5 +++++ easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb | 5 +++++ 5 files changed, 25 insertions(+) diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb index 74971c2b92..0ecf5d3f45 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goalf-1.1.0-no-OFED.eb @@ -28,4 +28,9 @@ unpack_options = '--strip-components=1' parallel = 1 # parallel build may fail +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb index 8699640db2..93406cb2aa 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.6.0-goolf-1.4.10.eb @@ -29,4 +29,9 @@ unpack_options = '--strip-components=1' # parallel build fails parallel = 1 +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb index a7621be492..cfdb1760fd 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.7.0-goolf-1.4.10.eb @@ -29,4 +29,9 @@ unpack_options = '--strip-components=1' # parallel build fails parallel = 1 +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb index e1b2b7b42c..cb35b40757 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.4.10.eb @@ -37,4 +37,9 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb index 388ed0d1a5..287a7c1d2b 100644 --- a/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb +++ b/easybuild/easyconfigs/c/Chapel/Chapel-1.8.0-goolf-1.6.10.eb @@ -37,4 +37,9 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'PATH': 'util', + 'CHPL_HOME': '', +} + moduleclass = 'lang' -- GitLab From d6fa0ff85c2bf50b217cca90dad6b8a26128c0c6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 13:58:01 +0100 Subject: [PATCH 343/566] HDF5: updated to 1.8.12 with ictce-5.5.0 --- .../h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb | 21 +++++++++++++++++++ .../s/Szip/Szip-2.1-ictce-5.5.0.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb new file mode 100644 index 0000000000..0edef61eb4 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.12' + +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +patches = ['configure_libtool.patch'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.5.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..d2fa1bb4ae --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.5.0.eb @@ -0,0 +1,21 @@ +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': 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' -- GitLab From 0741474cdc0c3405bb415a798d7baa13292523b6 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 13:58:55 +0100 Subject: [PATCH 344/566] h5py: updated to 2.2.1 with ictce 5.5.0 --- .../h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb new file mode 100644 index 0000000000..9f0f4603f5 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.2.1' + +homepage = 'http://code.google.com/p/h5py/' +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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'usempi': True} + +source_urls = ['http://h5py.googlecode.com/files/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.5' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('HDF5', '1.8.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], +} + +moduleclass = 'data' -- GitLab From 3008b5694d08c230d38ebefef07fd45fbd4ea746 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 14:33:52 +0100 Subject: [PATCH 345/566] mpi4py: new version and new download url --- .../mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb new file mode 100644 index 0000000000..10bcd119a6 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3.1' + +homepage = 'https://code.google.com/p/mpi4py/' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'mpi' -- GitLab From 2e95bf8198455dd6cf323cb34cc7adc9b6937c7a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 14:36:24 +0100 Subject: [PATCH 346/566] mpi4py: correct homepage url --- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 10bcd119a6..07e1ecd0dc 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'mpi4py' version = '1.3.1' -homepage = 'https://code.google.com/p/mpi4py/' +homepage = 'https://bitbucket.org/mpi4py/mpi4py' description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.""" -- GitLab From e02e1137996fc9d58be47c7c4e415e5500a337ce Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 14:52:42 +0100 Subject: [PATCH 347/566] HDF5: use MPI --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb index 0edef61eb4..1e14350d7c 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb @@ -6,7 +6,7 @@ description = """HDF5 is a unique technology suite that makes possible the manag extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 35c6875943c24cfe689600acbd38624f3ca42b2b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 18:23:26 +0100 Subject: [PATCH 348/566] Greenlet updated to 0.4.2 with ictce-5.5.0 --- ...Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb | 39 +++++++++++++++++++ ...md64_predefined_in_prepocessor-0.4.2.patch | 11 ++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb create mode 100644 easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb new file mode 100644 index 0000000000..2de415b2d7 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'Greenlet' +version = '0.4.2' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that + supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single + or a few OS-level threads) and are synchronized with data exchanges on "channels". + A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit + scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +python = "Python" +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ] + +patches = [ + 'icc_no_amd64_predefined_in_prepocessor-%(version)s.patch', + ] + +sanity_check_paths = { + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, + ], + 'dirs': [] + } + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch b/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch new file mode 100644 index 0000000000..0afb624caf --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch @@ -0,0 +1,11 @@ +--- slp_platformselect.h.orig 2014-01-06 23:48:38.000000000 +0100 ++++ slp_platformselect.h 2014-01-31 18:05:36.125349420 +0100 +@@ -8,7 +8,7 @@ + #include "platform/switch_x64_msvc.h" /* MS Visual Studio on X64 */ + #elif defined(__GNUC__) && defined(__amd64__) && defined(__ILP32__) + #include "platform/switch_x32_unix.h" /* gcc on amd64 with x32 ABI */ +-#elif defined(__GNUC__) && defined(__amd64__) ++#elif defined(__GNUC__) && defined(__x86_64__) + #include "platform/switch_amd64_unix.h" /* gcc on amd64 */ + #elif defined(__GNUC__) && defined(__i386__) + #include "platform/switch_x86_unix.h" /* gcc on X86 */ -- GitLab From 8bd00dac229a588a187e8518dfa7b9594de20d3c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 18:24:27 +0100 Subject: [PATCH 349/566] Update PyZMQ to python 2.7.5 with ictce-5.5.0 --- .../o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb | 26 +++++++++++++++ ...Q-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb | 31 +++++++++++++++++ .../util-linux-2.24.1-ictce-5.5.0.eb | 30 +++++++++++++++++ .../z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb | 33 +++++++++++++++++++ 4 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb new file mode 100644 index 0000000000..d23dd609d1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb @@ -0,0 +1,26 @@ +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': 'ictce', 'version': '5.5.0'} + +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-ictce-5.5.0-Python-2.7.5-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb new file mode 100644 index 0000000000..398114576d --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.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': 'ictce', 'version': '5.5.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[0:2]) +zmqversion = '2.2.0' + +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-2.24.1-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..533a0dcc2f --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb @@ -0,0 +1,30 @@ +name = 'util-linux' +version = '2.24.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +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 +# 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='${prefix}/share/bash-completion/completions' " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'] + } + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..cb028a5c0d --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb @@ -0,0 +1,33 @@ +name = 'ZeroMQ' +version = '2.2.0' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.24.1') + ] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'] + } + +moduleclass = 'devel' -- GitLab From eda90d1ba8279b8ed58a3bed1443e74b9d6f1613 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 31 Jan 2014 18:24:54 +0100 Subject: [PATCH 350/566] SCOOP: updated to 0.6.2 with ictce-5.5.0 --- .../SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb new file mode 100644 index 0000000000..cedd07f1dd --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'SCOOP' +version = '0.6.2' + +homepage = 'http://code.google.com/p/scoop/' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ["http://scoop.googlecode.com/files/"] +sources = ["%(namelower)s-%(version)s.release.tar.gz"] + +python = 'Python' +pythonversion = '2.7.5' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +versionsuffix = '-%s-%s' % (python, pythonversion) +zmqapi = 2 + +dependencies = [ + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.2', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), + ] + +sanity_check_paths = { + 'dirs': [], + 'files': [('lib/python%(pyv)s/site-packages/' + 'scoop-%(version)s.release-py%(pyv)s.egg') % + {'pyv': pythonshortversion, + 'version': version } + ] + } + +moduleclass = 'tools' -- GitLab From abc3c1be285ef5689f74d9bfba71b008d6009b32 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 3 Feb 2014 10:43:32 +0100 Subject: [PATCH 351/566] Added GMP with GCC-4.8.2 for Clang --- .../easyconfigs/g/GMP/GMP-5.1.3-GCC-4.8.2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.3-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.3-GCC-4.8.2.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-GCC-4.8.2.eb new file mode 100644 index 0000000000..191277eee5 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.3-GCC-4.8.2.eb @@ -0,0 +1,23 @@ +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': 'GCC', 'version': '4.8.2'} + +sources = [SOURCELOWER_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 59746bf234a1c8d8264806c259de66b9085fd406 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 4 Feb 2014 11:52:33 +0100 Subject: [PATCH 352/566] h5py: now actually with mpi support --- .../h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb index 9f0f4603f5..5419efd76b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'h5py' version = '2.2.1' -homepage = 'http://code.google.com/p/h5py/' +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.""" @@ -11,7 +11,7 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'usempi': True} -source_urls = ['http://h5py.googlecode.com/files/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' @@ -19,9 +19,12 @@ pythonver = '2.7.5' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +installopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.12'), + ('mpi4py', '1.3.1', versionsuffix), ] sanity_check_paths = { -- GitLab From 30eb849ea179e8587bafdcb8560aa9f4326d407d Mon Sep 17 00:00:00 2001 From: Forai Date: Wed, 5 Feb 2014 15:26:04 +0100 Subject: [PATCH 353/566] SOAPdenovo2 --- .../SOAPdenovo2-2.40-goolf-1.4.10.eb | 41 +++++++++++++++++ .../SOAPdenovo2-2.40-ictce-5.3.0.eb | 40 +++++++++++++++++ .../s/SOAPdenovo2/fix-unistd-includes.patch | 44 +++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb new file mode 100644 index 0000000000..d2d7ca3568 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = '240' + +homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' +description = """SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +patches = ['fix-unistd-includes.patch'] + + +# like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz +sources = ['%s-src-r%s.tgz' % (name, version)] +source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] + + +maxparallel=1 + + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], + 'dirs': [], +} + + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb new file mode 100644 index 0000000000..a023adde1e --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb @@ -0,0 +1,40 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = '240' + +homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' +description = """SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +patches = ['fix-unistd-includes.patch'] + + +# like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz +sources = ['%s-src-r%s.tgz' % (name, version)] +source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] + + +maxparallel=1 + + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], + 'dirs': [], +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch b/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch new file mode 100644 index 0000000000..eafb78fe83 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch @@ -0,0 +1,44 @@ +diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/build_preArc.cpp SOAPdenovo2-src-r240/sparsePregraph/build_preArc.cpp +--- SOAPdenovo2-src-r240.orig/sparsePregraph/build_preArc.cpp 2013-11-11 11:03:42.236283000 +0100 ++++ SOAPdenovo2-src-r240/sparsePregraph/build_preArc.cpp 2013-11-11 11:12:22.841393000 +0100 +@@ -21,12 +21,14 @@ + */ + + ++#include + #include "stdinc.h" + #include "build_preArc.h" + #include "seq_util.h" + #include "global.h" + #include "multi_threads.h" + ++ + #include + #include "bam.h" + #include "faidx.h" +diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/multi_threads.cpp SOAPdenovo2-src-r240/sparsePregraph/multi_threads.cpp +--- SOAPdenovo2-src-r240.orig/sparsePregraph/multi_threads.cpp 2013-11-11 11:03:41.749247000 +0100 ++++ SOAPdenovo2-src-r240/sparsePregraph/multi_threads.cpp 2013-11-11 11:10:04.695845000 +0100 +@@ -20,6 +20,7 @@ + * + */ + ++#include + #include "multi_threads.h" + #include "global.h" + #include "build_graph.h" +Only in SOAPdenovo2-src-r240/sparsePregraph: multi_threads.cpp.orig +diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp +--- SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:03:42.243266000 +0100 ++++ SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:10:30.945711000 +0100 +@@ -20,6 +20,7 @@ + * + */ + ++#include + #include "global.h" + #include "stdinc.h" + #include "core.h" +Only in SOAPdenovo2-src-r240/sparsePregraph: pregraph_sparse.cpp.orig +Only in SOAPdenovo2-src-r240/sparsePregraph: pregraph_sparse.cpp.rej +Only in SOAPdenovo2-src-r240.orig: uninstd-h-fix.h -- GitLab From 41b560a8d99214f2c4a2492c7e32e73c666404e3 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 5 Feb 2014 16:16:33 +0100 Subject: [PATCH 354/566] fix quote business Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb | 2 +- easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb index eed358ec55..f08911ac1e 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb @@ -7,7 +7,7 @@ version = '1.3.0' homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' description = """Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, - with extensions for "single program, multiple data" (SPMD) programming. + with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.""" diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb index 1cb61c35ec..384c54d6b1 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb @@ -7,7 +7,7 @@ version = '1.5.0' homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' description = """Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, - with extensions for "single program, multiple data" (SPMD) programming. + with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.""" -- GitLab From add37d47dd6ae004fcb237ca970fecf61f0b7d3f Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Wed, 5 Feb 2014 16:21:45 +0100 Subject: [PATCH 355/566] fix quotes in descriptions, for Lmod cache compatibility Signed-off-by: Fotis Georgatos --- .../Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 6 +++--- .../g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb | 6 +++--- .../g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb | 6 +++--- .../g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb | 6 +++--- .../g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb | 2 +- .../i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb | 2 +- .../easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb | 2 +- .../easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb | 2 +- .../p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb | 2 +- .../easyconfigs/p/Primer3/Primer3-2.3.0-goolf-1.4.10.eb | 2 +- .../easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb | 2 +- .../easyconfigs/p/Primer3/Primer3-2.3.0-ictce-5.3.0.eb | 2 +- .../x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb | 2 +- .../easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb | 2 +- .../easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb | 2 +- .../easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb | 2 +- 23 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d24861f722..e0ef726298 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -5,9 +5,9 @@ version = '0.4.0' homepage = 'https://github.com/python-greenlet/greenlet' description = """The greenlet package is a spin-off of Stackless, a version of CPython that - supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single - or a few OS-level threads) and are synchronized with data exchanges on "channels". - A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit + supports micro-threads called 'tasklets'. Tasklets run pseudo-concurrently (typically in a single + or a few OS-level threads) and are synchronized with data exchanges on 'channels'. + A 'greenlet', on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb index 59de038289..54a12ec5a6 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,9 +5,9 @@ version = '0.4.0' homepage = 'https://github.com/python-greenlet/greenlet' description = """The greenlet package is a spin-off of Stackless, a version of CPython that -supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single -or a few OS-level threads) and are synchronized with data exchanges on "channels". -A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +supports micro-threads called 'tasklets'. Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on 'channels'. +A 'greenlet', on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. """ toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb index 079811b174..d97e5f360a 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -5,9 +5,9 @@ version = '0.4.0' homepage = 'https://github.com/python-greenlet/greenlet' description = """The greenlet package is a spin-off of Stackless, a version of CPython that - supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single - or a few OS-level threads) and are synchronized with data exchanges on "channels". - A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit + supports micro-threads called 'tasklets'. Tasklets run pseudo-concurrently (typically in a single + or a few OS-level threads) and are synchronized with data exchanges on 'channels'. + A 'greenlet', on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb index 49b94ba41f..8daf2640d5 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb @@ -5,9 +5,9 @@ version = '0.4.0' homepage = 'https://github.com/python-greenlet/greenlet' description = """The greenlet package is a spin-off of Stackless, a version of CPython that - supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single - or a few OS-level threads) and are synchronized with data exchanges on "channels". - A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit + supports micro-threads called 'tasklets'. Tasklets run pseudo-concurrently (typically in a single + or a few OS-level threads) and are synchronized with data exchanges on 'channels'. + A 'greenlet', on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb index 1f22264a23..dc7e4b916a 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.2.3' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb index f03d5ac65f..5636300f58 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goolf-1.4.10.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.2.3' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb index e5c7bb899d..d473bf8554 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.2.3' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb index 64379dcbec..c370646492 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-5.3.0.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.2.3' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb index cd304a31b0..fca617a485 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.4.0' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb index 4780aece0d..ac31ff9416 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-5.3.0.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.4.0' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb index 568873fa47..f664330089 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb @@ -2,7 +2,7 @@ name = 'g2clib' version = '1.4.0' homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ("C" version).""" +description = """Library contains GRIB2 encoder/decoder ('C' version).""" toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'opt': True} diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb index f2c8d1274e..d3db545e1a 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goalf-1.1.0-no-OFED.eb @@ -14,7 +14,7 @@ name = 'Infernal' version = '1.1rc1' homepage = 'http://infernal.janelia.org/' -description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +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'} 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 25d1562163..51e22a99b8 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 @@ -14,7 +14,7 @@ name = 'Infernal' version = '1.1rc1' homepage = 'http://infernal.janelia.org/' -description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +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} diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb index 81e6ea4a46..49c4ff18a2 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-4.0.6.eb @@ -14,7 +14,7 @@ name = 'Infernal' version = '1.1rc1' homepage = 'http://infernal.janelia.org/' -description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +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'} 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 14693175a9..e9de6ee650 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 @@ -14,7 +14,7 @@ name = 'Infernal' version = '1.1rc1' homepage = 'http://infernal.janelia.org/' -description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +description = """Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.""" diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb index 642cc1ae68..e193532b76 100644 --- a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goalf-1.1.0-no-OFED.eb @@ -2,7 +2,7 @@ name = 'Primer3' version = '2.3.0' homepage = 'http://primer3.sourceforge.net' -description = """Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). +description = """Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.""" diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goolf-1.4.10.eb index f23e805270..744c1f126c 100644 --- a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-goolf-1.4.10.eb @@ -2,7 +2,7 @@ name = 'Primer3' version = '2.3.0' homepage = 'http://primer3.sourceforge.net' -description = """Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). +description = """Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.""" diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb index c6d73b18f6..cfa0ccd59d 100644 --- a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-4.0.6.eb @@ -2,7 +2,7 @@ name = 'Primer3' version = '2.3.0' homepage = 'http://primer3.sourceforge.net' -description = """Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). +description = """Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.""" diff --git a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-5.3.0.eb index 1596c5404e..a79e65bdea 100644 --- a/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Primer3/Primer3-2.3.0-ictce-5.3.0.eb @@ -2,7 +2,7 @@ name = 'Primer3' version = '2.3.0' homepage = 'http://primer3.sourceforge.net' -description = """Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). +description = """Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.""" diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb index 842e1cde97..dfbf3d0849 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb @@ -3,7 +3,7 @@ version = '3.95-0.1' homepage = 'http://cran.r-project.org/web/packages/XML' description = """This package provides many approaches for both reading and creating XML (and HTML) documents - (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".""" + (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath 'interpreter'.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb index dbd5ba5e89..366fa8a2aa 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb @@ -3,7 +3,7 @@ version = '3.95-0.1' homepage = 'http://cran.r-project.org/web/packages/XML' description = """This package provides many approaches for both reading and creating XML (and HTML) documents -(including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".""" +(including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath 'interpreter'.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb index 67a54f40cd..695f7960bc 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb @@ -3,7 +3,7 @@ version = '3.95-0.1' homepage = 'http://cran.r-project.org/web/packages/XML' description = """This package provides many approaches for both reading and creating XML (and HTML) documents - (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".""" + (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath 'interpreter'.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb index 16a2b8f853..e5358dc0d2 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb @@ -3,7 +3,7 @@ version = '3.95-0.1' homepage = 'http://cran.r-project.org/web/packages/XML' description = """This package provides many approaches for both reading and creating XML (and HTML) documents - (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter".""" + (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath 'interpreter'.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -- GitLab From c01edc3eaf7c33c7cc8e85d533ffe4391f7825a6 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 5 Feb 2014 17:26:24 +0100 Subject: [PATCH 356/566] FASTX-Toolkit-0.0.14-goolf-1.4.10.eb --- .../FASTX-Toolkit-0.0.14-goolf-1.4.10.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb new file mode 100644 index 0000000000..4bc8783a8a --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb @@ -0,0 +1,43 @@ +## +# 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 = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools +for Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +altname = name.lower().replace('-','_') +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['%s-%s.tar.bz2' % (altname, version)] + +dependencies = [('libgtextutils', '0.6.1')]; + +sanity_check_paths = { + 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', + 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', + 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', + 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', + 'to_fasta', 'quality_filter', 'quality_trimmer', + 'masker']], + 'dirs': ['.'] + } + +moduleclass = 'bio' -- GitLab From ccd0dbc800450287c78b1e7023053fb243774b34 Mon Sep 17 00:00:00 2001 From: Forai Date: Thu, 6 Feb 2014 13:47:50 +0100 Subject: [PATCH 357/566] removed superfluous lines in patch. --- easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch b/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch index eafb78fe83..5813a42d62 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch +++ b/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch @@ -27,7 +27,6 @@ diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/multi_threads.cpp SOAPden #include "multi_threads.h" #include "global.h" #include "build_graph.h" -Only in SOAPdenovo2-src-r240/sparsePregraph: multi_threads.cpp.orig diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp --- SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:03:42.243266000 +0100 +++ SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:10:30.945711000 +0100 @@ -39,6 +38,3 @@ diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp SOAPd #include "global.h" #include "stdinc.h" #include "core.h" -Only in SOAPdenovo2-src-r240/sparsePregraph: pregraph_sparse.cpp.orig -Only in SOAPdenovo2-src-r240/sparsePregraph: pregraph_sparse.cpp.rej -Only in SOAPdenovo2-src-r240.orig: uninstd-h-fix.h -- GitLab From 5f5156ee8ba9ca2898af1668789d406b1eabc933 Mon Sep 17 00:00:00 2001 From: Forai Date: Thu, 6 Feb 2014 13:50:59 +0100 Subject: [PATCH 358/566] fixed white space issues. --- .../s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb | 11 +++++------ .../s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb | 10 +++++----- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb index d2d7ca3568..55510047f9 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb @@ -13,22 +13,23 @@ name = 'SOAPdenovo2' version = '240' homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' -description = """SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.""" +description = """SOAPdenovo is a novel short-read assembly method that can build a +de novo draft assembly for human-sized genomes. The program is specially designed to +assemble Illumina short reads. It creates new opportunities for building reference +sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. +SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} patches = ['fix-unistd-includes.patch'] - # like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz sources = ['%s-src-r%s.tgz' % (name, version)] source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] - maxparallel=1 - files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] sanity_check_paths = { @@ -36,6 +37,4 @@ sanity_check_paths = { 'dirs': [], } - - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb index a023adde1e..f46b096cc9 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb @@ -13,22 +13,23 @@ name = 'SOAPdenovo2' version = '240' homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' -description = """SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.""" +description = """SOAPdenovo is a novel short-read assembly method that can build a +de novo draft assembly for human-sized genomes. The program is specially designed to +assemble Illumina short reads. It creates new opportunities for building reference +sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. +SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} patches = ['fix-unistd-includes.patch'] - # like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz sources = ['%s-src-r%s.tgz' % (name, version)] source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] - maxparallel=1 - files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] sanity_check_paths = { @@ -36,5 +37,4 @@ sanity_check_paths = { 'dirs': [], } - moduleclass = 'bio' -- GitLab From e3024f17b845795b7f75a1d5fdeb09759a05ed8d Mon Sep 17 00:00:00 2001 From: jhale Date: Thu, 6 Feb 2014 16:23:38 +0100 Subject: [PATCH 359/566] Adjusted style as suggested by boegel --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 7 +++++-- .../easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb | 6 ++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb | 6 ++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 6 ++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb | 6 ++++-- easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 6 ++++-- 6 files changed, 25 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index 4aa2994cd6..de79c4daae 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -6,8 +6,11 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/' + \ + '%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index 99561006f5..2d4e7c17a1 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -6,8 +6,10 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index 295259e31e..f83f3ffb6a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -6,8 +6,10 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 0af92be3f4..ffa5551d14 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -7,8 +7,10 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] # enforce use of -O1, required because of compiler bug that triggers 'internal error: 0_381' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index e294af2d8b..e05c77a46b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -6,8 +6,10 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index ff0c690069..654eb56d93 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -6,8 +6,10 @@ description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} -backup_url = 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' -source_urls = ['http://origin.releases.qt-project.org/qt4/source/', backup_url] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] -- GitLab From 2a549170881f2060a1bd9d7175e2a0b4aa8105af Mon Sep 17 00:00:00 2001 From: jhale Date: Thu, 6 Feb 2014 16:26:03 +0100 Subject: [PATCH 360/566] Join split url --- easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index de79c4daae..15b02947ee 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -8,8 +8,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/' + \ - '%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -- GitLab From e8a2c63d81949f9fa751a88a9aa9acd9f19997e9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 6 Feb 2014 16:48:28 +0100 Subject: [PATCH 361/566] add latest and greatest Lmod/Lua pair Signed-off-by: Fotis Georgatos --- .../l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb | 22 +++++++++++++++++ .../l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb | 24 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb new file mode 100644 index 0000000000..14c2d00848 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb @@ -0,0 +1,22 @@ +name = "Lmod" +version = "5.2.5" + +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/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb new file mode 100644 index 0000000000..2d4f7773d7 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8-GCC-4.8.2.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': '4.8.2'} + +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" -- GitLab From bf78655313b0bc553fc2ca3501d5a720b17d7497 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 6 Feb 2014 22:13:28 +0100 Subject: [PATCH 362/566] style fixes --- .../FASTX-Toolkit-0.0.14-goolf-1.4.10.eb | 30 +++++++++---------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb index 4bc8783a8a..d529b00f96 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-goolf-1.4.10.eb @@ -14,30 +14,30 @@ name = 'FASTX-Toolkit' version = '0.0.14' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' -description = """The FASTX-Toolkit is a collection of command line tools -for Short-Reads FASTA/FASTQ files preprocessing.""" +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} altname = name.lower().replace('-','_') source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] -sources = ['%s-%s.tar.bz2' % (altname, version)] +sources = ['%s-%%(version)s.tar.bz2' % altname] dependencies = [('libgtextutils', '0.6.1')]; sanity_check_paths = { - 'files': ['bin/fastx_%s' % x for x in ['clipper', 'trimmer', 'quality_stats', - 'artifacts_filter', 'reverse_complement', - 'collapser', 'uncollapser', 'renamer', - 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', - 'nucleotide_distribution_line_graph.sh']] + - ['bin/fasta_%s' % x for x in ['clipping_histogram.pl', 'formatter', - 'nucleotide_changer']] + - ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', - 'to_fasta', 'quality_filter', 'quality_trimmer', - 'masker']], - 'dirs': ['.'] - } + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] + } moduleclass = 'bio' -- GitLab From e7cdefae3c80b5d8eed384fcc204edd3d51b8363 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 11 Feb 2014 21:25:31 +0100 Subject: [PATCH 363/566] add patch for v1.4.5, to show openmpi fancyness Signed-off-by: Fotis Georgatos --- .../OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch new file mode 100644 index 0000000000..fec0e69c83 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch @@ -0,0 +1,11 @@ +--- opal/etc/openmpi-mca-params.conf.orig 2009-12-08 21:36:08.000000000 +0100 ++++ opal/etc/openmpi-mca-params.conf 2013-03-17 08:13:21.216969244 +0100 +@@ -56,3 +56,8 @@ + + # See "ompi_info --param all all" for a full listing of Open MPI MCA + # parameters available and their default values. ++ ++# FG, 20130317; customization for University of Luxembourg systems ++btl_openib_if_exclude=mlx4_1 ++btl_openib_warn_nonexistent_if=0 ++plm_rsh_agent=oarsh -- GitLab From d4560c5c2cefb3dcb122a661074b2791b977e7f9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 11 Feb 2014 22:37:43 +0100 Subject: [PATCH 364/566] Revert "add patch for v1.4.5, to show openmpi fancyness" This reverts commit e7cdefae3c80b5d8eed384fcc204edd3d51b8363. --- .../OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch b/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch deleted file mode 100644 index fec0e69c83..0000000000 --- a/easybuild/easyconfigs/o/OpenMPI/openmpi-mca-params.conf-1.4.5-local.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- opal/etc/openmpi-mca-params.conf.orig 2009-12-08 21:36:08.000000000 +0100 -+++ opal/etc/openmpi-mca-params.conf 2013-03-17 08:13:21.216969244 +0100 -@@ -56,3 +56,8 @@ - - # See "ompi_info --param all all" for a full listing of Open MPI MCA - # parameters available and their default values. -+ -+# FG, 20130317; customization for University of Luxembourg systems -+btl_openib_if_exclude=mlx4_1 -+btl_openib_warn_nonexistent_if=0 -+plm_rsh_agent=oarsh -- GitLab From 705c82dc671510eedaac1a49203ef29dd73b0147 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Feb 2014 21:46:56 +0100 Subject: [PATCH 365/566] include leading space in multiline description --- .../Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb | 2 +- .../d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb | 2 +- .../Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb | 2 +- .../d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb | 2 +- .../d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb | 2 +- .../d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb | 2 +- .../d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb | 2 +- .../d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb | 2 +- .../d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb | 2 +- .../d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb | 2 +- .../d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb | 2 +- .../d/Doxygen/Doxygen-1.8.3.1-ictce-5.5.0.eb | 18 ++++++++++++++++++ .../d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb | 2 +- .../d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb | 2 +- 14 files changed, 31 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb index 94124552fa..bb8cdbd66d 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goalf-1.1.0-no-OFED.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb index 50e6f2e0f5..d411b81fc2 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-goolf-1.4.10.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb index 2b4093a0c4..84f174b33d 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-3.2.2.u3.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb index 6fe341a2e4..5c9972551e 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.0.6.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb index 0a291437d5..a4f03bdb80 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-4.1.13.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb index 46e392d855..b2ae051cf0 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.1.1-ictce-5.3.0.eb @@ -3,7 +3,7 @@ version = '1.8.1.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb index 4e0322abc4..feaca896ce 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-4.1.13.eb @@ -3,7 +3,7 @@ version = '1.8.2' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb index 2793cce845..3d9629901c 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.2-ictce-5.3.0.eb @@ -3,7 +3,7 @@ version = '1.8.2' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb index 9b648008e6..07faae3865 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb @@ -3,7 +3,7 @@ version = '1.8.3.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb index b9145b9d9d..f588777511 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-4.1.13.eb @@ -3,7 +3,7 @@ version = '1.8.3.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb index f5c2ee7700..8194f931b7 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.3.0.eb @@ -3,7 +3,7 @@ version = '1.8.3.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.5.0.eb new file mode 100644 index 0000000000..5c549c9f51 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '5.5.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb index 17c6df3ade..b4ebaf0c87 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-iqacml-3.7.3.eb @@ -3,7 +3,7 @@ version = '1.8.3.1' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'iqacml', 'version': '3.7.3'} diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb index ac0d35a6d5..ded4982b00 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.6-ictce-5.5.0.eb @@ -3,7 +3,7 @@ version = '1.8.6' 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.""" + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -- GitLab From 6baef33f91c15d847b10965e276f5adf30a083d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Feb 2014 21:56:41 +0100 Subject: [PATCH 366/566] use VSCPythonPackage easyblock for all VSC Python packages (makes sense, right?) --- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) 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 bb10e35430..2b5b458800 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 @@ -56,6 +56,7 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', ...), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb index e5bcfce5d5..4129a58d5a 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb @@ -1,4 +1,4 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'VSCPythonPackage' name = 'vsc-base' version = '1.6.9' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index fb13fb6328..f6b363d857 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -1,4 +1,4 @@ -easyblock = 'VersionIndependentPythonPackage' +easyblock = 'VSCPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -- GitLab From 5fdc068dc370ee52fde3b47285570453b3a264b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Feb 2014 22:09:11 +0100 Subject: [PATCH 367/566] get rid of placeholder six extension --- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 1 - 1 file changed, 1 deletion(-) 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 2b5b458800..bb10e35430 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 @@ -56,7 +56,6 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), - ('six', ...), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], -- GitLab From b562fbbc2aa71d1a6e7b2c501272a9363bdac95d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 08:46:50 +0100 Subject: [PATCH 368/566] style fixes and source URL template for PyZMQ --- .../PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- ....2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb | 14 +++++++------- ....2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb | 14 +++++++------- ...PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb | 14 +++++++------- ...PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb | 14 +++++++------- ...PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb | 14 +++++++------- ...PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb | 14 +++++++------- .../PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb | 14 +++++++------- .../PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb | 14 +++++++------- 9 files changed, 58 insertions(+), 58 deletions(-) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb index 6939bcf426..a08cfce3cb 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.0.1-ictce-5.5.0-Python-2.7.6.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -24,7 +24,7 @@ options = {'modulename': 'zmq'} sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb index f39ba62b1d..6f127b706d 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '2.2.0' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb index e0f4d8199e..e1c29fe7ab 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '3.2.2' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb index d7b0dabc3f..9943daf903 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '2.2.0' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb index 64d61708c2..11781825a5 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-goolf-1.4.10-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '3.2.2' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb index b2c698d89a..ef798bdb27 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq2.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '2.2.0' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb index 63b8df0e9e..5e5a1f0511 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-4.1.13-Python-2.7.3-zmq3.eb @@ -6,7 +6,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -17,15 +17,15 @@ zmqversion = '3.2.2' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb index 4f2003dfe2..829290eef2 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq2.eb @@ -7,7 +7,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -18,15 +18,15 @@ zmqversion = '2.2.0' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb index 92979bea53..402506e6f6 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.3.0-Python-2.7.3-zmq3.eb @@ -7,7 +7,7 @@ description = """Python bindings for ZeroMQ""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ["http://pypi.python.org/packages/source/%s/%s/" % (name.lower()[0], name.lower())] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] python = 'Python' @@ -18,15 +18,15 @@ zmqversion = '3.2.2' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' -- GitLab From 60def82a79a580bbfeabcad75b18cfe5e60d3a15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 08:48:57 +0100 Subject: [PATCH 369/566] use SOURCE_TGZ in all Python easyconfigs --- 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 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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 28d55c2c9b..78902f06e7 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 @@ -11,7 +11,7 @@ numpyversion = '1.8.0' scipyversion = '0.13.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 a66adf51e6..156f284b28 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 @@ -11,7 +11,7 @@ numpyversion = '1.8.0' scipyversion = '0.13.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # libffi build in python is still broken, see http://bugs.python.org/issue4130 patches = ['python-2.7_libffi-include-xmmintrin.patch'] 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 fa31f87152..2570b71290 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 @@ -11,7 +11,7 @@ numpyversion = '1.8.0' scipyversion = '0.13.1' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] patches = ['python-2.7_libffi-include-xmmintrin.patch'] -- GitLab From 9c9ad0bf5d6d53a5242c28c9747f553f46d5a7eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 08:51:30 +0100 Subject: [PATCH 370/566] style fixes in SCOOP easyconfigs --- .../s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb index 750cd29e08..4789736f17 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb @@ -5,7 +5,7 @@ version = '0.5.3' homepage = 'http://code.google.com/p/scoop/' description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module -allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb index 691005bdb4..8ffb56ec18 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb @@ -5,7 +5,7 @@ version = '0.6.2' homepage = 'http://code.google.com/p/scoop/' description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module -allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -- GitLab From 2651d2f6f76deb4220a173a5871edf108c7cd3a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 08:54:38 +0100 Subject: [PATCH 371/566] cosmetic fixes to vsc-base easyconfigs --- easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb | 5 +---- easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb index 4129a58d5a..23ef4a12e7 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb @@ -9,11 +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 = ['https://github.com/hpcugent/vsc-base/archive/'] options = {'modulename': 'vsc.utils'} diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb index 7f81750f1e..a9424b7998 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb @@ -9,11 +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 = ['https://github.com/hpcugent/vsc-base/archive/'] options = {'modulename': 'vsc.utils'} -- GitLab From f327748d65e31e4795eda796aecb8308c241efeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 08:56:06 +0100 Subject: [PATCH 372/566] moar style/typo fixes --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 4 +--- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb | 4 +--- .../v/vsc-processcontrol/vsc-processcontrol-1.0.eb | 6 ++---- 3 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index f6b363d857..2f81b82d91 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -10,9 +10,7 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] -source_urls = [ - 'https://github.com/hpcugent/vsc-mympirun/archive/', -] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [('vsc-base', '1.6.9')] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb index 8a7e36cbc8..5617b0766f 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb @@ -10,9 +10,7 @@ description = """VSC-tools is a set of Python libraries and scripts that are com toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] -source_urls = [ - 'https://github.com/hpcugent/vsc-mympirun/archive/', -] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] dependencies = [ ('vsc-base', '1.7.3'), diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb index a8c92aec1c..2b715acacf 100644 --- a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb @@ -5,15 +5,13 @@ version = '1.0' homepage = 'http://hpcugent.github.com/vsc-processcontrol/' description = """vsc-processcontrol is a module to abstract process control like scheduler settings and affinity - from actual implementations like vsc.affintiy and psutil.""" + from actual implementations like vsc.affinity and psutil.""" # we build this to work with every python version toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] -source_urls = [ - 'https://github.com/hpcugent/vsc-processcontrol/archive/', -] +source_urls = ['https://github.com/hpcugent/vsc-processcontrol/archive/'] dependencies = [('vsc-base', '1.7.3')] -- GitLab From 58955d867fde40b7f2fd9d0f66746bae81d60813 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 11:49:12 +0100 Subject: [PATCH 373/566] use PYPI_SOURCE in Cython easyconfigs --- .../c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 1 + 10 files changed, 10 insertions(+), 9 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 de9d824b0b..111c644bc1 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 666edc42c2..5bcaed9bfc 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 16232ee493..9f373a0235 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 c638c7d869..0e90880443 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 7bab5be1c2..5b3b81efb9 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 b3b3468120..cf243045a0 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 ec5d60fe4e..5538d35119 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 3e23a5c022..91a404a0f3 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 3234e4ff25..00f9f4b739 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 @@ -9,7 +9,7 @@ description = """The Cython language makes writing C extensions for the Python l toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://pypi.python.org/packages/source/C/Cython/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' 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 bb10e35430..2b5b458800 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 @@ -56,6 +56,7 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), + ('six', ...), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], -- GitLab From 885d5638f2cc102453a8f9050838a99e806ade9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 11:52:26 +0100 Subject: [PATCH 374/566] use pylibdir in sanity_check_paths in Cython easyconfigs --- .../c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 5 +++-- .../c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb | 5 +++-- .../c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb | 5 +++-- .../c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb | 4 ++-- .../c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb | 4 ++-- .../c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb | 4 ++-- .../c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb | 4 ++-- .../c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- 9 files changed, 21 insertions(+), 18 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 111c644bc1..83aec1d936 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 @@ -15,13 +15,14 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 5bcaed9bfc..892d56aaa1 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 @@ -15,13 +15,14 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 9f373a0235..b81a538f5c 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 @@ -15,13 +15,14 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 0e90880443..6e94f41099 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 5b3b81efb9..5d1302c3c1 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 cf243045a0..ebccd555bb 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 5538d35119..3c845e9845 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 91a404a0f3..544e217059 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' 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 00f9f4b739..6d9476ba0f 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 @@ -21,8 +21,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [(python, pythonver)] sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'lib/python%s/site-packages/%%(namelower)s.py' % pythonshortver], - 'dirs': ['lib/python%s/site-packages/%%(name)s' % pythonshortver], + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % pylibdir], + 'dirs': ['%s/%%(name)s' % pylibdir], } moduleclass = 'lang' -- GitLab From 6a424be309a0f802bacab9f8f6e10c42c5f6b297 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 12:24:45 +0100 Subject: [PATCH 375/566] reorder toolchainopts (for compatibility with another PR) --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb index a30ee3a186..0a10444693 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0.eb @@ -6,7 +6,7 @@ description = """HDF5 is a unique technology suite that makes possible the manag extremely large and complex data collections.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -- GitLab From 0e627e24dadf6facd23e27f869e177dce75b2b3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 12:25:59 +0100 Subject: [PATCH 376/566] use GOOGLECODE_SOURCE constant for numexpr source URLs --- .../n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb index d5a11e2a58..4606d670d0 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -12,7 +12,7 @@ description = """The numexpr package evaluates multiple-operator array expressio toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} -source_urls = ['http://numexpr.googlecode.com/files/'] +source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 5d945019b9..23dc125463 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -9,11 +9,10 @@ description = """The numexpr package evaluates multiple-operator array expressio code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'usempi': True} -source_urls = ['http://numexpr.googlecode.com/files/'] +source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb index 4f89921346..585a1680b7 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.2.2-ictce-5.5.0-Python-2.7.6.eb @@ -12,7 +12,7 @@ description = """The numexpr package evaluates multiple-operator array expressio toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'usempi': True} -source_urls = ['http://numexpr.googlecode.com/files/'] +source_urls = [GOOGLECODE_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -- GitLab From 985b7b1ad4e8f13bd5906d4afdcfee83de708415 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 12:42:14 +0100 Subject: [PATCH 377/566] add missing patch file --- .../h/HDF5/HDF5-1.8.12_configure_ictce.patch | 131 ++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_configure_ictce.patch diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_configure_ictce.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_configure_ictce.patch new file mode 100644 index 0000000000..1877a925ef --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12_configure_ictce.patch @@ -0,0 +1,131 @@ +--- hdf5-1.8.12/configure.orig 2013-11-21 16:14:04.000000000 +0100 ++++ hdf5-1.8.12/configure 2014-01-13 13:16:28.486670037 +0100 +@@ -5260,7 +5260,7 @@ + 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=$2 +@@ -5304,7 +5304,7 @@ + fi + if test -z "$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=$2 +@@ -5533,7 +5533,7 @@ + ac_link='$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 "$ac_tool_prefix"; then +- for ac_prog in f90 pgf90 slf90 f95 g95 xlf95 efc ifort ftn ++ for ac_prog in f90 pgf90 slf90 f95 g95 xlf95 efc ifort mpif77 mpif90 ftn + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5577,7 +5577,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in f90 pgf90 slf90 f95 g95 xlf95 efc ifort ftn ++ for ac_prog in f90 pgf90 slf90 f95 g95 xlf95 efc ifort mpif77 mpif90 ftn + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -7769,7 +7769,7 @@ + mpicc) + ## The mpich compiler. Use mpiexec from the same directory if it + ## exists. +- PARALLEL=mpicc ++ PARALLEL="$CC_BASENAME" + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for mpiexec" >&5 + $as_echo_n "checking for mpiexec... " >&6; } + +@@ -7831,7 +7831,7 @@ + *mpif90*) + ## The Fortran mpich compiler. Use mpiexec from the same directory + ## if it exists. +- PARALLEL=mpif90 ++ PARALLEL="$FC" + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for mpiexec" >&5 + $as_echo_n "checking for mpiexec... " >&6; } + +@@ -12565,7 +12565,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc*| mpicc* | ifort*| mpif77* | mpif90* ) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -13201,11 +13201,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${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=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64*| mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64*| mpif77*,ia64* | mpif90*,ia64* ) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort*| mpif77* | mpif90* ) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13687,7 +13687,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_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 "$_lt_dar_can_shared" = "yes"; then +@@ -16685,7 +16685,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_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 "$_lt_dar_can_shared" = "yes"; then +@@ -19596,7 +19596,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc*| mpicc* | ifort*| mpif77* | mpif90* ) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -20217,11 +20217,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${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=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64*| mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64*| mpif77*,ia64* | mpif90*,ia64* ) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort*| mpif77* | mpif90* ) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20675,7 +20675,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_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 9bb05b2775e396091061f4331c1d47e256b86fbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 14:59:59 +0100 Subject: [PATCH 378/566] take out placeholder extension 'six' (again) --- easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 1 - 1 file changed, 1 deletion(-) 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 2b5b458800..bb10e35430 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 @@ -56,7 +56,6 @@ exts_list = [ ('Cython', '0.17.2', { 'source_urls': ['http://www.cython.org/release/'], }), - ('six', ...), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], -- GitLab From 1feb01b21ef54fa2fb61d2549352d322da4daf14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:01:38 +0100 Subject: [PATCH 379/566] style fixes in pandas and pyTables easyconfigs --- .../p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb | 2 +- .../p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb | 4 ++-- .../p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) 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 03c972512f..b38ad74c90 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 @@ -9,7 +9,7 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb index 4dcd85eb02..c5aa1dcd66 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pyTables/pyTables-2.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -15,8 +15,8 @@ description = """PyTables is a package for managing hierarchical datasets and de toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'usempi': True} -source_urls = [('http://sourceforge.net/projects/pytables/files/pytables/%s' % version, 'download')] -sources = ['tables-%s.tar.gz' % version] +source_urls = [SOURCEFORGE_SOURCE] +sources = ['tables-%(version)s.tar.gz'] python = 'Python' pythonver = '2.7.3' diff --git a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb index 8219cdaef1..9295347947 100644 --- a/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pyTables/pyTables-3.0.0-ictce-5.5.0-Python-2.7.6.eb @@ -15,8 +15,8 @@ description = """PyTables is a package for managing hierarchical datasets and de toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'usempi': True} -source_urls = [('http://sourceforge.net/projects/pytables/files/pytables/%s' % version, 'download')] -sources = ['tables-%s.tar.gz' % version] +source_urls = [SOURCEFORGE_SOURCE] +sources = ['tables-%(version)s.tar.gz'] python = 'Python' pythonver = '2.7.6' -- GitLab From afb111a835519386099b064ca81be667cc889340 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:05:43 +0100 Subject: [PATCH 380/566] style fix for scikit-learn --- .../scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb index b15833e4de..22f760cf88 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb @@ -10,7 +10,8 @@ it provides versatile tools for data mining and analysis in any field of science It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/s/scikit-learn/'] + +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" -- GitLab From 3bddb17f58b16aec870947384a4e60892cfe7373 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:17:16 +0100 Subject: [PATCH 381/566] make sure that --mpi build option is used h5py --- .../h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 3 ++- 9 files changed, 26 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 65a7014b20..f321a069fb 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -19,6 +19,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.7') diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb index 07429451c5..7c5593e46d 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb @@ -19,6 +19,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.7') diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb index a8e6f4abc3..99d122d4eb 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb @@ -18,6 +18,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.7'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb index 5c81d66386..d0c8ee67b4 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -18,6 +18,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index e9b09d3b51..b09d9d4e47 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -18,6 +18,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb index 33f5356c81..fc5502626f 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -19,6 +19,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb index a3bd601e67..06e44068ff 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb @@ -19,6 +19,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb index cd410ed70d..995c341024 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -19,6 +19,9 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) +# make sure that MPI features are enabled +makeopts = '--mpi' + dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb index 5419efd76b..3fd421a5a8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -19,7 +19,8 @@ pythonver = '2.7.5' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -installopts = '--mpi' +# make sure that MPI features are enabled +makeopts = '--mpi' dependencies = [ (python, pythonver), -- GitLab From bd47f3a0cda32d4b780e8716e74cca4d49c3d686 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:21:47 +0100 Subject: [PATCH 382/566] add mpi4py dependency for h5py, required for MPI support --- .../h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb | 1 + .../easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 2 +- 9 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f321a069fb..4e3371afcc 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -25,6 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.7') + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb index 7c5593e46d..4df83bbd1c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb @@ -25,6 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.7') + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb index 99d122d4eb..0d6f395cc9 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb @@ -24,6 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.7'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb index d0c8ee67b4..5df5af9d06 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -24,6 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index b09d9d4e47..7a551a0b1d 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -24,6 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb index fc5502626f..02bd36b338 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -25,6 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb index 06e44068ff..881a2f04c6 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb @@ -25,6 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb index 995c341024..79e383bb0e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -25,6 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb index 3fd421a5a8..5d08f30ca5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -25,7 +25,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), ('HDF5', '1.8.12'), - ('mpi4py', '1.3.1', versionsuffix), + ('mpi4py', '1.3', versionsuffix), # required for MPI support ] sanity_check_paths = { -- GitLab From 81c74f779dfac6644770eeaec5010306f4a1214e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:37:09 +0100 Subject: [PATCH 383/566] fix style issues in Greenlet easyconfigs --- ...et-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 14 +++++--------- .../Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb | 14 +++++--------- .../Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb | 17 ++++++----------- .../Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb | 17 ++++++----------- .../Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb | 17 ++++++----------- ..._amd64_predefined_in_prepocessor-0.4.2.patch | 11 ----------- 6 files changed, 28 insertions(+), 62 deletions(-) delete mode 100644 easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index d24861f722..9532285a30 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -21,16 +21,12 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -dependencies = [ - (python, pythonversion), - ] - +dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, - 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, - ], - 'dirs': [] - } + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb index 59de038289..e691784be6 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goolf-1.4.10-Python-2.7.3.eb @@ -21,16 +21,12 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -dependencies = [ - (python, pythonversion), - ] - +dependencies = [(python, pythonversion)] sanity_check_paths = { - 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, - 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, - ], - 'dirs': [] - } + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb index 079811b174..4061f88ae5 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb @@ -21,19 +21,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -dependencies = [ - (python, pythonversion), - ] +dependencies = [(python, pythonversion)] -patches = [ - 'icc_no_amd64_predefined_in_prepocessor.patch', - ] +patches = ['icc_no_amd64_predefined_in_prepocessor.patch'] sanity_check_paths = { - 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, - 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, - ], - 'dirs': [] - } + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb index 49b94ba41f..7fc1dea03a 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-5.3.0-Python-2.7.3.eb @@ -21,19 +21,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -dependencies = [ - (python, pythonversion), - ] +dependencies = [(python, pythonversion)] -patches = [ - 'icc_no_amd64_predefined_in_prepocessor.patch', - ] +patches = ['icc_no_amd64_predefined_in_prepocessor.patch'] sanity_check_paths = { - 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, - 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, - ], - 'dirs': [] - } + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb index 2de415b2d7..7d6a807731 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.5.eb @@ -21,19 +21,14 @@ pythonshortversion = ".".join(pythonversion.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pythonversion) -dependencies = [ - (python, pythonversion), - ] +dependencies = [(python, pythonversion)] -patches = [ - 'icc_no_amd64_predefined_in_prepocessor-%(version)s.patch', - ] +patches = ['Greenlet-%(version)s_icc_no_amd64_predefined_in_prepocessor.patch'] sanity_check_paths = { - 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, - 'lib/python%s/site-packages/greenlet.so' % pythonshortversion, - ], - 'dirs': [] - } + 'files': ['include/python%s/greenlet/greenlet.h' % pythonshortversion, + 'lib/python%s/site-packages/greenlet.so' % pythonshortversion], + 'dirs': [], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch b/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch deleted file mode 100644 index 0afb624caf..0000000000 --- a/easybuild/easyconfigs/g/Greenlet/icc_no_amd64_predefined_in_prepocessor-0.4.2.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- slp_platformselect.h.orig 2014-01-06 23:48:38.000000000 +0100 -+++ slp_platformselect.h 2014-01-31 18:05:36.125349420 +0100 -@@ -8,7 +8,7 @@ - #include "platform/switch_x64_msvc.h" /* MS Visual Studio on X64 */ - #elif defined(__GNUC__) && defined(__amd64__) && defined(__ILP32__) - #include "platform/switch_x32_unix.h" /* gcc on amd64 with x32 ABI */ --#elif defined(__GNUC__) && defined(__amd64__) -+#elif defined(__GNUC__) && defined(__x86_64__) - #include "platform/switch_amd64_unix.h" /* gcc on amd64 */ - #elif defined(__GNUC__) && defined(__i386__) - #include "platform/switch_x86_unix.h" /* gcc on X86 */ -- GitLab From d301cbd5a5101aa2a4440411f1480759c3bea3f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:38:27 +0100 Subject: [PATCH 384/566] style fixes for PyZMQ --- .../PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb index 398114576d..603c912f0d 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-2.2.0.1-ictce-5.5.0-Python-2.7.5-zmq2.eb @@ -17,15 +17,15 @@ zmqversion = '2.2.0' versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) dependencies = [ - (python, pythonversion), - ('ZeroMQ', zmqversion), - ] + (python, pythonversion), + ('ZeroMQ', zmqversion), +] options = {'modulename': 'zmq'} sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion] - } + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pythonshortversion], +} moduleclass = 'devel' -- GitLab From 073659ff6ca759f3c51abe40ef7283a03fd4c9a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:43:34 +0100 Subject: [PATCH 385/566] fix style issues for SCOOP --- ...-0.5.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 20 +++++++----------- .../SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb | 18 +++++++--------- .../SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb | 18 +++++++--------- .../SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb | 19 +++++++---------- .../SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb | 21 +++++++------------ .../SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb | 6 ++++-- 6 files changed, 41 insertions(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index cbfc0fc2a7..a523938124 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -14,23 +14,19 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 dependencies = [ - (python, pythonversion), # python with builtin argparse - ('Greenlet', '0.4.0', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), - ] + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.0', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), +] sanity_check_paths = { - 'files': [], - 'dirs': [('lib/python%(pyv)s/site-packages/' - 'scoop-%(version)s-py%(pyv)s.egg/scoop/') % - {'pyv': pythonshortversion, - 'version': version } - ] - } + 'files': [], + 'dirs': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s-py%(pyv)s.egg/scoop/' % {'pyv': pyshortver}], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb index 4789736f17..778cef0fac 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb @@ -19,18 +19,14 @@ versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 dependencies = [ - (python, pythonversion), # python with builtin argparse - ('Greenlet', '0.4.0', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), - ] + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.0', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), +] sanity_check_paths = { - 'files': [], - 'dirs': [('lib/python%(pyv)s/site-packages/' - 'scoop-%(version)s-py%(pyv)s.egg/scoop/') % - {'pyv': pythonshortversion, - 'version': version } - ] - } + 'files': [], + 'dirs': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s-py%(pyv)s.egg/scoop/' % {'pyv': pyshortver}], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb index 6359677a92..c636af662e 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb @@ -19,18 +19,14 @@ versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 dependencies = [ - (python, pythonversion), # python with builtin argparse - ('Greenlet', '0.4.0', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), - ] + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.0', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), +] sanity_check_paths = { - 'files': [], - 'dirs': [('lib/python%(pyv)s/site-packages/' - 'scoop-%(version)s-py%(pyv)s.egg/scoop/') % - {'pyv': pythonshortversion, - 'version': version } - ] - } + 'files': [], + 'dirs': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s-py%(pyv)s.egg/scoop/' % {'pyv': pyshortver}], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb index 8a88b6106a..4f555a09c2 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb @@ -7,7 +7,6 @@ homepage = 'http://code.google.com/p/scoop/' description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ["http://scoop.googlecode.com/files/"] @@ -20,18 +19,14 @@ versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 dependencies = [ - (python, pythonversion), # python with builtin argparse - ('Greenlet', '0.4.0', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), - ] + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.0', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), +] sanity_check_paths = { - 'files': [], - 'dirs': [('lib/python%(pyv)s/site-packages/' - 'scoop-%(version)s-py%(pyv)s.egg/scoop/') % - {'pyv': pythonshortversion, - 'version': version } - ] - } + 'files': [], + 'dirs': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s-py%(pyv)s.egg/scoop/' % {'pyv': pyshortver}], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb index cedd07f1dd..0794de7781 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.5.eb @@ -7,7 +7,6 @@ homepage = 'http://code.google.com/p/scoop/' description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" - toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ["http://scoop.googlecode.com/files/"] @@ -15,23 +14,19 @@ sources = ["%(namelower)s-%(version)s.release.tar.gz"] python = 'Python' pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 dependencies = [ - (python, pythonversion), # python with builtin argparse - ('Greenlet', '0.4.2', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), - ] + (python, pythonversion), # python with builtin argparse + ('Greenlet', '0.4.2', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), +] sanity_check_paths = { - 'dirs': [], - 'files': [('lib/python%(pyv)s/site-packages/' - 'scoop-%(version)s.release-py%(pyv)s.egg') % - {'pyv': pythonshortversion, - 'version': version } - ] - } + 'dirs': [], + 'files': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s.release-py%(pyv)s.egg' % {'pyv': pyshortver}], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb index 8ffb56ec18..964359f51b 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb @@ -20,10 +20,12 @@ versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ (python, pythonversion), # python with builtin argparse ('Greenlet', '0.4.2', versionsuffix), - ('PyZMQ', '14.0.1', versionsuffix), + ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), ] sanity_check_paths = { - 'files': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s.release-py%(pyv)s.egg' % {'pyv': pythonshortversion}], 'dirs': [], + 'files': ['lib/python%(pyv)s/site-packages/scoop-%%(version)s.release-py%(pyv)s.egg' % {'pyv': pyshortver}], } + +moduleclass = 'tools' -- GitLab From 8248ff458daa6ecf8f022b50f515d94ce9fec22b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:46:30 +0100 Subject: [PATCH 386/566] fix style issues for util-linux --- .../util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb | 8 ++++---- .../u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb | 8 ++++---- .../u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb | 8 ++++---- .../u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb | 9 ++++----- .../u/util-linux/util-linux-2.24-ictce-5.5.0.eb | 2 +- .../u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb | 9 ++++----- 6 files changed, 21 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb index d63c05d4aa..282691e211 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goalf-1.1.0-no-OFED.eb @@ -6,7 +6,7 @@ description = """Set of Linux utilities""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -20,8 +20,8 @@ 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'] - } + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb index c6cf3bbdc6..2181cfe1cc 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-goolf-1.4.10.eb @@ -6,7 +6,7 @@ description = """Set of Linux utilities""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -20,8 +20,8 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'] - } + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb index 709d0a0204..5bcfe76a71 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-4.1.13.eb @@ -6,7 +6,7 @@ description = """Set of Linux utilities""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -20,8 +20,8 @@ configopts += "--with-systemdsystemunitdir='${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'] - } + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb index 5efe20cea9..6fa9dfbdc6 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.3.0.eb @@ -4,10 +4,9 @@ version = '2.22.2' homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' description = """Set of Linux utilities""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -21,8 +20,8 @@ configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'] - } + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb index 08d7675cec..696815202f 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24-ictce-5.5.0.eb @@ -6,7 +6,7 @@ description = """Set of Linux utilities""" toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['%s/v%%(version)s' % homepage] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb index 533a0dcc2f..77d061f0e0 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.24.1-ictce-5.5.0.eb @@ -4,10 +4,9 @@ version = '2.24.1' homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' description = """Set of Linux utilities""" - toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['%s/v%s'%(homepage,'.'.join(version.split('.')[0:2]) )] +source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] # disable account related utilities (they need OS dependant pam-devel files) @@ -23,8 +22,8 @@ configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/complet dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], - 'dirs': ['include', 'bin', 'share', 'sbin'] - } + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} moduleclass = 'tools' -- GitLab From 707497ad2050a75d57ed763750b52a39f7eb1a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:49:14 +0100 Subject: [PATCH 387/566] fix style issues for ZeroMQ --- .../z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb | 12 ++++++------ .../z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb | 12 ++++++------ .../z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.3.0.eb | 13 ++++++------- .../z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb | 13 ++++++------- .../z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb | 12 ++++++------ .../z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb | 14 ++++++-------- .../z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb | 15 ++++++--------- 7 files changed, 42 insertions(+), 49 deletions(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb index 9daba3c85e..27a2cb351d 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-goalf-1.1.0-no-OFED.eb @@ -20,13 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2') - ] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb index a58d4fd084..a24777e7cd 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-4.1.13.eb @@ -20,13 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2') - ] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.3.0.eb index cede9c77fd..c50ac8ac7d 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.3.0.eb @@ -9,7 +9,6 @@ description = """ZeroMQ looks like an embeddable networking library but acts lik 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': 'ictce', 'version': '5.3.0'} source_urls = ['http://download.zeromq.org/'] @@ -21,13 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2') - ] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb index cb028a5c0d..b356788e95 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-2.2.0-ictce-5.5.0.eb @@ -9,7 +9,6 @@ description = """ZeroMQ looks like an embeddable networking library but acts lik products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.""" - toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = ['http://download.zeromq.org/'] @@ -21,13 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.24.1') - ] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb index a774e68300..117938148c 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-goalf-1.1.0-no-OFED.eb @@ -20,13 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2') - ] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb index 5cace57994..c184da63a2 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb @@ -20,15 +20,13 @@ configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%. configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ - ('OpenPGM', '5.2.122'), - ('util-linux', '2.22.2') - ] - -patches = ['stream_engine_ictce_storage_class_first.patch'] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb index e4cacef1c5..fe4983bf46 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb @@ -9,7 +9,6 @@ description = """ZeroMQ looks like an embeddable networking library but acts lik 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': 'ictce', 'version': '5.3.0'} source_urls = ['http://download.zeromq.org/'] @@ -21,15 +20,13 @@ 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') - ] - -patches = ['stream_engine_ictce_storage_class_first.patch'] + ('OpenPGM', '5.2.122'), + ('util-linux', '2.22.2'), +] sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], - 'dirs': ['include', 'lib'] - } + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} moduleclass = 'devel' -- GitLab From 65f82266a878fb2a21faa6fada30fcfed8e30cbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 15:59:50 +0100 Subject: [PATCH 388/566] add HDF5 dep compatible with zlib 1.2.8, required for h5py --- .../HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb | 26 +++++++++++++++++++ .../h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 2 +- 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb new file mode 100644 index 0000000000..bf02342e7c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-5.5.0-zlib-1.2.8.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.12' +versionsuffix = '-zlib-1.2.8' + +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': 'ictce', 'version': '5.5.0'} +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 = [ + 'HDF5-1.8.12_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb index 5d08f30ca5..c14fb5eb8f 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -24,7 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), - ('HDF5', '1.8.12'), + ('HDF5', '1.8.12', '-zlib-1.2.8'), ('mpi4py', '1.3', versionsuffix), # required for MPI support ] -- GitLab From 65274a8ae5c09fc973e036a9064253788ebf50ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 16:00:07 +0100 Subject: [PATCH 389/566] fix mpi4py 1.3 version --- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 07e1ecd0dc..e595d5b5ed 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'mpi4py' -version = '1.3.1' +version = '1.3' homepage = 'https://bitbucket.org/mpi4py/mpi4py' description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for -- GitLab From edfc483740ee66c21a900987b1f3c38c43e4b2d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 16:08:41 +0100 Subject: [PATCH 390/566] fix PyZMQ bump --- .../easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb index 964359f51b..3d3cbf7c0a 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb @@ -20,7 +20,7 @@ versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ (python, pythonversion), # python with builtin argparse ('Greenlet', '0.4.2', versionsuffix), - ('PyZMQ', '2.2.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), + ('PyZMQ', '14.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), ] sanity_check_paths = { -- GitLab From cea94b0fcd5637862f3487f9f3f516e64c528810 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 16:13:14 +0100 Subject: [PATCH 391/566] fix SCOOP easyconfig w.r.t. pyshortver and PyZMQ versionsuffix --- .../s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb index 3d3cbf7c0a..d684a52592 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-ictce-5.5.0-Python-2.7.6.eb @@ -14,13 +14,13 @@ sources = ['%s-%s.release.tar.gz' % (name.lower(), version)] python = 'Python' pythonversion = '2.7.6' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) dependencies = [ (python, pythonversion), # python with builtin argparse ('Greenlet', '0.4.2', versionsuffix), - ('PyZMQ', '14.0.1', '%s-zmq%s' % (versionsuffix, zmqapi)), + ('PyZMQ', '14.0.1', versionsuffix), ] sanity_check_paths = { -- GitLab From b6691cc962453f2e407e656820914199a37ccb49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 16:53:40 +0100 Subject: [PATCH 392/566] fix parsing of SCOOP easyconfigs --- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 5 ++++- .../m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb | 5 ++++- .../m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb | 5 ++++- .../m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 5 ++++- .../m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 5 ++++- .../s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- 8 files changed, 23 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index 10229d821c..92e62f75ef 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,10 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://mpi4py.googlecode.com/files/'] +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index 168f873fe3..5ecf122608 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -9,7 +9,10 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['https://mpi4py.googlecode.com/files/'] +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index a4f99586ea..67abf3ddf8 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -9,7 +9,10 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['https://mpi4py.googlecode.com/files/'] +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 8ff1173727..4988e7670a 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -9,7 +9,10 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://mpi4py.googlecode.com/files/'] +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 07e1ecd0dc..2e17022290 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -9,7 +9,10 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = [BITBUCKET_DOWNLOADS] +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb index 778cef0fac..b60889a72b 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-goolf-1.4.10-Python-2.7.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb index c636af662e..3f302d78e2 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-4.1.13-Python-2.7.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb index 4f555a09c2..154be5b9d1 100644 --- a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.5.3-ictce-5.3.0-Python-2.7.3.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] python = 'Python' pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyshortver = ".".join(pythonversion.split(".")[:-1]) versionsuffix = '-%s-%s' % (python, pythonversion) zmqapi = 2 -- GitLab From 12fc212d92a36b0ccb82814ea73e1cf5b98f4994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 17:04:47 +0100 Subject: [PATCH 393/566] fix typos --- .../h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 4e3371afcc..653f7ba173 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,7 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), - ('HDF5', '1.8.7') + ('HDF5', '1.8.7'), ('mpi4py', '1.3', versionsuffix), # required for MPI support ] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb index 4df83bbd1c..88f1a0722b 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb @@ -24,7 +24,7 @@ makeopts = '--mpi' dependencies = [ (python, pythonver), - ('HDF5', '1.8.7') + ('HDF5', '1.8.7'), ('mpi4py', '1.3', versionsuffix), # required for MPI support ] -- GitLab From 453d725964fa8656f66adb4e99041aaa12c32c5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 17:15:32 +0100 Subject: [PATCH 394/566] use SOURCEFORGE_SOURCE constant in numpy source URLs --- .../n/numpy/numpy-1.6.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb | 3 +-- .../n/numpy/numpy-1.6.2-iqacml-3.7.3-Python-2.7.3.eb | 2 +- .../n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb | 2 +- 6 files changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index b3aafe69b0..3cff78d9de 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb index 8106dc54bf..f1dcf152ee 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb @@ -9,7 +9,7 @@ NumPy can also be used as an efficient multi-dimensional container of generic da defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb index 5ce2cfa794..32146789ef 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-4.0.6-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb index e9f933cddf..0ea594ac42 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-ictce-5.3.0-Python-2.7.3.eb @@ -8,10 +8,9 @@ description = """NumPy is the fundamental package for scientific computing with 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': 'ictce', 'version': '5.3.0'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.6.2_distutils_multiple-lib-dirs.patch'] diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-iqacml-3.7.3-Python-2.7.3.eb b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-iqacml-3.7.3-Python-2.7.3.eb index 86800602aa..53dc5e3860 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.6.2-iqacml-3.7.3-Python-2.7.3.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.6.2-iqacml-3.7.3-Python-2.7.3.eb @@ -10,7 +10,7 @@ defined. This allows NumPy to seamlessly and speedily integrate with a wide vari toolchain = {'name': 'iqacml', 'version': '3.7.3'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb index df7582a273..722f3cab2c 100644 --- a/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/n/numpy/numpy-1.7.1-ictce-4.1.13-Python-2.7.5.eb @@ -10,7 +10,7 @@ description = """NumPy is the fundamental package for scientific computing with toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = [('http://sourceforge.net/projects/numpy/files/NumPy/%(version)s', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['numpy-1.7.1_distutils_multiple-lib-dirs.patch'] -- GitLab From 929a12a50177027207cdb4e4622543abc80b2404 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 17:18:03 +0100 Subject: [PATCH 395/566] moar constants --- 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 +- .../python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) 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 0a4ab2b959..e5c911cbe3 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.1' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 38956ed8cb..18501aa0f5 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.1' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ 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 c1fb8acaac..2bc16986cf 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 @@ -11,7 +11,7 @@ numpyversion = '1.7.1' scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = ['%(name)s-%(version)s.tgz'] +sources = [SOURCE_TGZ] # python needs bzip2 to build the bz2 package dependencies = [ diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb index 6f00563718..90bb4098db 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """The dateutil module provides powerful extensions to the datetim toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb index fae72a3762..37d02ed949 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """The dateutil module provides powerful extensions to the datetim toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://pypi.python.org/packages/source/p/%(name)s/'] +source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" -- GitLab From accd1dcf91b7401b79a7062b61f27bf01fbd4a03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 17:44:58 +0100 Subject: [PATCH 396/566] add missing mpi4py easyconfig required for deps --- ...py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb new file mode 100644 index 0000000000..0a66342f9b --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3' + +homepage = 'https://code.google.com/p/mpi4py/' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for +the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + +source_urls = [ + BITBUCKET_DOWNLOADS + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'mpi' -- GitLab From 252f2394e5d18132f355266f55dd02b909599951 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 17:53:51 +0100 Subject: [PATCH 397/566] fix typos --- .../m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb | 2 +- .../m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb | 2 +- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb | 2 +- .../easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index 92e62f75ef..d7ce479c30 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -10,7 +10,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index 5ecf122608..52e2739364 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -10,7 +10,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index 67abf3ddf8..5878a3a0a6 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -10,7 +10,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 4988e7670a..989b264cf7 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -10,7 +10,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 2e17022290..e60fe4ce5b 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -10,7 +10,7 @@ description = """MPI for Python (mpi4py) provides bindings of the Message Passin toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] -- GitLab From 5fce60a0e76be79228f6e7a486e68aea37fbe5df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 20:07:20 +0100 Subject: [PATCH 398/566] fix typo --- .../m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 0a66342f9b..832a044412 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,7 +10,7 @@ the Python programming language, allowing any Python program to exploit multiple toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ - BITBUCKET_DOWNLOADS + BITBUCKET_DOWNLOADS, GOOGLECODE_SOURCE, ] sources = [SOURCE_TAR_GZ] -- GitLab From 1ee055fd2833ff2cce19927cfab625be93237950 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 20:31:40 +0100 Subject: [PATCH 399/566] add missing util-linux easyconfig --- .../util-linux-2.22.2-ictce-5.5.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..4e19abd21c --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.22.2-ictce-5.5.0.eb @@ -0,0 +1,27 @@ +name = 'util-linux' +version = '2.22.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +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 +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 fb472f1f11dc4d44002edbeae7f891a4ed816e10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Feb 2014 21:59:14 +0100 Subject: [PATCH 400/566] fix zlib dep for matplotlib to avoid conflicts --- .../m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb index 8edf2b22c2..e0996041b8 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb @@ -21,7 +21,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('zlib', '1.2.8'), + ('zlib', '1.2.7'), ('freetype', '2.5.0.1'), ('libpng', '1.6.6'), ] -- GitLab From 79fa5fca5c35b60b46e584e5b99c01de002dbf6c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 13 Feb 2014 23:10:44 +0100 Subject: [PATCH 401/566] Clang-3.4: use polly --- easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index 5a750d9a0c..f753226de8 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -54,4 +54,6 @@ moduleclass = 'compiler' assertions = False +usepolly = True + build_targets = ['X86'] -- GitLab From 983319e417d7fa7fd2ec1a8edd1e643c36401413 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 00:33:20 +0100 Subject: [PATCH 402/566] creatively fix dep conflicts for matplotlib --- .../f/freetype/freetype-2.5.2-ictce-5.5.0.eb | 21 +++++++++++++++++++ .../l/libpng/libpng-1.6.9-ictce-5.5.0.eb | 17 +++++++++++++++ ...tplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb | 2 +- ...tplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- 4 files changed, 41 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.9-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb new file mode 100644 index 0000000000..578bf6e2b3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.2-ictce-5.5.0.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.2' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.9')] + +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/libpng/libpng-1.6.9-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.9-ictce-5.5.0.eb new file mode 100644 index 0000000000..37cc1311ee --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.9-ictce-5.5.0.eb @@ -0,0 +1,17 @@ +name = 'libpng' +version = '1.6.9' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.7')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb index e0996041b8..8edf2b22c2 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.5.eb @@ -21,7 +21,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), - ('zlib', '1.2.7'), + ('zlib', '1.2.8'), ('freetype', '2.5.0.1'), ('libpng', '1.6.6'), ] 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 5ee25a7abe..0e33120d40 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 @@ -22,8 +22,8 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [ (python, pythonversion), ('zlib', '1.2.7'), - ('freetype', '2.5.0.1'), - ('libpng', '1.6.6'), + ('freetype', '2.5.2'), + ('libpng', '1.6.9'), ] # is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? -- GitLab From 68df8cbd1646070c85c3a9b6687f3f5b51edf952 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 00:35:37 +0100 Subject: [PATCH 403/566] add latest OpenSSL version as a dependency for recent Python versions --- .../OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb | 21 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb | 21 +++++++++++++++++++ .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb | 21 +++++++++++++++++++ .../easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb | 21 +++++++++++++++++++ .../Python-2.7.5-goalf-1.5.12-no-OFED.eb | 1 + .../p/Python/Python-2.7.5-goolf-1.4.10.eb | 1 + .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 1 + .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 1 + .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 1 + .../p/Python/Python-2.7.5-iqacml-3.7.3.eb | 1 + .../p/Python/Python-2.7.6-goolf-1.4.10.eb | 1 + .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 1 + .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 1 + .../Python-3.2.3-goalf-1.1.0-no-OFED.eb | 1 + .../p/Python/Python-3.2.3-goolf-1.4.10.eb | 1 + .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 1 + .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 17 files changed, 97 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb new file mode 100644 index 0000000000..456f22d4c8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.1.0-no-OFED.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb new file mode 100644 index 0000000000..a894ebdd82 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goolf-1.4.10.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb new file mode 100644 index 0000000000..9f0fa27941 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb new file mode 100644 index 0000000000..af043c1fe5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' 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 5488b61962..3006668423 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f'), ] # order is important! 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 b70534400f..1b98bf29c0 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f'), ] # order is important! 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 e50d8ca057..8b8d853690 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 @@ -22,6 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 dbf075363b..c078168f17 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 @@ -22,6 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 1cd0602935..2a3eda5912 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 @@ -22,6 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 a4eb4e3cc9..e2c8a50128 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 @@ -23,6 +23,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('CBLAS', '20110120'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 78902f06e7..c452b12042 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f'), ] # order is important! 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 156f284b28..8c45c89aaa 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 @@ -22,6 +22,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 2570b71290..36d26d760e 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 @@ -21,6 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 b57481552a..7c1af324fa 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f'), ] # order is important! 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 6e6ef740c7..c92d41d278 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f'), ] # order is important! 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 7c8244621d..612b677b0c 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 @@ -21,6 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! 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 039d169ed3..d0002124cc 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 @@ -4,7 +4,6 @@ version = '3.2.3' homepage = 'http://python.org/' description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} @@ -20,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), + ('OpenSSL', '1.0.1f', '', True), ] # order is important! -- GitLab From fbbe5146aa0782713d29a294c72647b60d0858a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 09:30:11 +0100 Subject: [PATCH 404/566] get rid of dummy toolchain OpenSSL build --- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb | 21 ------------------- .../p/Python/Python-2.7.5-ictce-4.1.13.eb | 2 +- .../p/Python/Python-2.7.5-ictce-5.3.0.eb | 2 +- .../p/Python/Python-2.7.5-ictce-5.5.0.eb | 2 +- .../p/Python/Python-2.7.6-ictce-4.1.13.eb | 2 +- .../p/Python/Python-2.7.6-ictce-5.5.0.eb | 2 +- .../p/Python/Python-3.2.3-ictce-4.0.6.eb | 2 +- .../p/Python/Python-3.2.3-ictce-5.3.0.eb | 2 +- 8 files changed, 7 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb deleted file mode 100644 index af043c1fe5..0000000000 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'OpenSSL' -version = '1.0.1f' - -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': 'dummy', 'version': 'dummy'} -toolchainopts = {'pic': True, 'opt': True, 'optarch': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.openssl.org/source/'] - -dependencies = [('zlib', '1.2.7')] - -# makefile is not suitable for parallel build -parallel = 1 -runtest = 'test' - -moduleclass = 'system' 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 8b8d853690..d3bc991a29 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 @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 c078168f17..d23bfc901d 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 @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 2a3eda5912..cf04d1d5c0 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 @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 8c45c89aaa..da0f05502b 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 @@ -22,7 +22,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 36d26d760e..ac145f5b93 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 @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 612b677b0c..ff8ab76523 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 @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! 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 d0002124cc..eb4de74217 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! -- GitLab From b34c3af35e3e4a68b896cc61f430521a21c27347 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 09:31:51 +0100 Subject: [PATCH 405/566] add OpenSSL easyconfigs for ictce --- .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb | 23 ++++ .../o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb | 2 + .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb | 23 ++++ .../o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb | 23 ++++ .../o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch | 115 ++++++++++++++++++ 5 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb new file mode 100644 index 0000000000..1f75edf44c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.0.6.eb @@ -0,0 +1,23 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'ictce', 'version': '4.0.6'} +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'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb index 9f0fa27941..00fb598e1d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-4.1.13.eb @@ -12,6 +12,8 @@ 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'] + dependencies = [('zlib', '1.2.7')] # makefile is not suitable for parallel build diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb new file mode 100644 index 0000000000..317cd9b4de --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'ictce', 'version': '5.3.0'} +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'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb new file mode 100644 index 0000000000..c755fa9a4a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'ictce', 'version': '5.5.0'} +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'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch new file mode 100644 index 0000000000..a0492d9306 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch @@ -0,0 +1,115 @@ +diff -ru openssl-1.0.1f.orig/Configure openssl-1.0.1f/Configure +--- openssl-1.0.1f.orig/Configure 2014-01-06 14:47:42.000000000 +0100 ++++ openssl-1.0.1f/Configure 2014-02-14 08:41:42.000000000 +0100 +@@ -351,16 +351,16 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-DTERMIO -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 -DTERMIO -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 -DTERMIO -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 -DTERMIO -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 -DTERMIO -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### + "linux-generic64","gcc:-DTERMIO -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${no_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -DTERMIO -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -DTERMIO -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-ecc","ecc:-DL_ENDIAN -DTERMIO -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -DTERMIO -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -DTERMIO -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -DTERMIO -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 -DTERMIO -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1410,6 +1410,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1417,13 +1418,18 @@ + } + if ($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-1.0.1f.orig/crypto/aes/aes_x86core.c openssl-1.0.1f/crypto/aes/aes_x86core.c +--- openssl-1.0.1f.orig/crypto/aes/aes_x86core.c 2014-01-06 14:47:42.000000000 +0100 ++++ openssl-1.0.1f/crypto/aes/aes_x86core.c 2014-02-14 08:45:04.000000000 +0100 +@@ -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-1.0.1f.orig/crypto/des/des_locl.h openssl-1.0.1f/crypto/des/des_locl.h +--- openssl-1.0.1f.orig/crypto/des/des_locl.h 2014-01-06 14:47:42.000000000 +0100 ++++ openssl-1.0.1f/crypto/des/des_locl.h 2014-02-14 08:46:24.000000000 +0100 +@@ -160,8 +160,10 @@ + } \ + } + +-#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-1.0.1f.orig/crypto/md32_common.h openssl-1.0.1f/crypto/md32_common.h +--- openssl-1.0.1f.orig/crypto/md32_common.h 2014-01-06 14:47:42.000000000 +0100 ++++ openssl-1.0.1f/crypto/md32_common.h 2014-02-14 08:47:12.000000000 +0100 +@@ -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-1.0.1f.orig/crypto/rc5/rc5_locl.h openssl-1.0.1f/crypto/rc5/rc5_locl.h +--- openssl-1.0.1f.orig/crypto/rc5/rc5_locl.h 2014-01-06 14:47:42.000000000 +0100 ++++ openssl-1.0.1f/crypto/rc5/rc5_locl.h 2014-02-14 08:43:37.000000000 +0100 +@@ -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 dee2cf9063615fc7954eb8acdfffcc33c0412142 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 09:40:02 +0100 Subject: [PATCH 406/566] add openssl/libssl OS dep, favored over explicit OpenSSL dependency --- .../p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb | 3 +++ .../p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb | 3 +++ .../easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb | 3 +++ .../easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb | 3 +++ .../easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb | 3 +++ .../easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb | 3 +++ .../easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb | 3 +++ .../easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb | 3 +++ .../easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb | 3 +++ .../easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb | 3 +++ .../easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb | 4 +++- 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 | 4 +++- easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb | 4 +++- 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 ++ .../easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb | 4 +++- easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb | 4 +++- 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 ++ 35 files changed, 98 insertions(+), 6 deletions(-) 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 f2464bd93a..279bdd8c99 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 @@ -16,6 +16,9 @@ dependencies = [ ('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')] + 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 82ec6c7d72..f9f346f7bc 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 @@ -16,6 +16,9 @@ dependencies = [ ('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')] + 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 0fbce53d37..66cb466a25 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 @@ -16,6 +16,9 @@ dependencies = [ ('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')] + 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 e25ef5a1c1..781b45ed3f 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 @@ -18,6 +18,9 @@ dependencies = [ ('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')] + 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 97c0820aec..c8bc196270 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 @@ -18,6 +18,9 @@ dependencies = [ ('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')] + 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 ed152a73d9..79512f826c 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 @@ -16,6 +16,9 @@ dependencies = [ ('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')] + 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 5176f9c1ae..f949db90c2 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 @@ -16,6 +16,9 @@ dependencies = [ ('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')] + 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 35492d5a7d..7a975980fe 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 dda0a20f74..c0a121ef71 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -77,4 +78,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 a86bdc6265..2e5b1c3cc2 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 851b072492..3cc5940708 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -77,4 +78,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 900b2bb97c..f8a7666f78 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 099c18d05f..262c91f061 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 374755e896..c22d902c71 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9-20130406'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 44476dd915..4e3149189f 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 bb10e35430..0f28917f5c 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 79a133dbd2..11ffa16a41 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 @@ -21,6 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 118e666646..97c9a23292 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 @@ -21,6 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 a517c35ce4..79e4bbcd67 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -77,4 +78,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 044223ddd0..1ccc5c12ca 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -77,4 +78,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 44a477057c..3a167c9f92 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 @@ -21,6 +21,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -79,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 bce6fdd959..1ad8450e3d 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 @@ -22,6 +22,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('CBLAS', '20110120'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -83,4 +84,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 3006668423..df55e62340 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -78,4 +78,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 1b98bf29c0..968045a415 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -80,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 d3bc991a29..464a9c0441 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 @@ -83,4 +83,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 d23bfc901d..54b6d1a65f 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 @@ -81,4 +81,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 cf04d1d5c0..d513f80632 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 @@ -81,4 +81,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 e2c8a50128..4a7605ab2c 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 @@ -23,7 +23,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('CBLAS', '20110120'), - ('OpenSSL', '1.0.1f', '', True), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -85,4 +85,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 c452b12042..44158cd159 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -80,4 +80,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 da0f05502b..6a17a47968 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 @@ -83,4 +83,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 ac145f5b93..9006100969 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 @@ -82,4 +82,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 7c1af324fa..236304395e 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -64,4 +64,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 c92d41d278..fbb78f9e84 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 @@ -19,7 +19,7 @@ dependencies = [ ('zlib', '1.2.7'), ('libreadline', '6.2'), ('ncurses', '5.9'), - ('OpenSSL', '1.0.1f'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -64,4 +64,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 ff8ab76523..c6cedb61ef 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 @@ -66,4 +66,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 eb4de74217..38875e2a4f 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 @@ -64,4 +64,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' -- GitLab From ddd5f21a023bd568efbabd613b32079bdb0fb5ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 11:30:11 +0100 Subject: [PATCH 407/566] add reference for OpenSSL patch --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch index a0492d9306..bc1d39fe2d 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f_icc-fixes.patch @@ -1,3 +1,4 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) diff -ru openssl-1.0.1f.orig/Configure openssl-1.0.1f/Configure --- openssl-1.0.1f.orig/Configure 2014-01-06 14:47:42.000000000 +0100 +++ openssl-1.0.1f/Configure 2014-02-14 08:41:42.000000000 +0100 -- GitLab From 302acbbd9b2d14982fe2ae9bebd1d067abec8f64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 11:32:20 +0100 Subject: [PATCH 408/566] add missing easyconfig --- .../OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..ac69ef38a5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1f-goalf-1.5.12-no-OFED.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1f' + +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': 'goalf', 'version': '1.5.12-no-OFED'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.7')] + +# makefile is not suitable for parallel build +parallel = 1 +runtest = 'test' + +moduleclass = 'system' -- GitLab From ff0ba2bd5f12d65df72188e9efa21f340cd6801a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 11:57:31 +0100 Subject: [PATCH 409/566] style fixes in ParMETIS description --- .../easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb | 8 ++++---- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb | 8 ++++---- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb | 8 ++++---- .../easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb index ff151de1b0..1f858cb94c 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-3.1.1-goolf-1.4.10.eb @@ -3,10 +3,10 @@ version = '3.1.1' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, -meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes -routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in -ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning -schemes.""" + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb index 7ba66e723b..ad06991953 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goolf-1.4.10.eb @@ -3,10 +3,10 @@ version = '4.0.2' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, -meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes -routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in -ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning -schemes.""" + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb index c745675e3d..ebbc3db5a2 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-goolf-1.4.10.eb @@ -3,10 +3,10 @@ version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, -meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes -routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in -ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning -schemes.""" + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb index 6c8b6f15d8..db08a4e643 100644 --- a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-ictce-5.5.0.eb @@ -3,10 +3,10 @@ version = '4.0.3' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, -meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes -routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in -ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning -schemes.""" + meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes + routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in + ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning + schemes.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} -- GitLab From e4b232f9ee2b0355f65b65d36cc407b083429d05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 12:08:06 +0100 Subject: [PATCH 410/566] add OpenSSL OS dep in Python 3.3.2 easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb | 3 +++ easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 3 +++ 3 files changed, 9 insertions(+) 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 e5c911cbe3..73c3832a10 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -41,4 +42,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 18501aa0f5..cef0a03fea 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -41,4 +42,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' 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 2bc16986cf..6312c62e4e 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 @@ -19,6 +19,7 @@ dependencies = [ ('zlib', '1.2.8'), ('libreadline', '6.2'), ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1f'), # OS dependency should be preferred for security reasons ] # order is important! @@ -41,4 +42,6 @@ exts_list = [ }), ] +osdependencies = [('openssl-devel', 'libssl-dev')] + moduleclass = 'lang' -- GitLab From f4b066e336ff093fa13608a508c60f9be77ba61f Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 14 Feb 2014 12:37:00 +0100 Subject: [PATCH 411/566] added required MAFFT_BINARIES env var --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index b608cfdee4..700a8e8695 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -22,6 +22,8 @@ skipsteps = ['configure'] start_dir = 'core' installopts = 'PREFIX=%(installdir)s' +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + sanity_check_paths = { 'files': ['bin/mafft'], 'dirs': [], -- GitLab From 95254ad7d2967c029b9c8e7150684311bb718f0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 14:24:07 +0100 Subject: [PATCH 412/566] minor style fixes in protobuf easyconfigs --- .../easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb | 4 ++-- .../easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb index 506350152b..7d1df26fcd 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.4.0a-goolf-1.4.10.eb @@ -7,11 +7,11 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['https://protobuf.googlecode.com/files/'] +source_urls = [GOOGLECODE_SOURCE] sanity_check_paths = { 'files': ['bin/protoc'], - 'dirs': [] + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb index 149c94d9e7..f6ab1b5fd2 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.4.10.eb @@ -7,11 +7,11 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCE_TAR_GZ] -source_urls = ['https://protobuf.googlecode.com/files/'] +source_urls = [GOOGLECODE_SOURCE] sanity_check_paths = { 'files': ['bin/protoc'], - 'dirs': [] + 'dirs': [], } moduleclass = 'devel' -- GitLab From f323768568a352e6758e7bed24735953b235905c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 14:44:53 +0100 Subject: [PATCH 413/566] minor style fixes in SOAPdenovo2 easyconfigs --- .../s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb | 11 ++++++----- .../s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb | 11 ++++++----- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb index 55510047f9..f5c3b3a3ef 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb @@ -25,16 +25,17 @@ toolchainopts = {'optarch': True, 'pic': True} patches = ['fix-unistd-includes.patch'] # like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz -sources = ['%s-src-r%s.tgz' % (name, version)] -source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] +sources = ['%(name)s-src-r%(version)s.tgz'] +source_urls = [SOURCEFORGE_SOURCE] -maxparallel=1 +# parallel build is broken +maxparallel = 1 files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] sanity_check_paths = { - 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], - 'dirs': [], + 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb index f46b096cc9..32ca2a4913 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb @@ -25,16 +25,17 @@ toolchainopts = {'optarch': True, 'pic': True} patches = ['fix-unistd-includes.patch'] # like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz -sources = ['%s-src-r%s.tgz' % (name, version)] -source_urls = ['http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/','download'] +sources = ['%(name)s-src-r%(version)s.tgz'] +source_urls = [SOURCEFORGE_SOURCE] -maxparallel=1 +# parallel build is broken +maxparallel = 1 files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] sanity_check_paths = { - 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], - 'dirs': [], + 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], + 'dirs': [], } moduleclass = 'bio' -- GitLab From c7ad2e46287942bd6d9acb56919a0b54ee65e7a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 16:06:35 +0100 Subject: [PATCH 414/566] fix name of XZ dir --- easybuild/easyconfigs/x/{xz => XZ}/XZ-5.0.5-goolf-1.4.10.eb | 0 easybuild/easyconfigs/x/{xz => XZ}/XZ-5.0.5-ictce-5.3.0.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/x/{xz => XZ}/XZ-5.0.5-goolf-1.4.10.eb (100%) rename easybuild/easyconfigs/x/{xz => XZ}/XZ-5.0.5-ictce-5.3.0.eb (100%) diff --git a/easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/x/xz/XZ-5.0.5-goolf-1.4.10.eb rename to easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/x/xz/XZ-5.0.5-ictce-5.3.0.eb rename to easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb -- GitLab From 0d1dc6939a3dd052b56d0978d85691b951872e74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 16:22:57 +0100 Subject: [PATCH 415/566] use constants for source_urls --- .../easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb | 2 +- .../easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb index a532d7cc6b..5a3e833ff0 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-goolf-1.4.10.eb @@ -9,7 +9,7 @@ description = """gperftools are for use by developers so that they can create mo toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://gperftools.googlecode.com/files'] +source_urls = [GOOGLECODE_SOURCE] dependencies = [ ('Automake', '1.13.4'), diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb index e7a1a41118..bdbfa99fd8 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.1-ictce-5.3.0.eb @@ -9,7 +9,7 @@ description = """gperftools are for use by developers so that they can create mo toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://gperftools.googlecode.com/files'] +source_urls = [GOOGLECODE_SOURCE] dependencies = [ ('Automake', '1.13.4'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 83cc56ad97..df2b6201e1 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ description = """The primary goal of libunwind is to define a portable and effic toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] +source_urls = [GNU_SAVANNAH_SOURCE] sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index d8952f399c..d3931fac83 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -11,7 +11,7 @@ description = """The primary goal of libunwind is to define a portable and effic toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] +source_urls = [GNU_SAVANNAH_SOURCE] sanity_check_paths = { 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], -- GitLab From c2c518c562190daea04c8862391ac56e98fd2dad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 16:24:50 +0100 Subject: [PATCH 416/566] add missing zlib easyconfig --- .../z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb new file mode 100644 index 0000000000..e008a0db4b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-goalf-1.5.12-no-OFED.eb @@ -0,0 +1,20 @@ +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': 'goalf', 'version': '1.5.12-no-OFED'} +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 7dd76cf442c8a0df24140a52db2de138680c9ad5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 14 Feb 2014 16:46:58 +0100 Subject: [PATCH 417/566] rename to ErlangOTP and make no-java explicit Signed-off-by: Fotis Georgatos --- .../ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/e/{Erlang/Erlang-R16B02-goolf-1.4.10.eb => ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb} (92%) diff --git a/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb similarity index 92% rename from easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb rename to easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb index f16d2df15b..6f89ce5300 100644 --- a/easybuild/easyconfigs/e/Erlang/Erlang-R16B02-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/ErlangOTP/ErlangOTP-R16B02-goolf-1.4.10-no-Java.eb @@ -7,8 +7,9 @@ # $Id$ ## -name = "Erlang" +name = "ErlangOTP" version = "R16B02" +versionsuffix = "-no-Java" homepage = 'http://www.erlang.org/' description = """Erlang is a programming language used to build massively scalable @@ -21,6 +22,8 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download/'] +configopts = ' --without-javac ' + builddependencies = [('Autoconf', '2.69')] dependencies = [('ncurses', '5.9')] -- GitLab From 2bb6186e6f457ac27c4edd2c4bb7a84f6d72b066 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 14 Feb 2014 16:51:38 +0100 Subject: [PATCH 418/566] bugfix ocaml source_url Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 3 ++- 1 file changed, 2 insertions(+), 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 cb3cc4532d..1e75cdcd62 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 @@ -19,7 +19,8 @@ description = """OCaml is a general purpose industrial-strength programming lang toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = ['ocaml-%(version)s.tar.gz'] -source_urls = ['http://caml.inria.fr/pub/distrib/ocaml-%(version_major_minor)s'] +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')] -- GitLab From e24edaeccfc45cf1457ce5b3601e31331e7f3ae0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 16:55:20 +0100 Subject: [PATCH 419/566] minor style fixes --- .../h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb | 2 +- .../m/Molekel/Molekel-5.4.0_Linux_x86_64.eb | 2 +- easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb | 12 ++++++------ 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb index ba4c7ce505..9701129849 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # fi. http://www.hdfgroup.org/ftp/HDF5/tools/h4toh5/bin/h4h5tools-2.2.1-linux-x86_64-static.tar.gz source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/bin' % name] -sources = ['%s-%s%s.tar.gz' % ('h4h5tools', version, versionsuffix)] +sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['h5toh4', 'h5toh4']], diff --git a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb index 4d43f45e84..d68a450d82 100644 --- a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0_Linux_x86_64.eb @@ -14,7 +14,7 @@ source_urls = ['ftp://ftp.cscs.ch/out/molekel/molekel_%(version_major_minor)s'] sanity_check_paths = { 'files': ["bin/Molekel"], - 'dirs': [] + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb index a94cde2423..6fc9490675 100644 --- a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb +++ b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb @@ -13,16 +13,16 @@ toolchain = {'version': 'dummy', 'name': 'dummy'} subdir = '_'.join(version.split('-')[0].split('.')) source_urls = ['http://ftp.vim.org/editors/NEdit/v%s/executables' % subdir ] -sources = ["nedit-%s%s.tar.gz" % (version, versionsuffix)] - -sanity_check_paths = { - 'files': ["nc", "nedit"], - 'dirs': [] -} +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] modextrapaths = { 'PATH': '', 'MANPATH': '', } +sanity_check_paths = { + 'files': ["nc", "nedit"], + 'dirs': [], +} + moduleclass = 'tools' -- GitLab From 4e8ce79a22acbb660ddec514a29c9c81078c0821 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 14 Feb 2014 17:15:32 +0100 Subject: [PATCH 420/566] fixed versionsuffix --- .../m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb index 700a8e8695..0fd4f0bb04 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.130-with-extensions-goolf-1.4.10.eb @@ -5,7 +5,7 @@ name = 'MAFFT' version = '7.130' -versionsuffix = 'with-extensions' +versionsuffix = '-with-extensions' homepage = 'http://mafft.cbrc.jp/alignment/software/' description = """MAFFT is a multiple sequence alignment program @@ -16,7 +16,7 @@ description = """MAFFT is a multiple sequence alignment program toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [homepage] -sources = ['%(namelower)s-%(version)s-%(versionsuffix)s-src.tgz'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] skipsteps = ['configure'] start_dir = 'core' -- GitLab From a7cd75983b80ff7e46dff261bcd3cbda026e9805 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 14 Feb 2014 17:20:32 +0100 Subject: [PATCH 421/566] fixed versionsuffix as @boegel suggested --- easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb index a224586986..a2500b9e04 100644 --- a/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/sickle/sickle-1.210-goolf-1.4.10.eb @@ -3,20 +3,20 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel -easyblock='MakeCp' +easyblock = 'MakeCp' name = "sickle" # version checked running "sickle --version" version = "1.210" # git_commit_id bab15f7d14b06400be37d50df7c092b1ec6fe0c5 -versionsuffix = "bab15f7" +versionsuffix = "-bab15f7" homepage = 'https://github.com/najoshi/sickle' description = """ Windowed Adaptive Trimming for fastq files using quality """ toolchain = {'name': 'goolf', 'version': '1.4.10'} -git_commit_id = versionsuffix +git_commit_id = versionsuffix[1:] sources = ['%s.tar.gz' % git_commit_id] source_urls = ['https://github.com/najoshi/sickle/archive/'] -- GitLab From 31bc689b853a102ca8fb9e2f384947fa1a27a30b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Feb 2014 18:33:27 +0100 Subject: [PATCH 422/566] disable parallel build for OCaml --- easybuild/easyconfigs/o/OCaml/OCaml-4.01.0-goolf-1.4.10.eb | 3 +++ 1 file changed, 3 insertions(+) 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 1e75cdcd62..d660b5e167 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 @@ -28,6 +28,9 @@ dependencies = [('ncurses', '5.9')] prefix_opt = "-prefix " makeopts = "world.opt" +# parallel build tends to break +parallel = 1 + sanity_check_paths = { 'files': ["bin/ocaml", "bin/ocamlc"], 'dirs': [] -- GitLab From 4e71d17073b43bc808591bffb5435a0994c81924 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 01:29:00 +0100 Subject: [PATCH 423/566] add Cufflinks-2.0.2-ictce-5.3.0.eb Signed-off-by: Fotis Georgatos --- .../Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb new file mode 100644 index 0000000000..c7a3e3e37c --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.0.2-ictce-5.3.0.eb @@ -0,0 +1,44 @@ +## +# 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 +# Jens Timmerman (Ghent University) +# 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 = '2.0.2' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cufflinks.cbcb.umd.edu/downloads/'] + +patches = ['Cufflinks-2.1.1_init-error.patch'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +configopts += ' --enable-intel64 ' +preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 4e42ac23a994b889b6be2b70198607e6909d4950 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 01:38:13 +0100 Subject: [PATCH 424/566] add HTSeq builds Signed-off-by: Fotis Georgatos --- ...HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb | 29 +++++++++++++++++++ .../HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb 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 new file mode 100644 index 0000000000..467ed7ee6d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.5.4p5' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +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' 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 new file mode 100644 index 0000000000..d593001ecd --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.5.4p5' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +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 89f625fc41f016e50734bee23b803be0582dae1c Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 01:55:53 +0100 Subject: [PATCH 425/566] add GMAP variants Signed-off-by: Fotis Georgatos --- .../g/GMAP/GMAP-2013-11-27-goolf-1.4.10.eb | 23 +++++++++++++++++++ .../g/GMAP/GMAP-2013-11-27-ictce-5.3.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-goolf-1.4.10.eb new file mode 100644 index 0000000000..809e34a7b8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +name = 'GMAP' +version = '2013-11-27' + +homepage = 'http://research-pub.gene.com/gmap/' +description = "A Genomic Mapping and Alignment Program for mRNA and EST Sequences" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = ['%(namelower)s-gsnap-%(version)s.tar.gz'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), +] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gmap", "bin/gsnap"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.3.0.eb new file mode 100644 index 0000000000..4e6d4dcdae --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP/GMAP-2013-11-27-ictce-5.3.0.eb @@ -0,0 +1,23 @@ +name = 'GMAP' +version = '2013-11-27' + +homepage = 'http://research-pub.gene.com/gmap/' +description = "A Genomic Mapping and Alignment Program for mRNA and EST Sequences" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = ['%(namelower)s-gsnap-%(version)s.tar.gz'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.7'), +] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gmap", "bin/gsnap"], + 'dirs': [], +} + +moduleclass = 'tools' -- GitLab From 44657ab838d41165542e22785ccc5dbf6d2187d0 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 01:58:06 +0100 Subject: [PATCH 426/566] uncomment Cufflinks in HPCBIOS_Bioinfo Signed-off-by: Fotis Georgatos --- .../h/HPCBIOS_Bioinfo/HPCBIOS_Bioinfo-20130829-ictce-5.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 1d4aeb5a5a..1ea22d3ff3 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 @@ -35,7 +35,7 @@ dependencies = [ ('biodeps', '1.6'), ('CD-HIT', '4.5.4', '-2011-03-07'), ('ClustalW2', '2.1'), -# ('Cufflinks', '2.0.2'), + ('Cufflinks', '2.0.2'), ('EMBOSS', '6.5.7'), ('FASTA', '36.3.5e'), ('FASTX-Toolkit', '0.0.13.2'), -- GitLab From c6a5659fd22717a305ffca3169bbd47da5297f39 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 02:37:43 +0100 Subject: [PATCH 427/566] handle ispc comments Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb | 29 ------------------- .../i/ispc/{ispc-1.5.0.eb => ispc-1.6.0.eb} | 5 +--- 2 files changed, 1 insertion(+), 33 deletions(-) delete mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb rename easybuild/easyconfigs/i/ispc/{ispc-1.5.0.eb => ispc-1.6.0.eb} (85%) diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb deleted file mode 100644 index f08911ac1e..0000000000 --- a/easybuild/easyconfigs/i/ispc/ispc-1.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ - -easyblock = 'Tarball' - -name = 'ispc' -version = '1.3.0' - -homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' -description = """Intel SPMD Program Compilers; An open-source compiler for high-performance - SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, - with extensions for 'single program, multiple data' (SPMD) programming. - Under the SPMD model, the programmer writes a program that generally appears - to be a regular serial program, though the execution model is actually that - a number of program instances execute in parallel on the hardware.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# eg. https://github.com/downloads/ispc/ispc/ispc-v1.3.0-linux.tar.gz -# or better for later: https://github.com/ispc/ispc/tarball/v1.3.0 -sources = ['ispc-v%(version)s-linux.tar.gz'] -source_urls = ['https://github.com/downloads/ispc/ispc/'] - -sanity_check_paths = { - 'files': ["ispc"], - 'dirs': [] -} - -modextrapaths = {'PATH': ''} - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb similarity index 85% rename from easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb rename to easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb index 384c54d6b1..5f9a44b8c2 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.5.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb @@ -1,8 +1,7 @@ - easyblock = 'Tarball' name = 'ispc' -version = '1.5.0' +version = '1.6.0' homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' description = """Intel SPMD Program Compilers; An open-source compiler for high-performance @@ -14,8 +13,6 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = {'name': 'dummy', 'version': 'dummy'} -# eg. https://github.com/downloads/ispc/ispc/ispc-v1.5.0-linux.tar.gz -# or better for later: https://github.com/ispc/ispc/tarball/v1.5.0 sources = ['ispc-v%(version)s-linux.tar.gz'] source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] -- GitLab From 1da403e0940b6e59554bfa8ac4d23bc15395f7bf Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sat, 15 Feb 2014 02:40:41 +0100 Subject: [PATCH 428/566] fix mcpp to include specific compiler Signed-off-by: Fotis Georgatos --- .../m/mcpp/{mcpp-2.7.2.eb => mcpp-2.7.2-GCC-4.7.2.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/m/mcpp/{mcpp-2.7.2.eb => mcpp-2.7.2-GCC-4.7.2.eb} (84%) diff --git a/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb b/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2-GCC-4.7.2.eb similarity index 84% rename from easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb rename to easybuild/easyconfigs/m/mcpp/mcpp-2.7.2-GCC-4.7.2.eb index 60b167dc2a..5a89179795 100644 --- a/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2.eb +++ b/easybuild/easyconfigs/m/mcpp/mcpp-2.7.2-GCC-4.7.2.eb @@ -1,4 +1,3 @@ - name = 'mcpp' version = '2.7.2' @@ -7,7 +6,7 @@ description = """MCPP is a portable C/C++ preprocessor, supporting GCC, Visual C Its source is highly configurable and can generate executables of various specs. It accompanies a validation suite to check preprocessor's conformance and quality exhaustively.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} # rewire towards your favourite compiler +toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = [SOURCE_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] -- GitLab From a97ee0525d9266c7eea2d703cf39dac2e0c077a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 13:11:59 +0100 Subject: [PATCH 429/566] only use --mpi for recent h5py versions (v2.2 and up) --- .../h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb | 3 --- .../easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb | 2 +- 9 files changed, 1 insertion(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 653f7ba173..b8f9029260 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -19,9 +19,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.7'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb index 88f1a0722b..ede8e25c17 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-goolf-1.4.10-Python-2.7.3.eb @@ -19,9 +19,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.7'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb index 0d6f395cc9..b7aec3d30e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.0.6-Python-2.7.3.eb @@ -18,9 +18,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.7'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb index 5df5af9d06..7a0e274285 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-4.1.13-Python-2.7.3.eb @@ -18,9 +18,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb index 7a551a0b1d..17626346c5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.0.1-ictce-5.3.0-Python-2.7.3.eb @@ -18,9 +18,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.10', '-gpfs'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb index 02bd36b338..b83b6afd0a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-goolf-1.4.10-Python-2.7.3.eb @@ -19,9 +19,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb index 881a2f04c6..00b462fa19 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-4.1.13-Python-2.7.3.eb @@ -19,9 +19,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb index 79e383bb0e..e2324d7186 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.1.3-ictce-5.3.0-Python-2.7.3.eb @@ -19,9 +19,6 @@ pythonver = '2.7.3' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled -makeopts = '--mpi' - dependencies = [ (python, pythonver), ('HDF5', '1.8.10'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb index c14fb5eb8f..fd76fc37b5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.2.1-ictce-5.5.0-Python-2.7.5.eb @@ -19,7 +19,7 @@ pythonver = '2.7.5' pythonshortver = '.'.join(pythonver.split('.')[0:2]) versionsuffix = '-%s-%s' % (python, pythonver) -# make sure that MPI features are enabled +# make sure that MPI features are enabled (new in h5py v2.2) makeopts = '--mpi' dependencies = [ -- GitLab From f1a033ba374a65035d0eafb3ec56747f0041c250 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 13:45:10 +0100 Subject: [PATCH 430/566] add required patch file for Python 3.3.2 with ictce --- .../easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb | 2 ++ .../easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb | 2 ++ .../p/Python/python-3.3_libffi-include-xmmintrin.patch | 10 ++++++++++ 3 files changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/python-3.3_libffi-include-xmmintrin.patch 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 cef0a03fea..8cd8056d73 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 @@ -13,6 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['python-3.3_libffi-include-xmmintrin.patch'] + # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), 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 6312c62e4e..27461c4521 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 @@ -13,6 +13,8 @@ scipyversion = '0.12.0' source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['python-3.3_libffi-include-xmmintrin.patch'] + # python needs bzip2 to build the bz2 package dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/python-3.3_libffi-include-xmmintrin.patch b/easybuild/easyconfigs/p/Python/python-3.3_libffi-include-xmmintrin.patch new file mode 100644 index 0000000000..79aaa325fc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/python-3.3_libffi-include-xmmintrin.patch @@ -0,0 +1,10 @@ +--- Python-3.3.2/Modules/_ctypes/libffi/src/x86/ffi64.c.orig 2014-02-15 13:40:51.000000000 +0100 ++++ Python-3.3.2/Modules/_ctypes/libffi/src/x86/ffi64.c 2014-02-15 13:40:58.000000000 +0100 +@@ -39,6 +39,7 @@ + #define MAX_SSE_REGS 8 + + #if defined(__INTEL_COMPILER) ++#include "xmmintrin.h" + #define UINT128 __m128 + #else + #if defined(__SUNPRO_C) -- GitLab From 745be3c1f7c1b0780ca89bfec6d79c4ff3b7e3bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 13:47:27 +0100 Subject: [PATCH 431/566] revert back to using VersionIndependentPythonPackage, to avoid failing sanity check --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 12550055eb..368c166390 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -1,4 +1,4 @@ -easyblock = 'VSCPythonPackage' +easyblock = 'VersionIndependentPythonPackage' name = 'vsc-mympirun' version = '3.2.1' -- GitLab From fc8a888f6d9cc31cfbf2e94cbed4158bd10ddfad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 13:50:34 +0100 Subject: [PATCH 432/566] fix sanity check for python-dateutil --- .../python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb index 90bb4098db..b51abe00cd 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-goolf-1.4.10-Python-2.7.3.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] py_short_ver = ".".join(pythonversion.split(".")[0:2]) -pylibdir = "lib/python%s/site-packages/%%(name)s" % py_short_ver +pylibdir = "lib/python%s/site-packages/python_dateutil" % py_short_ver sanity_check_paths = { 'files': ["%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver)], diff --git a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb index 37d02ed949..66b4d0b80c 100644 --- a/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-dateutil/python-dateutil-2.1-ictce-4.1.13-Python-2.7.3.eb @@ -19,7 +19,7 @@ versionsuffix = "-%s-%s" % (python, pythonversion) dependencies = [(python, pythonversion)] py_short_ver = ".".join(pythonversion.split(".")[0:2]) -pylibdir = "lib/python%s/site-packages/%%(name)s" % py_short_ver +pylibdir = "lib/python%s/site-packages/python_dateutil" % py_short_ver sanity_check_paths = { 'files': ["%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver)], -- GitLab From e5acdb2448e5b1003ccef583c9e66abab91380de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 13:59:29 +0100 Subject: [PATCH 433/566] add missing patch file for ZeroMQ 3.2.2 with ictce --- .../z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb | 2 ++ .../easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb | 2 ++ .../easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2_icc.patch | 12 ++++++++++++ 3 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2_icc.patch diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb index c184da63a2..7f28e21cd4 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-4.1.13.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} 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-${EBVERSIONOPENPGM%.*}" ' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb index fe4983bf46..4ab3604a00 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2-ictce-5.3.0.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://download.zeromq.org/'] sources = [SOURCELOWER_TAR_GZ] +patches = ['ZeroMQ-%(version)s_icc.patch'] + # --with-pgm will use shipped OpenPGM (in foreign subdir) configopts = '--with-pic --with-system-pgm ' configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2_icc.patch b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2_icc.patch new file mode 100644 index 0000000000..eeb3dca310 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.2_icc.patch @@ -0,0 +1,12 @@ +diff -ru zeromq-3.2.2.orig/src/stream_engine.hpp zeromq-3.2.2/src/stream_engine.hpp +--- zeromq-3.2.2.orig/src/stream_engine.hpp 2012-11-14 02:09:14.000000000 +0100 ++++ zeromq-3.2.2/src/stream_engine.hpp 2014-02-15 13:57:14.074526627 +0100 +@@ -94,7 +94,7 @@ + + // Size of the greeting message: + // Preamble (10 bytes) + version (1 byte) + socket type (1 byte). +- const static size_t greeting_size = 12; ++ static const size_t greeting_size = 12; + + // True iff we are registered with an I/O poller. + bool io_enabled; -- GitLab From ff35284bf9087683a8afc52f5bd57f7f4d0ce32a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Feb 2014 21:28:52 +0100 Subject: [PATCH 434/566] bump version to v1.11 and update release notes --- RELEASE_NOTES | 25 ++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 25 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d843a5fb38..be302f6580 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -1,9 +1,32 @@ This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package. For more detailed information, please see the git log. -The latest version of easybuild-easyconfig provides 2,203 easyconfig files, for 414 different software packages +The latest version of easybuild-easyconfig provides 2,319 easyconfig files, for 444 different software packages and 29 different (compiler) toolchains. +v1.11.0 (February 16th 2013) +---------------------------- + +feature + bugfix release +- added example easyconfig files for 30 new software packages: + argtable (#669), Clustal-Omega (#669), Coreutils (#582), GMT (#560), gperftools (#596), grep (#582), h4toh5 (#597), + libunwind (#596), Lmod (#600, #692), Lua (#600, #692), MAFFT (#654), Molekel (#597), NEdit (#597), + netcdf4-python (#660), nodejs (#678), OCaml (#704), patch (#582), PhyML (#664), + PRACE Common Production Environment (#599), protobuf (#680), python-dateutil (#438), sed (#582), sickle (#651), + Tesla-Deployment-Kit (#489), TREE-PUZZLE (#662), VCFtools (#626), Vim (#665), vsc-mympirun-scoop (#661), + vsc-processcontrol (#661), XZ (#582) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + - OpenSSL with ictce toolchain (#703) +- various enhancements, including: + - using more constants and templates (#613, #615) + - specify OS dependency for SSL support, with OpenSSL dependency as fallback (#703) +- various bug fixes, including: + - fix unit tests after (internal) framework API changes (#667, #672) + - fix homepage in vsc-mympirun easyconfig file (#681) + - align OpenMPI easyconfigs (#650) + - add additional source URL in Qt easyconfigs (#676) + - specify correct $PATH specification and define $CHPL_HOME for Chapel (#683) + v1.10.0 (December 24th 2013) ---------------------------- diff --git a/setup.py b/setup.py index 98addcaa37..88e12b07b3 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "1.11.0.0dev" +VERSION = "1.11.0.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 878cd81d9ffc6a6d6d8c2563bba89f186559ea35 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 16 Feb 2014 16:45:54 +0100 Subject: [PATCH 435/566] netloc is not really beta, misnomer from past work fixed Signed-off-by: Fotis Georgatos --- ...-0.5beta-gcccuda-2.6.10.eb => netloc-0.5-gcccuda-2.6.10.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/n/netloc/{netloc-0.5beta-gcccuda-2.6.10.eb => netloc-0.5-gcccuda-2.6.10.eb} (89%) diff --git a/easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb similarity index 89% rename from easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb index b8c85aae37..f570d5694f 100644 --- a/easybuild/easyconfigs/n/netloc/netloc-0.5beta-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/n/netloc/netloc-0.5-gcccuda-2.6.10.eb @@ -1,6 +1,5 @@ name = 'netloc' version = "0.5" -versionsuffix = "beta" homepage = 'http://www.open-mpi.org/software/netloc' description = """The Portable Network Locality (netloc) software package provides @@ -19,7 +18,7 @@ configopts = '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--with-jansson=$EBROOTJANSSON ' # jansson support # fi. http://www.open-mpi.org/software/netloc/v0.5/downloads/netloc-0.5.tar.gz -source_urls = [ homepage + '/v%(version_major_minor)s/downloads'] +source_urls = [homepage + '/v%(version_major_minor)s/downloads'] sources = [SOURCE_TAR_GZ] moduleclass = 'system' -- GitLab From baea30861fa9292e3ef1758384fe660ac0ae0bf7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Sun, 16 Feb 2014 19:22:55 +0100 Subject: [PATCH 436/566] template properly mvapich2 easyconfigs Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb | 2 +- easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb | 2 +- .../easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb index fd7d023894..6d98d3a032 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'ClangGCC', 'version': '1.1.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['mvapich2-%s.tgz' % version] +sources = [SOURCELOWER_TGZ] dependencies = [('Bison', '2.7')] diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb index 229478ec5e..e1fdfb364f 100644 --- a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb +++ b/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb @@ -7,7 +7,7 @@ description = "This is an MPI 3.0 implementation. It is based on MPICH2 and MVI toolchain = {'name': 'ClangGCC', 'version': '1.2.3'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['mvapich2-%s.tgz' % version] +sources = [SOURCELOWER_TGZ] dependencies = [('Bison', '2.7')] 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 b140cf37c7..51fd98fd16 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 @@ -8,7 +8,7 @@ toolchain = {'name': 'iccifort', 'version': '2011.13.367'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich2/'] -sources = ['mvapich2-%(version)s.tgz'] +sources = [SOURCELOWER_TGZ] builddependencies = [('Bison', '2.7', '', ('ictce', '4.1.13'))] -- GitLab From 12f3733a8d148fe0bfb1107f66e47f4b3d808d69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Feb 2014 10:25:42 +0100 Subject: [PATCH 437/566] bump version to v1.12.0.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 88e12b07b3..d090434633 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 = "1.11.0.0" +VERSION = "1.12.0.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 1b389ac10dccbdaba40ad6bbdec8e46b0ae7a037 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 25 Feb 2014 14:39:09 +0100 Subject: [PATCH 438/566] Clang: add patch for very long uid numbers --- .../c/Clang/Clang-3.4-GCC-4.8.2.eb | 1 + .../c/Clang/Clang-3.4-llvm-ar-uid.patch | 42 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-3.4-llvm-ar-uid.patch diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb index f753226de8..da75a7816f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-GCC-4.8.2.eb @@ -36,6 +36,7 @@ patches = [ # 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', ] builddependencies = [('CMake', '2.8.12')] diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.4-llvm-ar-uid.patch b/easybuild/easyconfigs/c/Clang/Clang-3.4-llvm-ar-uid.patch new file mode 100644 index 0000000000..77af143b39 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.4-llvm-ar-uid.patch @@ -0,0 +1,42 @@ +# part of svn rev 199222. Fixes issue with very long uid numbers +diff -urN llvm-3.4.orig/tools/llvm-ar/llvm-ar.cpp llvm-3.4/tools/llvm-ar/llvm-ar.cpp +--- llvm-3.4.orig/tools/llvm-ar/llvm-ar.cpp 2013-11-08 13:35:56.000000000 +0100 ++++ llvm-3.4/tools/llvm-ar/llvm-ar.cpp 2014-02-24 13:22:18.335265229 +0100 +@@ -578,14 +578,21 @@ + } + + template +-static void printWithSpacePadding(raw_ostream &OS, T Data, unsigned Size) { ++static void printWithSpacePadding(raw_fd_ostream &OS, T Data, unsigned Size, ++ bool MayTruncate = false) { + uint64_t OldPos = OS.tell(); + OS << Data; + unsigned SizeSoFar = OS.tell() - OldPos; +- assert(Size >= SizeSoFar && "Data doesn't fit in Size"); +- unsigned Remaining = Size - SizeSoFar; +- for (unsigned I = 0; I < Remaining; ++I) +- OS << ' '; ++ if (Size > SizeSoFar) { ++ unsigned Remaining = Size - SizeSoFar; ++ for (unsigned I = 0; I < Remaining; ++I) ++ OS << ' '; ++ } else if (Size < SizeSoFar) { ++ assert(MayTruncate && "Data doesn't fit in Size"); ++ // Some of the data this is used for (like UID) can be larger than the ++ // space available in the archive format. Truncate in that case. ++ OS.seek(OldPos + Size); ++ } + } + + static void print32BE(raw_fd_ostream &Out, unsigned Val) { +@@ -600,8 +607,8 @@ + unsigned GID, unsigned Perms, + unsigned Size) { + printWithSpacePadding(Out, ModTime.toEpochTime(), 12); +- printWithSpacePadding(Out, UID, 6); +- printWithSpacePadding(Out, GID, 6); ++ printWithSpacePadding(Out, UID, 6, true); ++ printWithSpacePadding(Out, GID, 6, true); + printWithSpacePadding(Out, format("%o", Perms), 8); + printWithSpacePadding(Out, Size, 10); + Out << "`\n"; -- GitLab From 7b318c621cd12c0b36620344af46f700f87f4928 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Feb 2014 21:00:03 +0100 Subject: [PATCH 439/566] bump version to v1.11.1.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 88e12b07b3..c31a5dfad5 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 = "1.11.0.0" +VERSION = "1.11.1.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 572be72b127ba9754c9bb8498307add0d1ba6922 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Feb 2014 23:57:52 +0100 Subject: [PATCH 440/566] added 4 bowtie2 ebconfigs using MakeCp generic block --- .../b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 32 ++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 32 ++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 32 ++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 33 +++++++++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb new file mode 100644 index 0000000000..55dd34dc9d --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.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 + +easyblock='MakeCp' + +name = 'Bowtie2' +version = '2.0.5' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), + "doc", "example",] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb new file mode 100644 index 0000000000..d88124dee6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.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 + +easyblock='MakeCp' + +name = 'Bowtie2' +version = '2.0.6' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), + "doc", "example",] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..a296555869 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.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 + +easyblock='MakeCp' + +name = 'Bowtie2' +version = '2.1.0' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), + "doc", "example",] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..a035f0594b --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# 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 = 'Bowtie2' +version = '2.2.0' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s", "scripts/*"], 'bin'), + "doc", "example",] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 58d052fda2e39930565c10ec357f21c0e51ab423 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 27 Feb 2014 00:41:14 +0100 Subject: [PATCH 441/566] copy full "scripts" folder and add it to PATH --- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 6 ++++-- .../easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 6 ++++-- 4 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 55dd34dc9d..6dfbe76f04 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -21,12 +21,14 @@ sources = ['%s-%s-source.zip' % (name.lower(), version)] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), - "doc", "example",] + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), + "doc", "example", "scripts",] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'dirs': [], } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index d88124dee6..b798bacc86 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -21,12 +21,14 @@ sources = ['%s-%s-source.zip' % (name.lower(), version)] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), - "doc", "example",] + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), + "doc", "example", "scripts"] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'dirs': [], } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index a296555869..209ceb96ba 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -21,12 +21,14 @@ sources = ['%s-%s-source.zip' % (name.lower(), version)] source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] files_to_copy = [ - (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect", "scripts/*"], 'bin'), - "doc", "example",] + (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), + "doc", "example","scripts"] sanity_check_paths = { 'files': ["bin/bowtie2-align", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'dirs': [], } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index a035f0594b..2c983dec7b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -22,12 +22,14 @@ source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", - "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s", "scripts/*"], 'bin'), - "doc", "example",] + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts"] sanity_check_paths = { 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], 'dirs': [], } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' -- GitLab From ece9ec07b5e4ada7c7db8d66cfcdd82d33e509b8 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 27 Feb 2014 13:45:29 +0100 Subject: [PATCH 442/566] removed "scripts" folder from $PATH --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 3 ++- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 6dfbe76f04..57283b6361 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -29,6 +29,7 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH': 'scripts'} +# to add scripts folder to $PATH just uncomment this line +#modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index b798bacc86..401552dfac 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -29,6 +29,7 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH': 'scripts'} +# to add scripts folder to $PATH just uncomment this line +#modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 209ceb96ba..8686bbb43c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -29,6 +29,7 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH': 'scripts'} +# to add scripts folder to $PATH just uncomment this line +#modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 2c983dec7b..1ae7dd0f5e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -30,6 +30,7 @@ sanity_check_paths = { 'dirs': [], } -modextrapaths = {'PATH': 'scripts'} +# to add scripts folder to $PATH just uncomment this line +#modextrapaths = {'PATH': 'scripts'} moduleclass = 'bio' -- GitLab From d0c81f2b6e7d54958740bdb201890c8249db75ce Mon Sep 17 00:00:00 2001 From: build Date: Fri, 28 Feb 2014 14:17:33 +0200 Subject: [PATCH 443/566] Contributing new intel release --- .../easyconfigs/i/icc/icc-2013_sp1.2.144.eb | 18 +++++++++++ easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb | 21 +++++++++++++ .../i/ifort/ifort-2013_sp1.2.144.eb | 18 +++++++++++ .../easyconfigs/i/imkl/imkl-11.1.2.144.eb | 30 +++++++++++++++++++ .../easyconfigs/i/impi/impi-4.1.3.048.eb | 19 ++++++++++++ 5 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb create mode 100644 easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb new file mode 100644 index 0000000000..b742c2c7e4 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -0,0 +1,18 @@ +name = 'icc' +version = '2013_sp1.2.144' + +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'] + +# compiler class +moduleclass = 'compiler' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb new file mode 100644 index 0000000000..452f2e72f1 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '6.2.5' + +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 = '2.144' +compver = '2013_sp1.%s' % suff + +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.3.048'), + ('imkl', '11.1.%s' % suff), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb new file mode 100644 index 0000000000..058b29e416 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -0,0 +1,18 @@ +name = 'ifort' +version = '2013_sp1.2.144' + +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'] + +# compiler class +moduleclass = 'compiler' + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb new file mode 100644 index 0000000000..991935e8b0 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -0,0 +1,30 @@ +name = 'imkl' +version = '11.1.2.144' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mkl_%(version)s.tgz'] + +# deps for interface build +compver = '2013_sp1.2.144' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '4.1.3.048') +] + +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-4.1.3.048.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb new file mode 100644 index 0000000000..bf918f875b --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.3.048' + +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': 'dummy', 'version': 'dummy'} + +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 5473ee6d129dff29e063736a7ee8f39855bb4afc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Feb 2014 15:10:56 +0100 Subject: [PATCH 444/566] bump version to v1.11.1, 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 be302f6580..48872f366f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -4,6 +4,11 @@ For more detailed information, please see the git log. The latest version of easybuild-easyconfig provides 2,319 easyconfig files, for 444 different software packages and 29 different (compiler) toolchains. +v1.11.1 (February 28th 2013) +---------------------------- + +(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework + v1.11.0 (February 16th 2013) ---------------------------- diff --git a/setup.py b/setup.py index c31a5dfad5..eac0265495 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 = "1.11.1.0dev" +VERSION = "1.11.1.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 4bd8c9315d02ce7bd1a9e0d508d3f4ff1bff089b Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Tue, 4 Mar 2014 10:49:26 +0100 Subject: [PATCH 445/566] Add netifaces and netaddr. These are dependencies for the forthcoming hanythingondemand version. --- ...netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb | 24 ++++++++++++++++++ .../netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb | 25 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb create mode 100644 easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb 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 new file mode 100644 index 0000000000..dd70ce8320 --- /dev/null +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'netaddr' +version = '0.7.10' + +homepage = 'https://pypi.python.org/pypi/netaddr' +description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network +addresses""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.6' +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-0.8-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb new file mode 100644 index 0000000000..3bbd0c1fca --- /dev/null +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'netifaces' +version = '0.8' + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://alastairs-place.net/projects/netifaces/'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.6' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netifaces'} -- GitLab From 7010cff282b963205a671783f9dd66b97ef1594a Mon Sep 17 00:00:00 2001 From: "i.gutheil" Date: Fri, 7 Mar 2014 10:01:11 +0100 Subject: [PATCH 446/566] Support for ELPA --- .../e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 31 +++++++++++++ .../easyconfigs/e/ELPA/ELPA_fix-tests.patch | 44 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA_fix-tests.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb new file mode 100644 index 0000000000..df7b134658 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +name = 'ELPA' +version = '2013.11' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'usempi': True} + + +sources = ['%sJUROPA3.tar.gz' % version] + +patches = ['ELPA_fix-tests.patch'] + +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +makeopts = ' V=1 LIBS="$LIBSCALAPACK"' #FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBBLAS"' +start_dir = '%s_%s' % (name, version) + +builddependencies = [('Automake', '1.13.4')] + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA_fix-tests.patch b/easybuild/easyconfigs/e/ELPA/ELPA_fix-tests.patch new file mode 100644 index 0000000000..18fa2236a7 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA_fix-tests.patch @@ -0,0 +1,44 @@ +diff -ru ELPA_2013.11.orig/test/test_complex2.F90 ELPA_2013.11/test/test_complex2.F90 +--- ELPA_2013.11.orig/test/test_complex2.F90 2014-01-29 09:29:35.544248000 +0100 ++++ ELPA_2013.11/test/test_complex2.F90 2014-02-21 13:48:09.662072163 +0100 +@@ -79,6 +79,7 @@ + integer i, mpierr, my_blacs_ctxt, sc_desc(9), info, nprow, npcol + + integer, external :: numroc ++ integer :: iargc + + real*8 err, errmax + real*8, allocatable :: ev(:), xr(:,:) +diff -ru ELPA_2013.11.orig/test/test_complex.F90 ELPA_2013.11/test/test_complex.F90 +--- ELPA_2013.11.orig/test/test_complex.F90 2014-01-29 09:29:35.534699000 +0100 ++++ ELPA_2013.11/test/test_complex.F90 2014-02-21 13:48:33.118418351 +0100 +@@ -78,6 +78,7 @@ + integer i, mpierr, my_blacs_ctxt, sc_desc(9), info, nprow, npcol + + integer, external :: numroc ++ integer :: iargc + + real*8 err, errmax + real*8, allocatable :: ev(:), xr(:,:) +diff -ru ELPA_2013.11.orig/test/test_real2.F90 ELPA_2013.11/test/test_real2.F90 +--- ELPA_2013.11.orig/test/test_real2.F90 2014-01-29 09:29:35.573319000 +0100 ++++ ELPA_2013.11/test/test_real2.F90 2014-02-21 13:48:51.240387595 +0100 +@@ -80,6 +80,7 @@ + integer i, mpierr, my_blacs_ctxt, sc_desc(9), info, nprow, npcol + + integer, external :: numroc ++ integer :: iargc + + real*8 err, errmax + real*8, allocatable :: a(:,:), z(:,:), tmp1(:,:), tmp2(:,:), as(:,:), ev(:) +diff -ru ELPA_2013.11.orig/test/test_real.F90 ELPA_2013.11/test/test_real.F90 +--- ELPA_2013.11.orig/test/test_real.F90 2014-01-29 09:29:35.563829000 +0100 ++++ ELPA_2013.11/test/test_real.F90 2014-02-21 13:49:05.466094157 +0100 +@@ -79,6 +79,7 @@ + integer i, mpierr, my_blacs_ctxt, sc_desc(9), info, nprow, npcol + + integer, external :: numroc ++ integer :: iargc + + real*8 err, errmax + real*8, allocatable :: a(:,:), z(:,:), tmp1(:,:), tmp2(:,:), as(:,:), ev(:) -- GitLab From 9b5fa0ebac73c2a0b24838d769684db03c293458 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 10 Mar 2014 19:47:39 +0100 Subject: [PATCH 447/566] upgraded to vcftools-0.1.12. Added new man pages released in 0.1.12 to MANPATH --- ...CFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000..0d59c2f0e7 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,39 @@ +# 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 = 'VCFtools' +version = '0.1.12' + +easyblock = 'MakeCp' + +homepage = "http://vcftools.sourceforge.net/" +description = """The aim of VCFtools is to provide + methods for working with VCF files: validating, + merging, comparing and calculate some basic population + genetic statistics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin", "lib", "examples", (["bin/man1"], 'man')] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 4b4a145b87a3f641172b56b385bfcb0b5e9420cf Mon Sep 17 00:00:00 2001 From: "i.gutheil" Date: Tue, 11 Mar 2014 15:26:59 +0100 Subject: [PATCH 448/566] added autoconf and automake with ictce-5.5.0 toolchain --- .../a/Autoconf/Autoconf-2.69-ictce-5.5.0.eb | 22 ++++++++++++++++ .../a/Automake/Automake-1.13.4-ictce-5.5.0.eb | 26 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.5.0.eb new file mode 100644 index 0000000000..80861e6d4f --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +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': 'ictce', 'version': '5.5.0'} + +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-1.13.4-ictce-5.5.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb new file mode 100644 index 0000000000..b587eedafb --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.13.4-ictce-5.5.0.eb @@ -0,0 +1,26 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Alan O'Cais +# $Id$ +# +## + +name = 'Automake' +version = '1.13.4' + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +dependencies = [('Autoconf', '2.69')] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [], +} + +moduleclass = 'devel' -- GitLab From 7c5fbaa142d838950d8ad337033de2f9c9881f4a Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 11 Mar 2014 15:45:40 +0100 Subject: [PATCH 449/566] ebconfig for precompiled APBS-1.4-linux-static-x86_64 --- .../a/APBS/APBS-1.4-linux-static-x86_64.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb diff --git a/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb new file mode 100644 index 0000000000..730a5cb604 --- /dev/null +++ b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb @@ -0,0 +1,28 @@ +# 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 = 'APBS' +version = '1.4' +versionsuffix = '-linux-static-x86_64' + +easyblock = 'PackedBinary' + +homepage = 'http://www.poissonboltzmann.org/apbs' +description = """ APBS is a software package for modeling biomolecular solvation + through solution of the Poisson-Boltzmann equation (PBE), one of the most popular + continuum models for describing electrostatic interactions between molecular solutes + in salty, aqueous media. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/apbs'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From c6e7e3ce2bde44abd815ecad295e221641e50515 Mon Sep 17 00:00:00 2001 From: "i.gutheil" Date: Tue, 11 Mar 2014 16:24:18 +0100 Subject: [PATCH 450/566] added ELPA-2013.11-ictce-5.3.0.eb --- .../e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb new file mode 100644 index 0000000000..f5078c7b57 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +name = 'ELPA' +version = '2013.11' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True} + + +sources = ['%sJUROPA3.tar.gz' % version] + +patches = ['ELPA_fix-tests.patch'] + +configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' +makeopts = ' V=1 LIBS="$LIBSCALAPACK"' #FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBBLAS"' +start_dir = '%s_%s' % (name, version) + +builddependencies = [('Automake', '1.13.4')] + +parallel = 1 + +moduleclass = 'math' -- GitLab From d24f6bf857980da298ed86bde1fedb89a61e0808 Mon Sep 17 00:00:00 2001 From: build Date: Wed, 12 Mar 2014 15:50:09 +0200 Subject: [PATCH 451/566] Adding changes --- easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb | 2 +- easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb | 2 +- .../easyconfigs/i/impi/{impi-4.1.3.048.eb => impi-4.1.3.049.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/i/impi/{impi-4.1.3.048.eb => impi-4.1.3.049.eb} (96%) diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb index 452f2e72f1..005ab77007 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -14,7 +14,7 @@ compver = '2013_sp1.%s' % suff dependencies = [ ('icc', compver), ('ifort', compver), - ('impi', '4.1.3.048'), + ('impi', '4.1.3.049'), ('imkl', '11.1.%s' % suff), ] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 991935e8b0..03e70ed442 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -16,7 +16,7 @@ compver = '2013_sp1.2.144' dependencies = [ ('icc', compver), ('ifort', compver), - ('impi', '4.1.3.048') + ('impi', '4.1.3.049') ] dontcreateinstalldir = 'True' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb similarity index 96% rename from easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb rename to easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index bf918f875b..e55725a62a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.048.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -1,5 +1,5 @@ name = 'impi' -version = '4.1.3.048' +version = '4.1.3.049' homepage = 'http://software.intel.com/en-us/intel-mpi-library/' description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message -- GitLab From dd7ae865de48f81d49df503600f246a3708b34ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Mar 2014 15:25:50 +0100 Subject: [PATCH 452/566] fix source specifications for ELPA + minor style fixes --- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb | 9 +++++---- easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb index f5078c7b57..c34c5462cb 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.3.0.eb @@ -12,17 +12,18 @@ version = '2013.11' homepage = 'http://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" + toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'usempi': True} - -sources = ['%sJUROPA3.tar.gz' % version] +# download at http://elpa.rzg.mpg.de/elpa-tar-archive +sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' -makeopts = ' V=1 LIBS="$LIBSCALAPACK"' #FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBBLAS"' -start_dir = '%s_%s' % (name, version) +makeopts = ' V=1 LIBS="$LIBSCALAPACK"' +start_dir = '%(name)s_%(version)s' builddependencies = [('Automake', '1.13.4')] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb index df7b134658..43da6936b9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2013.11-ictce-5.5.0.eb @@ -12,17 +12,18 @@ version = '2013.11' homepage = 'http://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" + toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'usempi': True} - -sources = ['%sJUROPA3.tar.gz' % version] +# download at http://elpa.rzg.mpg.de/elpa-tar-archive +sources = ['%(name)s_%(version)s.006_20140312.tar.gz'] patches = ['ELPA_fix-tests.patch'] configopts = '--with-generic-simple --disable-shared FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBSCALAPACK"' -makeopts = ' V=1 LIBS="$LIBSCALAPACK"' #FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" LIBS="$LIBBLAS"' -start_dir = '%s_%s' % (name, version) +makeopts = ' V=1 LIBS="$LIBSCALAPACK"' +start_dir = '%(name)s_%(version)s' builddependencies = [('Automake', '1.13.4')] -- GitLab From ee5824d6a1dc9bd36b6d470fb9a77cbd6a1647e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Mar 2014 16:31:22 +0100 Subject: [PATCH 453/566] add gzip easyconfig to test use of ictce/6.2.5 toolchain --- .../g/gzip/gzip-1.6-ictce-6.2.5.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb new file mode 100644 index 0000000000..8c3304ae5f --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-ictce-6.2.5.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC +# Authors:: Thekla Loizou +# 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_06-19.html +## + +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = ['http://ftpmirror.gnu.org/gzip'] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' -- GitLab From fa2bd0dc9c0f99389717c068b7ea97bc2c397f14 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 13 Mar 2014 16:40:32 +0100 Subject: [PATCH 454/566] add sourceme & README.TXT for Lmod Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/README.TXT | 31 +++++++++++++++++++++++++ easybuild/easyconfigs/l/Lmod/sourceme | 26 +++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/README.TXT create mode 100644 easybuild/easyconfigs/l/Lmod/sourceme diff --git a/easybuild/easyconfigs/l/Lmod/README.TXT b/easybuild/easyconfigs/l/Lmod/README.TXT new file mode 100644 index 0000000000..ad2d283ddc --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/README.TXT @@ -0,0 +1,31 @@ + +Summary: + +This directory contains (hopefully) sufficient gear in order to let you +bootstrap towards the Lmod implementation of environment modules. + +Howto: + +Assuming you have successfully used the bootstrap procedure of EasyBuild, +you should be able to initiate a recursive build of the following bits: + +l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb +l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb +n/ncurses/ncurses-5.9-GCC-4.8.2.eb +g/GCC/GCC-4.8.2.eb + +This set is expected to be the needed substrate to launch you towards Lmod, +which gets activated with the script sitting in the same directory: + +`source sourceme` # N.B. it does direct env. var. assignments; that's intentional + +Then try: + +`ml av` # ie. Lmod equivalent to `module avail` + +You should now be able to try alternative Lmod/Lua versions, such as 3.x variety and so on so forth. + +enjoy, +Fotis + +2014-03-13 diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme new file mode 100644 index 0000000000..c934dd7d78 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -0,0 +1,26 @@ +## Contributed by Fotis Georgatos , as means to help others wishing to ride on Lmod +# +# This script helps to implement policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html +# +# prereq: Lua/5.1.4-8-GCC-4.8.2 +# prereq: Lmod/5.2.5-GCC-4.8.2 + +## Remember to change the following, as per individual case +EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"/opt/apps/HPCBIOS.20131224"} +#EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} + +TOOLCHAIN="GCC-4.8.2" +VERSIONLUA="5.1.4-8" +VERSIONLMOD="5.2.5" + +PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN +PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD + +export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH +source $PREFIXLMOD/init/profile + +export PAGER=cat # Keep it simple, for a start +unset LMOD_IGNORE_CACHE # Lmod cache should be working now +export LMOD_COLORIZE=YES # YMMV + +echo 'Now, try fi. `module avail -d compiler` or `ml av` and observe output' -- GitLab From f374d3fb4da4872ae8cc375baf17e2cfc4d03372 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 13 Mar 2014 16:47:31 +0100 Subject: [PATCH 455/566] add hint on Lmod & buildsets relation Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/README.TXT | 10 ++++++---- easybuild/easyconfigs/l/Lmod/sourceme | 4 ++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/README.TXT b/easybuild/easyconfigs/l/Lmod/README.TXT index ad2d283ddc..d371af9bfb 100644 --- a/easybuild/easyconfigs/l/Lmod/README.TXT +++ b/easybuild/easyconfigs/l/Lmod/README.TXT @@ -15,15 +15,17 @@ n/ncurses/ncurses-5.9-GCC-4.8.2.eb g/GCC/GCC-4.8.2.eb This set is expected to be the needed substrate to launch you towards Lmod, -which gets activated with the script sitting in the same directory: +which gets activated with the `sourceme` script sitting in the same directory: -`source sourceme` # N.B. it does direct env. var. assignments; that's intentional +`source sourceme` # N.B. it does direct assignments on environment variables; that's very intentional Then try: -`ml av` # ie. Lmod equivalent to `module avail` +`ml av` # ie. the Lmod equivalent to `module avail` ; it should work -You should now be able to try alternative Lmod/Lua versions, such as 3.x variety and so on so forth. +If so, you implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html +Lmod's caching can help to work with *buildsets*; ref. https://fosdem.org/2014/schedule/event/hpc_devroom_hpcbios/ +You should now be able to try alternative Lmod/Lua versions, such as 3.x variety, enable cache, and so on so forth. enjoy, Fotis diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index c934dd7d78..515aafba07 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -6,8 +6,8 @@ # prereq: Lmod/5.2.5-GCC-4.8.2 ## Remember to change the following, as per individual case -EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"/opt/apps/HPCBIOS.20131224"} -#EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} +EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} +#EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"/opt/apps/HPCBIOS.20131224"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" -- GitLab From e398892e207124e6a2956bff00b87cd3280538f1 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 13 Mar 2014 17:01:08 +0100 Subject: [PATCH 456/566] prereqs pedantic comment Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/README.TXT | 2 +- easybuild/easyconfigs/l/Lmod/sourceme | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/README.TXT b/easybuild/easyconfigs/l/Lmod/README.TXT index d371af9bfb..6e4cf47e00 100644 --- a/easybuild/easyconfigs/l/Lmod/README.TXT +++ b/easybuild/easyconfigs/l/Lmod/README.TXT @@ -25,7 +25,7 @@ Then try: If so, you implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html Lmod's caching can help to work with *buildsets*; ref. https://fosdem.org/2014/schedule/event/hpc_devroom_hpcbios/ -You should now be able to try alternative Lmod/Lua versions, such as 3.x variety, enable cache, and so on so forth. +You should now be able to try alternative Lmod/Lua versions, such as 3.x variety, toggle cache, and so forth. enjoy, Fotis diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 515aafba07..3f7c86e156 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -2,8 +2,10 @@ # # This script helps to implement policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html # -# prereq: Lua/5.1.4-8-GCC-4.8.2 # prereq: Lmod/5.2.5-GCC-4.8.2 +# prereq: Lua/5.1.4-8-GCC-4.8.2 +# +# build prereqs, take a note: GCC/4.8.2 & ncurses/5.9 ## Remember to change the following, as per individual case EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} -- GitLab From 427aa96c7c53cbea2abbae8a5143674d0e57c973 Mon Sep 17 00:00:00 2001 From: pub Date: Thu, 13 Mar 2014 20:11:52 +0100 Subject: [PATCH 457/566] iomkl-6.6.2.eb toolchain and dependencies --- .../g/gzip/gzip-1.6-iomkl-6.6.2.eb | 22 +++++++++++ .../hwloc-1.8.1-iccifort-2013_sp1.2.144.eb | 17 +++++++++ .../i/iccifort/iccifort-2013_sp1.2.144.eb | 16 ++++++++ .../i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb | 35 +++++++++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb | 23 +++++++++++ .../OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 38 +++++++++++++++++++ 6 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb new file mode 100644 index 0000000000..fe81686c74 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb @@ -0,0 +1,22 @@ +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'iomkl', 'version': '6.6.2'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = ['http://ftpmirror.gnu.org/gzip'] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb new file mode 100644 index 0000000000..4578e9944c --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb @@ -0,0 +1,17 @@ +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': 'iccifort', 'version': '2013_sp1.2.144'} + +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/iccifort/iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb new file mode 100644 index 0000000000..c51fb8ee78 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2013_sp1.2.144' + +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/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb new file mode 100644 index 0000000000..7c293cda0a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -0,0 +1,35 @@ +name = 'imkl' +version = '11.1.2.144' + +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': 'dummy', 'version': 'dummy'} + +sources = ['l_mkl_%(version)s.tgz'] + +compver = '2013_sp1.2.144' +comp = ('iccifort', compver) + +# deps for interface build +mpi = 'OpenMPI' +mpiver = '1.6.5' +versionsuffix = '-%s-%s' % (mpi, mpiver) + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (mpi, mpiver, '', comp), +] + +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-6.6.2.eb b/easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb new file mode 100644 index 0000000000..7c34f7ee3c --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-6.6.2.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '6.6.2' + +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 = '2013_sp1.2.144' +comp = ('iccifort', compver) +ompi = 'OpenMPI' +ompiver = '1.6.5' + +dependencies = [ + ('icc', compver), + ('ifort', compver), + (ompi, ompiver, '', comp), + ('imkl', '11.1.2.144', '-%s-%s' % (ompi, ompiver)), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000..6f2cfbd602 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -0,0 +1,38 @@ +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': 'iccifort', 'version': '2013_sp1.2.144'} + +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 + +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, shared_lib_ext) for libfile in ["mca_common_sm", "mpi_cxx", + "mpi_f77", "mpi_f90", + "mpi", "ompitrace", "open-pal", + "otfaux", + "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' -- GitLab From 32989180b34a055248d58f7c96298a753f0d8a78 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 13 Mar 2014 22:33:24 +0100 Subject: [PATCH 458/566] goolf-1.4.10-no-OFED.eb and dependencies --- .../f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb | 32 ++++++++++++ .../g/gompi/gompi-1.4.10-no-OFED.eb | 26 ++++++++++ .../g/goolf/goolf-1.4.10-no-OFED.eb | 44 ++++++++++++++++ ...0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb | 51 +++++++++++++++++++ .../OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 31 +++++++++++ ....10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 25 +++++++++ 6 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb new file mode 100644 index 0000000000..7e4ef9ffc4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.4.10-no-OFED.eb @@ -0,0 +1,32 @@ +name = 'FFTW' +version = '3.3.3' + +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': '1.4.10-no-OFED'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb b/easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb new file mode 100644 index 0000000000..50c30a5ac2 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.4.10-no-OFED.eb @@ -0,0 +1,26 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.4.10' +versionsuffix = '-no-OFED' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.7.2' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.6.4' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, versionsuffix, comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb new file mode 100644 index 0000000000..756c57643b --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb @@ -0,0 +1,44 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.4.10' +versionsuffix = '-no-OFED' + +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 = '4.7.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.6' +blas = '%s-%s' % (blaslib, blasver) +blas_suff = '-LAPACK-3.4.2' + +# 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) + + +# toolchain used to build goalf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s%s" % (version, versionsuffix) +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', '1.6.4', versionsuffix, comp), + (blaslib, blasver, blas_suff, comp_mpi_tc), + ('FFTW', '3.3.3', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blas_suff), comp_mpi_tc) +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..f64ed2e18b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-no-OFED-LAPACK-3.4.2.eb @@ -0,0 +1,51 @@ +name = 'OpenBLAS' +version = '0.2.6' + +lapackver = '3.4.2' +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': '1.4.10-no-OFED'} + +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 = [ + 'OpenBLAS-%s_Makefile-LAPACK-sources.patch' % version, + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +makeopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb new file mode 100644 index 0000000000..17f945a10e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -0,0 +1,31 @@ +name = 'OpenMPI' +version = '1.6.4' +versionsuffix = '-no-OFED' + +homepage = 'http://www.open-mpi.org/' +description = "The Open MPI Project is an open source MPI-2 implementation." + +toolchain = {'name': 'GCC', 'version': '4.7.2'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.6.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_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/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.eb new file mode 100644 index 0000000000..5e0e14ba2c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-no-OFED-OpenBLAS-0.2.6-LAPACK-3.4.2.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': '1.4.10-no-OFED'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s.tgz'] + +blaslib = 'OpenBLAS' +blasver = '0.2.6' +blassuff = '-LAPACK-3.4.2' + +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 dd86580c59a204aae887d6f768ab53a983ae0490 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 13 Mar 2014 22:43:14 +0100 Subject: [PATCH 459/566] removed unneded comments and blank lines --- easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb index 756c57643b..e7b5fd7db4 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.4.10-no-OFED.eb @@ -19,13 +19,7 @@ blasver = '0.2.6' blas = '%s-%s' % (blaslib, blasver) blas_suff = '-LAPACK-3.4.2' -# 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) - - -# toolchain used to build goalf dependencies +# toolchain used to build goolf-1.4.10-no-OFED dependencies comp_mpi_tc_name = 'gompi' comp_mpi_tc_ver = "%s%s" % (version, versionsuffix) comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) -- GitLab From 3554b1d0980b4ff5990d84426f14103bec6d1313 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 13 Mar 2014 22:45:52 +0100 Subject: [PATCH 460/566] added gzip-1.6-goolf-1.4.10-no-OFED.eb for testing --- .../g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb new file mode 100644 index 0000000000..00881818f0 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb @@ -0,0 +1,22 @@ +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'goolf', 'version': '1.4.10-no-OFED'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = ['http://ftpmirror.gnu.org/gzip'] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' -- GitLab From 11d06675225018aecc55a9f3a09dd7939d97461a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Mar 2014 10:04:44 +0100 Subject: [PATCH 461/566] add easyconfig files for slalib-c --- .../s/slalib-c/slalib-c-0.0-goolf-1.4.10.eb | 23 +++++++++++++++++++ .../s/slalib-c/slalib-c-0.0-ictce-5.5.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-goolf-1.4.10.eb b/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..433f61d41e --- /dev/null +++ b/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'slalib-c' +version = '0.0' + +homepage = 'http://star-www.rl.ac.uk/star/docs/sun67.htx/sun67.html' +description = "SLALIB is a library used by writers of positional-astronomy applications." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# only available for download per request, cfr. ftp://legacy.gsfc.nasa.gov/heasarc/software/slalib-info.html +sources = [SOURCE_TAR_BZ2] + +skipsteps = ['configure', 'install'] +makeopts = 'INSTALL_DIR=%(installdir)s SLA_LIB_DIR=%(installdir)s/lib/ CCOMPC="$CC" CFLAGC="-c -pedantic $CFLAGS"' + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["include/slalib.h", "include/slamac.h", "lib/libsla.a"], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-ictce-5.5.0.eb b/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-ictce-5.5.0.eb new file mode 100644 index 0000000000..8b59888038 --- /dev/null +++ b/easybuild/easyconfigs/s/slalib-c/slalib-c-0.0-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'slalib-c' +version = '0.0' + +homepage = 'http://star-www.rl.ac.uk/star/docs/sun67.htx/sun67.html' +description = "SLALIB is a library used by writers of positional-astronomy applications." + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +# only available for download per request, cfr. ftp://legacy.gsfc.nasa.gov/heasarc/software/slalib-info.html +sources = [SOURCE_TAR_BZ2] + +skipsteps = ['configure', 'install'] +makeopts = 'INSTALL_DIR=%(installdir)s SLA_LIB_DIR=%(installdir)s/lib/ CCOMPC="$CC" CFLAGC="-c -pedantic $CFLAGS"' + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["include/slalib.h", "include/slamac.h", "lib/libsla.a"], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 7e4790d5d6c4ecf6303abddb26d811fb72cdf9fa Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 14 Mar 2014 16:49:56 +0100 Subject: [PATCH 462/566] fixed indentation --- easybuild/easyconfigs/i/iccifort/iccifort-2011.13.367.eb | 6 +++--- easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2011.13.367.eb index fdb9bb58b9..76b5884dca 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2011.13.367.eb @@ -9,8 +9,8 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('icc', version), - ('ifort', version), - ] + ('icc', version), + ('ifort', version), +] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb index c51fb8ee78..85878e8ca1 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb @@ -9,8 +9,8 @@ description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and toolchain = {'name': 'dummy', 'version': 'dummy'} dependencies = [ - ('icc', version), - ('ifort', version), - ] + ('icc', version), + ('ifort', version), +] moduleclass = 'toolchain' -- GitLab From 4f0cae67686003babdb918ed19737fb07bf35fb9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 14 Mar 2014 17:00:26 +0100 Subject: [PATCH 463/566] switched to GNU_SOURCE template --- easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb index fe81686c74..9763d27a88 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb @@ -7,7 +7,7 @@ description = "gzip (GNU zip) is a popular data compression program as a replace toolchain = {'name': 'iomkl', 'version': '6.6.2'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz -source_urls = ['http://ftpmirror.gnu.org/gzip'] +source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # make sure the gzip, gunzip and compress binaries are available after installation -- GitLab From 62223fdc3d31bcc876a15fc4a37760bc174deda8 Mon Sep 17 00:00:00 2001 From: Ewan Higgs Date: Mon, 17 Mar 2014 14:37:47 +0100 Subject: [PATCH 464/566] Add ViennaRNA 2.1.6 ictce-5.5.0 build. --- .../ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb | 45 +++++++++++++++++++ .../v/ViennaRNA/ViennaRNA-2.1.6_ictce.patch | 26 +++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6_ictce.patch diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb new file mode 100644 index 0000000000..f0df356467 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -0,0 +1,45 @@ +## +# 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 = 'ViennaRNA' +version = '2.1.6' + +homepage = 'http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0' } +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA/packages/source'] + +patches = ['ViennaRNA-2.1.6_ictce.patch'] + +# Prevents the "make install" step from trying to copy to _global_ perl dir and thus make easybuild fail. +configopts = '--without-perl' +# Alternatively, you may want to use the following to copy the perl-module to a "local" directory +# Code NOT yet tested, therefor left here for future recycling +#preconfigopts = 'PERLPREFIX="/path/where/the/perl/module/shoud/go"' + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6_ictce.patch b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6_ictce.patch new file mode 100644 index 0000000000..ff068d76be --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6_ictce.patch @@ -0,0 +1,26 @@ +--- ViennaRNA-2.1.6/Kinfold/cache.c.orig 2014-03-17 14:07:33.308562799 +0100 ++++ ViennaRNA-2.1.6/Kinfold/cache.c 2014-03-17 14:07:48.808965449 +0100 +@@ -56,7 +56,6 @@ + 61,59,53,47,43,41,37,31,29,23,17,13,11,7,3,1}; + + /* key must not be longer than 128 */ +-#pragma inline (cache_f) + unsigned cache_f(char *x) { + register char *s; + register int i; +@@ -80,6 +79,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x); + if ((c=cachetab[cacheval])) + if (strcmp(c->structure,x)==0) return c; +@@ -92,6 +92,7 @@ + int cacheval; + cache_entry *c; + ++ #pragma inline (cache_f) + cacheval=cache_f(x->structure); + if ((c=cachetab[cacheval])) { + free(c->structure); -- GitLab From 3eaa3275e3ad379056e9a4ea58acce82404038fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 11:52:29 +0100 Subject: [PATCH 465/566] fix Qt source_urls, add Qt easyconfig with ictce 4.1.13 --- .../q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb | 2 +- .../q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb | 5 ++++- .../easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb | 17 +++++++++++++++++ 8 files changed, 27 insertions(+), 7 deletions(-) create mode 100755 easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index 15b02947ee..feb10d4a75 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index 2d4e7c17a1..e8472dac11 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index f83f3ffb6a..c489c5aa68 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index ffa5551d14..4a7a10534b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -9,7 +9,7 @@ toolchainopts = {'lowopt': True} # use -O1 source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index e05c77a46b..a411477c0b 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 654eb56d93..3c0ae0a9af 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -8,7 +8,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(major_minor_version)s/%(version)s/' + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index faddb7d77e..9e49fd8ca8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -5,7 +5,10 @@ homepage = 'http://qt-project.org/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gmpolf', 'version': '1.4.8'} -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb new file mode 100755 index 0000000000..bc5d1c87ff --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.5' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' -- GitLab From 3c1f1dde78eb019eac5664983bd186d18f341068 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Mar 2014 16:41:13 +0100 Subject: [PATCH 466/566] add missing patch file for Qt v4.8.5 with ictce/4.1.13 --- .../easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb | 2 ++ .../easyconfigs/q/Qt/Qt-4.8.5_ictce-qUnused.patch | 15 +++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.5_ictce-qUnused.patch diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb index bc5d1c87ff..312d6b1990 100755 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -12,6 +12,8 @@ source_urls = [ ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] +patches = ['Qt-4.8.5_ictce-qUnused.patch'] + dependencies = [('GLib', '2.34.3')] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5_ictce-qUnused.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.5_ictce-qUnused.patch new file mode 100644 index 0000000000..e881808fd2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5_ictce-qUnused.patch @@ -0,0 +1,15 @@ +see https://qt.gitorious.net/qt/qtbase/commit/d3951a5b0f4fe9731d1512668b43f51bd98bd84e +and http://lists.qt-project.org/pipermail/interest/2013-September/008591.html +diff --git a/src/corelib/global/qglobal.h b/src/corelib/global/qglobal.h +index 7d91fa3..cc0e6a1 100644 +--- a/src/corelib/global/qglobal.h ++++ b/src/corelib/global/qglobal.h +@@ -820,7 +820,7 @@ Q_CORE_EXPORT bool qSharedBuild(); + Avoid "unused parameter" warnings + */ + +-#if defined(Q_CC_INTEL) && !defined(Q_OS_WIN) || defined(Q_CC_RVCT) ++#if defined(Q_CC_RVCT) + template + inline void qUnused(T &x) { (void)x; } + # define Q_UNUSED(x) qUnused(x); -- GitLab From 77d339cb10d9e252953caac6a1fbf3684a9a3f25 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 19 Mar 2014 19:54:49 +0100 Subject: [PATCH 467/566] added goolf-1.6.5.eb. Still missing deps --- easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb | 37 ++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb new file mode 100644 index 0000000000..00585a3dca --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.6.5' + +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 = '4.8.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +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', '4.8.2'), + ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.1.0 + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.3', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' -- GitLab From 012a003cab7c239c230b453c66a8a3bf45251657 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 19 Mar 2014 23:05:48 +0100 Subject: [PATCH 468/566] added dependencies --- .../f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb | 32 ++++++++++++ easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb | 25 ++++++++++ ...OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb | 50 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 36 +++++++++++++ ...gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb | 25 ++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb new file mode 100644 index 0000000000..94287ee108 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb @@ -0,0 +1,32 @@ +name = 'FFTW' +version = '3.3.3' + +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': '1.6.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb b/easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb new file mode 100644 index 0000000000..bbd1e9fa7d --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb @@ -0,0 +1,25 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.6.5' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.2' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.6.5' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..2ac7e82d71 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb @@ -0,0 +1,50 @@ +name = 'OpenBLAS' +version = '0.2.8' + +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': '1.6.5'} + +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' +makeopts = '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' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' 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 new file mode 100644 index 0000000000..4b87a8687a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -0,0 +1,36 @@ +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': '4.8.2'} + +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 + +# 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, shared_lib_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/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..4d6a349030 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-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': '1.6.5'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +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 282fa941d5cff3d8800f75dd358ed51326367b1b Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 19 Mar 2014 23:37:09 +0100 Subject: [PATCH 469/566] goolf-1.6.5-no-OFED goolf-1.6.5-no-OFED --- .../f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb | 32 ++++++++++++ .../g/gompi/gompi-1.6.5-no-OFED.eb | 26 ++++++++++ .../g/goolf/goolf-1.6.5-no-OFED.eb | 38 ++++++++++++++ ...-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb | 50 +++++++++++++++++++ .../OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 30 +++++++++++ ...6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb | 25 ++++++++++ 6 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb create mode 100644 easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb new file mode 100644 index 0000000000..86c18c4f19 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb @@ -0,0 +1,32 @@ +name = 'FFTW' +version = '3.3.3' + +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': '1.6.5-no-OFED'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb new file mode 100644 index 0000000000..3595845212 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb @@ -0,0 +1,26 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '1.6.5' +versionsuffix = '-no-OFED' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compname = 'GCC' +compver = '4.8.2' +comp = (compname, compver) + +mpilib = 'OpenMPI' +mpiver = '1.6.5' + +# compiler toolchain dependencies +dependencies = [ + comp, + (mpilib, mpiver, versionsuffix, comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb new file mode 100644 index 0000000000..4bf7e91c94 --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb @@ -0,0 +1,38 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.6.5' +versionsuffix = '-no-OFED' + +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 = '4.8.2' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +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%s" % (version, versionsuffix) +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', '4.8.2'), + ('OpenMPI', '1.6.5', '-no-OFED', comp), # part of gompi-1.1.0 + (blaslib, blasver, blassuff, comp_mpi_tc), + ('FFTW', '3.3.3', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..c446511bf9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb @@ -0,0 +1,50 @@ +name = 'OpenBLAS' +version = '0.2.8' + +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': '1.6.5-no-OFED'} + +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' +makeopts = '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' % shared_lib_ext], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb new file mode 100644 index 0000000000..189fba5f29 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -0,0 +1,30 @@ +name = 'OpenMPI' +version = '1.6.5' +versionsuffix = '-no-OFED' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '4.8.2'} + +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 --without-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 + +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, shared_lib_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/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb new file mode 100644 index 0000000000..a24ac08f75 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-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': '1.6.5-no-OFED'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.8' +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 8a61cb164f42e24816f426cb72e47586b849b563 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 19 Mar 2014 23:38:54 +0100 Subject: [PATCH 470/566] added gzip-1.6-goolf-1.6.5-no-OFED.eb for testing --- .../g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb new file mode 100644 index 0000000000..8c43c42f94 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC +# Authors:: Thekla Loizou +# 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_06-19.html +## + +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'goolf', 'version': '1.6.5-no-OFED'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' -- GitLab From d2990e9543d10418b0996d1d7a2a21f4cf3a318c Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 19 Mar 2014 23:40:12 +0100 Subject: [PATCH 471/566] added gzip-1.6-goolf-1.6.5.eb for testing --- .../g/gzip/gzip-1.6-goolf-1.6.5.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb new file mode 100644 index 0000000000..dd296a9acd --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC +# Authors:: Thekla Loizou +# 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_06-19.html +## + +name = 'gzip' +version = '1.6' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'goolf', 'version': '1.6.5'} + +# eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +# run 'gzip -h' and 'gzip --version' after installation +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' -- GitLab From 3d567f03786991456fa78b963a8791af6fa6013e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Mar 2014 16:49:19 +0100 Subject: [PATCH 472/566] fix defining tmp_logdir config setting --- test/easyconfigs/suite.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 0c775762c4..dbb1a006c9 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -38,7 +38,6 @@ import tempfile import unittest from vsc import fancylogger -import easybuild.tools.config as config import test.easyconfigs.easyconfigs as e # initialize logger for all the unit tests @@ -48,7 +47,7 @@ os.remove(log_fn) fancylogger.logToFile(log_fn) fancylogger.setLogLevelDebug() -config.variables['tmp_logdir'] = tempfile.mkdtemp(prefix='easyconfigs_test_') +os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') # call suite() for each module and then run them all SUITE = unittest.TestSuite([x.suite() for x in [e]]) @@ -65,7 +64,8 @@ except ImportError, err: res = unittest.TextTestRunner().run(SUITE) fancylogger.logToFile(log_fn, enable=False) -shutil.rmtree(config.variables['tmp_logdir']) +shutil.rmtree(os.environ['EASYBUILD_TMP_LOGDIR']) +del os.environ['EASYBUILD_TMP_LOGDIR'] for f in glob.glob('%s*' % log_fn): os.remove(f) -- GitLab From b9b6b7acdad9d547f6c0a5a3a7e443483cddc39f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Mar 2014 16:49:48 +0100 Subject: [PATCH 473/566] add test for checking locations of easyconfig files --- test/easyconfigs/easyconfigs.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c7a289a50f..ec1d53f7b5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -157,6 +157,22 @@ class EasyConfigTest(TestCase): conflicts = True self.assertFalse(conflicts, "No conflicts detected") + def test_easyconfig_locations(self): + """Make sure all easyconfigs files are in the right location.""" + easyconfig_dirs_regex = re.compile('.*/easybuild/easyconfigs/[a-z]/[^/]+$') + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + for (dirpath, _, filenames) in os.walk(topdir): + # ignore git/svn dirs + if '/.git/' in dirpath or '.svn' in dirpath: + continue + # check whether list of .eb files is non-empty + easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + if easyconfig_files: + # check whether path matches required pattern + if not easyconfig_dirs_regex.match(dirpath): + # only exception: TEMPLATE.eb + if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): + self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) def template_easyconfig_test(self, spec): """Test whether all easyconfigs can be initialized.""" -- GitLab From 30ac03c588fb027198a3d07858a9bf09db824772 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Mar 2014 16:56:53 +0100 Subject: [PATCH 474/566] fix remark --- 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 ec1d53f7b5..bb68a41844 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -163,7 +163,7 @@ class EasyConfigTest(TestCase): topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) for (dirpath, _, filenames) in os.walk(topdir): # ignore git/svn dirs - if '/.git/' in dirpath or '.svn' in dirpath: + if '/.git/' in dirpath or '/.svn/' in dirpath: continue # check whether list of .eb files is non-empty easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] -- GitLab From 87a4e33adf4aaccd14203aef7a4908e5e2f7125a Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 16:58:03 +0100 Subject: [PATCH 475/566] added hwloc support to OpenMPI-1.6.5-GCC-4.8.2.eb --- .../h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb | 17 +++++++++++++++++ .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 3 +++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..1a2541a79b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb @@ -0,0 +1,17 @@ +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': '4.8.2'} + +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/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 4b87a8687a..0dccde3d24 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 @@ -14,6 +14,9 @@ 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']: -- GitLab From 60c99978c319fc273a4027192a199c2486dfffd1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 16:59:26 +0100 Subject: [PATCH 476/566] updated to FFTW-3.3.4 --- .../f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb | 32 +++++++++++++++++++ easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb | 2 +- 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb new file mode 100644 index 0000000000..998fa89264 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb @@ -0,0 +1,32 @@ +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': '1.6.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [homepage] + +common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', + 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb index 00585a3dca..2dcbbded37 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb @@ -30,7 +30,7 @@ dependencies = [ ('GCC', '4.8.2'), ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.1.0 (blaslib, blasver, blassuff, comp_mpi_tc), - ('FFTW', '3.3.3', '', comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] -- GitLab From 41fb586ce713cf336e21d2f2865ceb3e715b7630 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 17:21:13 +0100 Subject: [PATCH 477/566] removed FFTW-3.3.3-gompi-1.6.5.eb --- .../f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb deleted file mode 100644 index 94287ee108..0000000000 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'FFTW' -version = '3.3.3' - -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': '1.6.5'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [homepage] - -common_configopts = "--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.a' % x for x in ['', '_mpi', '_omp', 'f', 'f_mpi', 'f_omp', - 'l', 'l_mpi', 'l_omp', 'q', 'q_omp']], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'numlib' -- GitLab From 30dac6aeb7df115df6631e6d9105c887b69ceda5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Mar 2014 17:22:51 +0100 Subject: [PATCH 478/566] fix remark w.r.t. regex --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bb68a41844..d617cee355 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -159,7 +159,7 @@ class EasyConfigTest(TestCase): def test_easyconfig_locations(self): """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile('.*/easybuild/easyconfigs/[a-z]/[^/]+$') + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[a-z]/[^/]+$') topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) for (dirpath, _, filenames) in os.walk(topdir): # ignore git/svn dirs @@ -169,7 +169,7 @@ class EasyConfigTest(TestCase): easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] if easyconfig_files: # check whether path matches required pattern - if not easyconfig_dirs_regex.match(dirpath): + if not easyconfig_dirs_regex.search(dirpath): # only exception: TEMPLATE.eb if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) -- GitLab From a8cc4c977027bee45797602e52a8531545f49186 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 17:29:41 +0100 Subject: [PATCH 479/566] added hwloc support to openmpi --- easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb | 10 +++++----- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 3 +++ 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb index 5b98a2e11a..ed98f4cf73 100644 --- a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb @@ -24,11 +24,11 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://git-core.googlecode.com/files'] -dependencies = [ - ('cURL', '7.29.0'), - ('expat', '2.1.0'), - ('gettext', '0.18.2'), -] +#dependencies = [ +# ('cURL', '7.29.0'), +# ('expat', '2.1.0'), +# ('gettext', '0.18.2'), +#] sanity_check_paths = { 'files': ['bin/git'], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 189fba5f29..792495946f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -15,6 +15,9 @@ patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-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')] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + -- GitLab From f93bb984a5eb9dc4219df94e09afecf258ab1da5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 17:46:58 +0100 Subject: [PATCH 480/566] updated to FFTW-3.3.4 --- ...gompi-1.6.5-no-OFED.eb => FFTW-3.3.4-gompi-1.6.5-no-OFED.eb} | 2 +- easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.3-gompi-1.6.5-no-OFED.eb => FFTW-3.3.4-gompi-1.6.5-no-OFED.eb} (98%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb similarity index 98% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb index 86c18c4f19..dea05843bc 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-gompi-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb @@ -1,5 +1,5 @@ name = 'FFTW' -version = '3.3.3' +version = '3.3.4' homepage = 'http://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb index 4bf7e91c94..dda99907c3 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb @@ -31,7 +31,7 @@ dependencies = [ ('GCC', '4.8.2'), ('OpenMPI', '1.6.5', '-no-OFED', comp), # part of gompi-1.1.0 (blaslib, blasver, blassuff, comp_mpi_tc), - ('FFTW', '3.3.3', '', comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), ] -- GitLab From 80f34117b2f8bea4e384845c491323b8472ea3fc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 20 Mar 2014 18:19:08 +0100 Subject: [PATCH 481/566] removed git-1.8.2-goolf-1.4.10.eb added by mistake --- .../g/git/git-1.8.2-goolf-1.4.10.eb | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb deleted file mode 100644 index ed98f4cf73..0000000000 --- a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb +++ /dev/null @@ -1,42 +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 -# 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 -## - -name = 'git' -version = '1.8.2' - -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': 'goolf', 'version': '1.4.10'} - -# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://git-core.googlecode.com/files'] - -#dependencies = [ -# ('cURL', '7.29.0'), -# ('expat', '2.1.0'), -# ('gettext', '0.18.2'), -#] - -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 a2237141d9a157c6a1ce2dfc2b63a6635e1d54f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Mar 2014 10:13:50 +0100 Subject: [PATCH 482/566] fix unit tests after changes in framework --- test/easyconfigs/easyconfigs.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d617cee355..bef4a1c195 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -60,6 +60,11 @@ class EasyConfigTest(TestCase): # 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')) + build_options = { + 'valid_module_classes': config.module_classes(), + 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + } + config.init_build_options(build_options=build_options) config.set_tmpdir() del eb_go @@ -79,13 +84,13 @@ class EasyConfigTest(TestCase): # parse all easyconfigs easyconfigs = [] for spec in specs: - easyconfigs.extend(process_easyconfig(spec, build_options={'validate': False})) + easyconfigs.extend(process_easyconfig(spec)) build_options = { 'robot_path': easyconfigs_path, 'force': True, } - self.ordered_specs = resolve_dependencies(easyconfigs, build_options=build_options) + self.ordered_specs = resolve_dependencies(easyconfigs) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" @@ -194,7 +199,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(False, "Obtained software name directly from easyconfig file") # parse easyconfig - ec = EasyConfig(spec, build_options={'validate': False}) + ec = EasyConfig(spec, validate=False) # sanity check for software name self.assertTrue(ec['name'], name) @@ -206,7 +211,7 @@ def template_easyconfig_test(self, spec): # instantiate easyblock with easyconfig file app_class = get_class(easyblock, name=name) - app = app_class(spec, build_options={'validate_ec': False}) + app = app_class(spec) # more sanity checks self.assertTrue(name, app.name) -- GitLab From eedb7060bc31602d6d2494e6fa2bf5e52d92c989 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Mar 2014 10:53:15 +0100 Subject: [PATCH 483/566] fix specifying robot_path/force build options --- test/easyconfigs/easyconfigs.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bef4a1c195..1b0e7da825 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -63,6 +63,8 @@ class EasyConfigTest(TestCase): build_options = { 'valid_module_classes': config.module_classes(), 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + 'robot_path': get_paths_for("easyconfigs")[0], + 'force': True, } config.init_build_options(build_options=build_options) config.set_tmpdir() @@ -86,10 +88,6 @@ class EasyConfigTest(TestCase): for spec in specs: easyconfigs.extend(process_easyconfig(spec)) - build_options = { - 'robot_path': easyconfigs_path, - 'force': True, - } self.ordered_specs = resolve_dependencies(easyconfigs) def test_dep_graph(self): -- GitLab From a584e0ac66f3c81d6cd9a612895cf56c725ff93f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Mar 2014 11:08:38 +0100 Subject: [PATCH 484/566] correct imports, avoid that all easyconfigs are being parsed twice --- test/easyconfigs/easyconfigs.py | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1b0e7da825..24cab7ba53 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -43,8 +43,7 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.framework.easyblock import EasyBlock, get_class from easybuild.framework.easyconfig.easyconfig import EasyConfig -from easybuild.framework.easyconfig.tools import get_paths_for -from easybuild.main import dep_graph, resolve_dependencies, process_easyconfig +from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig, resolve_dependencies from easybuild.tools import config from easybuild.tools.module_generator import det_full_module_name @@ -76,6 +75,7 @@ class EasyConfigTest(TestCase): # make sure a logger is present for main main._log = log ordered_specs = None + parsed_easyconfigs = [] def process_all_easyconfigs(self): """Process all easyconfigs and resolve inter-easyconfig dependencies.""" @@ -83,12 +83,12 @@ class EasyConfigTest(TestCase): easyconfigs_path = get_paths_for("easyconfigs")[0] specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - # parse all easyconfigs - easyconfigs = [] - for spec in specs: - easyconfigs.extend(process_easyconfig(spec)) + # parse all easyconfigs if they haven't been already + if not self.parsed_easyconfigs: + for spec in specs: + self.parsed_easyconfigs.extend(process_easyconfig(spec)) - self.ordered_specs = resolve_dependencies(easyconfigs) + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" @@ -197,7 +197,11 @@ def template_easyconfig_test(self, spec): self.assertTrue(False, "Obtained software name directly from easyconfig file") # parse easyconfig - ec = EasyConfig(spec, validate=False) + ecs = process_easyconfig(spec) + if len(ecs) == 1: + ec = ecs[0]['ec'] + else: + self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) # sanity check for software name self.assertTrue(ec['name'], name) @@ -242,6 +246,9 @@ def template_easyconfig_test(self, spec): app.close_log() os.remove(app.logfile) + # cache the parsed easyconfig, to avoid that it is parsed again + self.parsed_easyconfigs.append(ecs[0]) + # test passed, so set back to True single_tests_ok = True and prev_single_tests_ok -- GitLab From 4e7a9ae2136621000aa9b8f811dd9962c888ea57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Mar 2014 13:11:24 +0100 Subject: [PATCH 485/566] disable checking of OS deps --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 24cab7ba53..15f64e4aca 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -60,10 +60,11 @@ class EasyConfigTest(TestCase): eb_go = eboptions.parse_options() config.init(eb_go.options, eb_go.get_options_by_section('config')) build_options = { + 'check_osdeps': False, + 'force': True, + 'robot_path': get_paths_for("easyconfigs")[0], 'valid_module_classes': config.module_classes(), 'valid_stops': [x[0] for x in EasyBlock.get_steps()], - 'robot_path': get_paths_for("easyconfigs")[0], - 'force': True, } config.init_build_options(build_options=build_options) config.set_tmpdir() -- GitLab From 8fe5e38fcb79fa9c56213f478fe06f15996f3941 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 22 Mar 2014 20:28:49 +0100 Subject: [PATCH 486/566] change version of goolf v1.6.5 to goolf v1.5.14, to align with existing gompi 1.5.12 easyconfig --- .../{FFTW-3.3.4-gompi-1.6.5.eb => FFTW-3.3.4-gompi-1.5.14.eb} | 2 +- .../easyconfigs/g/gompi/{gompi-1.6.5.eb => gompi-1.5.14.eb} | 2 +- .../easyconfigs/g/goolf/{goolf-1.6.5.eb => goolf-1.5.14.eb} | 4 ++-- .../{gzip-1.6-goolf-1.6.5.eb => gzip-1.6-goolf-1.5.14.eb} | 2 +- ...K-3.5.0.eb => OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb} | 2 +- ...aLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb} | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-gompi-1.6.5.eb => FFTW-3.3.4-gompi-1.5.14.eb} (95%) rename easybuild/easyconfigs/g/gompi/{gompi-1.6.5.eb => gompi-1.5.14.eb} (95%) rename easybuild/easyconfigs/g/goolf/{goolf-1.6.5.eb => goolf-1.5.14.eb} (92%) rename easybuild/easyconfigs/g/gzip/{gzip-1.6-goolf-1.6.5.eb => gzip-1.6-goolf-1.5.14.eb} (95%) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb => OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb} (96%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb => ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb} (92%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb similarity index 95% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb index 998fa89264..1cf9159796 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14.eb @@ -5,7 +5,7 @@ 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': '1.6.5'} +toolchain = {'name': 'gompi', 'version': '1.5.14'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb similarity index 95% rename from easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb rename to easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb index bbd1e9fa7d..c42da3fda1 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.6.5.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'gompi' -version = '1.6.5' +version = '1.5.14' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb similarity index 92% rename from easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb rename to easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb index 2dcbbded37..89526c2d6c 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'goolf' -version = '1.6.5' +version = '1.5.14' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including @@ -28,7 +28,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ ('GCC', '4.8.2'), - ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.1.0 + ('OpenMPI', '1.6.5', '', comp), # part of gompi (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb similarity index 95% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb rename to easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb index dd296a9acd..e3c2131d4d 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14.eb @@ -16,7 +16,7 @@ version = '1.6' homepage = 'http://www.gnu.org/software/gzip/' description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" -toolchain = {'name': 'goolf', 'version': '1.6.5'} +toolchain = {'name': 'goolf', 'version': '1.5.14'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb similarity index 96% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index 2ac7e82d71..bdd5c179ef 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -7,7 +7,7 @@ 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': '1.6.5'} +toolchain = {'name': 'gompi', 'version': '1.5.14'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb similarity index 92% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-LAPACK-3.5.0.eb index 4d6a349030..2a0a7e12ce 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-OpenBLAS-0.2.8-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-OpenBLAS-0.2.8-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': '1.6.5'} +toolchain = {'name': 'gompi', 'version': '1.5.14'} toolchainopts = {'pic': True} source_urls = [homepage] -- GitLab From 79d80acf0b661347c53328b744367d2fa61c06ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 22 Mar 2014 20:35:15 +0100 Subject: [PATCH 487/566] change version of goolf v1.6.5-no-OFED to goolf v1.5.14-no-OFED, to align with existing gompi 1.5.12 easyconfig --- ...ompi-1.6.5-no-OFED.eb => FFTW-3.3.4-gompi-1.5.14-no-OFED.eb} | 2 +- .../g/gompi/{gompi-1.6.5-no-OFED.eb => gompi-1.5.14-no-OFED.eb} | 2 +- .../g/goolf/{goolf-1.6.5-no-OFED.eb => goolf-1.5.14-no-OFED.eb} | 2 +- ...-goolf-1.6.5-no-OFED.eb => gzip-1.6-goolf-1.5.14-no-OFED.eb} | 2 +- ...0.eb => OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb} | 2 +- ...K-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb} | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.4-gompi-1.6.5-no-OFED.eb => FFTW-3.3.4-gompi-1.5.14-no-OFED.eb} (95%) rename easybuild/easyconfigs/g/gompi/{gompi-1.6.5-no-OFED.eb => gompi-1.5.14-no-OFED.eb} (96%) rename easybuild/easyconfigs/g/goolf/{goolf-1.6.5-no-OFED.eb => goolf-1.5.14-no-OFED.eb} (98%) rename easybuild/easyconfigs/g/gzip/{gzip-1.6-goolf-1.6.5-no-OFED.eb => gzip-1.6-goolf-1.5.14-no-OFED.eb} (94%) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb => OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb} (95%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb => ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb} (90%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb similarity index 95% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb index dea05843bc..6c4efd7f74 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.14-no-OFED.eb @@ -5,7 +5,7 @@ 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': '1.6.5-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.5.14-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.14-no-OFED.eb similarity index 96% rename from easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb rename to easybuild/easyconfigs/g/gompi/gompi-1.5.14-no-OFED.eb index 3595845212..62bfbf3784 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.14-no-OFED.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'gompi' -version = '1.6.5' +version = '1.5.14' versionsuffix = '-no-OFED' homepage = '(none)' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb similarity index 98% rename from easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb rename to easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb index dda99907c3..e040a35e43 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb @@ -1,7 +1,7 @@ easyblock = "Toolchain" name = 'goolf' -version = '1.6.5' +version = '1.5.14' versionsuffix = '-no-OFED' homepage = '(none)' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb rename to easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb index 8c43c42f94..81dfe171a8 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.6.5-no-OFED.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb @@ -16,7 +16,7 @@ version = '1.6' homepage = 'http://www.gnu.org/software/gzip/' description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" -toolchain = {'name': 'goolf', 'version': '1.6.5-no-OFED'} +toolchain = {'name': 'goolf', 'version': '1.5.14-no-OFED'} # eg. http://ftp.gnu.org/gnu/gzip/gzip-1.6.tar.gz source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb similarity index 95% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb index c446511bf9..2b422ff45f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.5-no-OFED-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-no-OFED-LAPACK-3.5.0.eb @@ -7,7 +7,7 @@ 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': '1.6.5-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.5.14-no-OFED'} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb similarity index 90% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb index a24ac08f75..b55976ccac 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.6.5-no-OFED-OpenBLAS-0.2.8-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.14-no-OFED-OpenBLAS-0.2.8-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': '1.6.5-no-OFED'} +toolchain = {'name': 'gompi', 'version': '1.5.14-no-OFED'} toolchainopts = {'pic': True} source_urls = [homepage] -- GitLab From 9a6e7d8bf1beda2b521380f398e37093cd90e0de Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sun, 23 Mar 2014 13:00:24 +0100 Subject: [PATCH 488/566] fix in comments --- easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb index 2dcbbded37..6a57b900eb 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.5.eb @@ -28,7 +28,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ ('GCC', '4.8.2'), - ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.1.0 + ('OpenMPI', '1.6.5', '', comp), # part of gompi (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From 0026070443ccc7be9e38c8117bf294900805edaa Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sun, 23 Mar 2014 13:33:09 +0100 Subject: [PATCH 489/566] fixed comments --- easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb index e040a35e43..878a9f4474 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.14-no-OFED.eb @@ -29,7 +29,7 @@ comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) # because of toolchain preperation functions dependencies = [ ('GCC', '4.8.2'), - ('OpenMPI', '1.6.5', '-no-OFED', comp), # part of gompi-1.1.0 + ('OpenMPI', '1.6.5', '-no-OFED', comp), # part of gompi (blaslib, blasver, blassuff, comp_mpi_tc), ('FFTW', '3.3.4', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blassuff), comp_mpi_tc), -- GitLab From f6d3357893a5181cc0e2d04078f679f3173e86c4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sun, 23 Mar 2014 13:35:24 +0100 Subject: [PATCH 490/566] re-added git-1.8.2-goolf-1.4.10.eb --- .../g/git/git-1.8.2-goolf-1.4.10.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..5b98a2e11a --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-1.8.2-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# 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 +## + +name = 'git' +version = '1.8.2' + +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': 'goolf', 'version': '1.4.10'} + +# eg. http://git-core.googlecode.com/files/git-1.8.2.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://git-core.googlecode.com/files'] + +dependencies = [ + ('cURL', '7.29.0'), + ('expat', '2.1.0'), + ('gettext', '0.18.2'), +] + +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 1ae915bcfc8a83515eb713f2c5419d0b87dcb7fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Mar 2014 15:47:46 +0100 Subject: [PATCH 491/566] fix unit tests after changes in framework --- test/easyconfigs/easyconfigs.py | 28 ++++++++-------------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 15f64e4aca..8ac48f3bce 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -41,8 +41,9 @@ from unittest import TestCase, TestLoader, main import easybuild.main as main import easybuild.tools.options as eboptions -from easybuild.framework.easyblock import EasyBlock, get_class -from easybuild.framework.easyconfig.easyconfig import EasyConfig +from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.easyconfig import EasyConfig, fetch_parameter_from_easyconfig_file +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig, resolve_dependencies from easybuild.tools import config from easybuild.tools.module_generator import det_full_module_name @@ -71,8 +72,6 @@ class EasyConfigTest(TestCase): del eb_go log = fancylogger.getLogger("EasyConfigTest", fname=False) - name_regex = re.compile("^name\s*=\s*['\"](.*)['\"]$", re.M) - easyblock_regex = re.compile(r"^\s*easyblock\s*=['\"](.*)['\"]$", re.M) # make sure a logger is present for main main._log = log ordered_specs = None @@ -86,6 +85,7 @@ class EasyConfigTest(TestCase): # parse all easyconfigs if they haven't been already if not self.parsed_easyconfigs: + print "parsing ALL easyconfigs..." for spec in specs: self.parsed_easyconfigs.extend(process_easyconfig(spec)) @@ -186,17 +186,6 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - f = open(spec, 'r') - spectxt = f.read() - f.close() - - # determine software name directly from easyconfig file - res = self.name_regex.search(spectxt) - if res: - name = res.group(1) - else: - self.assertTrue(False, "Obtained software name directly from easyconfig file") - # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: @@ -205,16 +194,15 @@ def template_easyconfig_test(self, spec): self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) # 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 = self.easyblock_regex.search(spectxt) - if easyblock: - easyblock = easyblock.group(1) + easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock') # instantiate easyblock with easyconfig file - app_class = get_class(easyblock, name=name) - app = app_class(spec) + app_class = get_easyblock_class(easyblock, name=name) + app = app_class(ec) # more sanity checks self.assertTrue(name, app.name) -- GitLab From 925e3576ed836d517abed79832724f23d0582386 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Mar 2014 18:54:47 +0100 Subject: [PATCH 492/566] clean up print --- test/easyconfigs/easyconfigs.py | 1 - 1 file changed, 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8ac48f3bce..6490a96fde 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -85,7 +85,6 @@ class EasyConfigTest(TestCase): # parse all easyconfigs if they haven't been already if not self.parsed_easyconfigs: - print "parsing ALL easyconfigs..." for spec in specs: self.parsed_easyconfigs.extend(process_easyconfig(spec)) -- GitLab From f313c23427f119b170d6b173384c1252ba9253ad Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 24 Mar 2014 21:16:19 +0100 Subject: [PATCH 493/566] BayesTraits-1.0-linux32.eb BayesTraits-2.0-beta-linux64.eb --- .../b/BayesTraits/BayesTraits-1.0-linux32.eb | 32 +++++++++++++++++++ .../BayesTraits-2.0-beta-linux64.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb create mode 100644 easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb new file mode 100644 index 0000000000..49c78aa1c4 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.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 + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '1.0-linux32' + +homepage = 'http://www.evolution.reading.ac.uk/BayesTraitsV1.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.evolution.reading.ac.uk/Files/'] +sources = ['BayesTraits-Linux-Intel-V1.0.tar.gz'] + +sanity_check_paths = { + 'files': ['BayesTraits', 'Primates.trees', 'PPI.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH':''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb new file mode 100644 index 0000000000..940dfe4dc2 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.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 + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '2.0-Beta-Linux64' + +homepage = 'http://www.evolution.reading.ac.uk/BayesTraitsV1.html' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.evolution.reading.ac.uk/Files/'] +sources = ['BayesTraitsV2-Beta-Linux64.tar.gz'] + +sanity_check_paths = { + 'files': ['BayesTraits', 'Primates.trees', 'Mammal.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH':''} + +moduleclass = 'bio' -- GitLab From 877c17d0c0a3775c5c88ae90f3de7d1f8034efd4 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 24 Mar 2014 23:53:22 +0100 Subject: [PATCH 494/566] rSeq-0.2.0-goolf-1.4.10.eb --- .../r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..21ca0b75f9 --- /dev/null +++ b/easybuild/easyconfigs/r/rSeq/rSeq-0.2.0-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# 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 = 'rSeq' +version = '0.2.0' + +homepage = 'http://www-personal.umich.edu/~jianghui/rseq/' +description = """ rSeq is a set of tools for RNA-Seq data analysis. It consists of programs + that deal with many aspects of RNA-Seq data analysis, such as read quality assessment, + reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) estimation, etc. + There are also many other features that will be gradually added into rSeq in the future. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://www-personal.umich.edu/~jianghui/rseq/download/'] + +files_to_copy = [ + (["rseq", "seqmap"], 'bin') +] + +sanity_check_paths = { + 'files': ["bin/rseq", "bin/seqmap"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From f747e38682a3dc6017545129d08ac429527674cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Mar 2014 09:00:37 +0100 Subject: [PATCH 495/566] massively speed up unit tests by disabling all logging --- test/easyconfigs/suite.py | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index dbb1a006c9..6161221000 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -38,14 +38,12 @@ import tempfile import unittest from vsc import fancylogger +import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e -# initialize logger for all the unit tests -fd, log_fn = tempfile.mkstemp(prefix='easybuild-easyconfigs-tests-', suffix='.log') -os.close(fd) -os.remove(log_fn) -fancylogger.logToFile(log_fn) -fancylogger.setLogLevelDebug() +# disable all logging to significantly speed up tests +fancylogger.disableDefaultHandlers() +fancylogger.setLogLevel('APOCALYPTIC') os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') @@ -63,13 +61,9 @@ except ImportError, err: sys.stderr.write("WARNING: xmlrunner module not available, falling back to using unittest...\n\n") res = unittest.TextTestRunner().run(SUITE) -fancylogger.logToFile(log_fn, enable=False) shutil.rmtree(os.environ['EASYBUILD_TMP_LOGDIR']) del os.environ['EASYBUILD_TMP_LOGDIR'] -for f in glob.glob('%s*' % log_fn): - os.remove(f) - if not res.wasSuccessful(): sys.stderr.write("ERROR: Not all tests were successful.\n") sys.exit(2) -- GitLab From 83b844a107950040de6225ef1b52ab8f8ccdad1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Mar 2014 10:02:51 +0100 Subject: [PATCH 496/566] set log level on error, not apocalyptic --- test/easyconfigs/suite.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 6161221000..f936405be6 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -43,7 +43,7 @@ import test.easyconfigs.easyconfigs as e # disable all logging to significantly speed up tests fancylogger.disableDefaultHandlers() -fancylogger.setLogLevel('APOCALYPTIC') +fancylogger.setLogLevelError() os.environ['EASYBUILD_TMP_LOGDIR'] = tempfile.mkdtemp(prefix='easyconfigs_test_') -- GitLab From 85de18a5856e956b59e4533d7a5e3f4fa6fffd67 Mon Sep 17 00:00:00 2001 From: pescobar Date: Tue, 25 Mar 2014 17:21:36 +0100 Subject: [PATCH 497/566] PLINK-1.07-ictce-6.2.5.eb --- .../p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb new file mode 100644 index 0000000000..9206fbc286 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -0,0 +1,44 @@ +# 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 = 'PLINK' +version = '1.07' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = """ PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for + steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). + Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, + annotation and storage of results. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +# plink makefile is a little bit tricky so we pass every options as arguments +# review plink original makefile for details +# if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes +# have no internet access better leave it as is +makeopts = ' CXX_UNIX="icpc -fopenmp" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' +makeopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBVARBLAS_LAPACK_LIB_DIR/libmkl_lapack.a' + +files_to_copy = [ + (["plink", "gPLINK.jar"], 'bin'), + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["bin/plink", "bin/gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 35934d6fa8d2dc4718c7cfa5fff6f424a661d637 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Mar 2014 14:00:34 +0100 Subject: [PATCH 498/566] IsoInfer for goolf-1.4.10 ictce-6.2.5 and deps --- .../g/GLPK/GLPK-4.53-goolf-1.4.10.eb | 20 ++++++++ .../g/GLPK/GLPK-4.53-ictce-6.2.5.eb | 21 +++++++++ .../g/GMP/GMP-5.1.1-goolf-1.4.10.eb | 20 ++++++++ .../g/GMP/GMP-5.1.1-ictce-6.2.5.eb | 20 ++++++++ .../easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb | 16 +++++++ .../i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb | 47 +++++++++++++++++++ .../i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb | 47 +++++++++++++++++++ .../QuadProg++-1.2.1-goolf-1.4.10.eb | 23 +++++++++ .../QuadProg++-1.2.1-ictce-6.2.5.eb | 23 +++++++++ 9 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb create mode 100644 easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb new file mode 100644 index 0000000000..cb34428fa6 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-goolf-1.4.10.eb @@ -0,0 +1,20 @@ +name = 'GLPK' +version = '4.53' + +homepage = 'http://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': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] + +dependencies = [ + ('GMP', '5.1.1'), +] + +configopts = "--with-gmp" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb new file mode 100644 index 0000000000..6d0e9c123d --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.53-ictce-6.2.5.eb @@ -0,0 +1,21 @@ +name = 'GLPK' +version = '4.53' + +homepage = 'http://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': 'ictce', 'version': '6.2.5'} +toolchainopts = {'opt': True, 'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s'] + +dependencies = [ + ('GMP', '5.1.1'), +] + +configopts = "--with-gmp" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..aebac5b344 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-goolf-1.4.10.eb @@ -0,0 +1,20 @@ +name = 'GMP' +version = '5.1.1' + +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': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..0e349243f0 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-5.1.1-ictce-6.2.5.eb @@ -0,0 +1,20 @@ +name = 'GMP' +version = '5.1.1' + +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': 'ictce', 'version': '6.2.5'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb new file mode 100644 index 0000000000..c460ded159 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-1.16-ictce-6.2.5.eb @@ -0,0 +1,16 @@ +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': 'ictce', 'version': '6.2.5'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['http://ftpmirror.gnu.org/gsl/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..1ed83c4526 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors: Kenneth Hoste (UGent), Pablo Escobar Lopez (Unibas) + +easyblock = 'MakeCp' + +name = 'IsoInfer' +version = '0.9.1' + +homepage = 'http://www.cs.ucr.edu/~jianxing/IsoInfer.html' +description = """IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq + (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. + This version of IsoInfer uses a unified way to handle different types of short reads + with different lengths. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [ + SOURCELOWER_TAR_GZ, # main tarball first, so that start_dir is set correctly + 'graphlib-0.3.tar.gz', +] +source_urls = ['http://www.cs.ucr.edu/~jianxing'] + +dependencies = [ + ('QuadProg++', '1.2.1'), + ('GLPK', '4.53'), + ('GSL', '1.16') +] + +with_configure = True + +# build libgraph.a +graphlib_version = '0.3' +preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version +# build isoinfer, make sure we can link to libgraph.a +preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version + +files_to_copy = [ + (['src/isoinfer'], 'bin'), +] + +sanity_check_paths = { + 'files': ["bin/isoinfer"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..3f65089c09 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Authors: Kenneth Hoste (UGent), Pablo Escobar Lopez (Unibas) + +easyblock = 'MakeCp' + +name = 'IsoInfer' +version = '0.9.1' + +homepage = 'http://www.cs.ucr.edu/~jianxing/IsoInfer.html' +description = """IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq + (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. + This version of IsoInfer uses a unified way to handle different types of short reads + with different lengths. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +sources = [ + SOURCELOWER_TAR_GZ, # main tarball first, so that start_dir is set correctly + 'graphlib-0.3.tar.gz', +] +source_urls = ['http://www.cs.ucr.edu/~jianxing'] + +dependencies = [ + ('QuadProg++', '1.2.1'), + ('GLPK', '4.53'), + ('GSL', '1.16') +] + +with_configure = True + +# build libgraph.a +graphlib_version = '0.3' +preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version +# build isoinfer, make sure we can link to libgraph.a +preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version + +files_to_copy = [ + (['src/isoinfer'], 'bin'), +] + +sanity_check_paths = { + 'files': ["bin/isoinfer"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..dc4855b885 --- /dev/null +++ b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = 'QuadProg++' +version = '1.2.1' + +homepage = 'http://sourceforge.net/projects/quadprog/' +description = """ A C++ library for Quadratic Programming which implements the + Goldfarb-Idnani active-set dual method. At present it is limited to the solution + of strictly convex quadratic programs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s.tar.gz' % (name.lower().rstrip('++'), version)] +source_urls = ['http://downloads.sourceforge.net/project/quadprog/'] + +dependencies = [('Boost', '1.53.0')] + +configopts = ' --with-boost=$EBROOTBOOST' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb new file mode 100644 index 0000000000..1349b54e09 --- /dev/null +++ b/easybuild/easyconfigs/q/QuadProg++/QuadProg++-1.2.1-ictce-6.2.5.eb @@ -0,0 +1,23 @@ +# 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 = 'QuadProg++' +version = '1.2.1' + +homepage = 'http://sourceforge.net/projects/quadprog/' +description = """ A C++ library for Quadratic Programming which implements the + Goldfarb-Idnani active-set dual method. At present it is limited to the solution + of strictly convex quadratic programs. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +sources = ['%s-%s.tar.gz' % (name.lower().rstrip('++'), version)] +source_urls = ['http://downloads.sourceforge.net/project/quadprog/'] + +dependencies = [('Boost', '1.53.0')] + +configopts = ' --with-boost=$EBROOTBOOST' + +moduleclass = 'lib' -- GitLab From 73910773ccf82e5223ec2da1c0fe7b4e7f2180c8 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Mar 2014 17:17:17 +0100 Subject: [PATCH 499/566] added missing dependency Boost-1.53.0-ictce-6.2.5.eb --- .../b/Boost/Boost-1.53.0-ictce-6.2.5.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb new file mode 100644 index 0000000000..2d60c31b5b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-6.2.5.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '6.2.5'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' -- GitLab From 633ee246320c4fba3f8bf635ea48046e3c8b1579 Mon Sep 17 00:00:00 2001 From: pescobar Date: Wed, 26 Mar 2014 20:05:28 +0100 Subject: [PATCH 500/566] added missing dependency bzip2-1.0.6-ictce-6.2.5.eb --- .../b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb new file mode 100644 index 0000000000..c2e0a1e300 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.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': 'ictce', 'version': '6.2.5'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' -- GitLab From bb2b316ac7227eed1bf8bde152e96796dfab1e90 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Mar 2014 22:40:11 +0100 Subject: [PATCH 501/566] tweak BOINC easyconfig, use glob support available for files_to_copy --- .../easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb index cd332e88ad..ffdbd66265 100644 --- a/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb +++ b/easybuild/easyconfigs/b/BOINC/BOINC-7.0.65-goolf-1.4.10-client.eb @@ -23,11 +23,12 @@ with_configure = True preconfigopts = './_autosetup &&' configopts = '--disable-server --disable-manager --enable-client' -files_to_copy = [(['client/boinc','client/boinccmd'], 'bin')] +# copy boinc and boinccmd binaries +files_to_copy = [(['client/boin*[cd]'], 'bin')] # make sure the binary are available after installation sanity_check_paths = { - 'files': ["bin/boinc",], + 'files': ["bin/boinc", "bin/boinccmd"], 'dirs': [], } -- GitLab From 64f14a192da543b29541539c7bf21e2f0d892a14 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 28 Mar 2014 15:31:37 +0100 Subject: [PATCH 502/566] eXpress-1.5.1-goolf-1.4.10.eb and patch --- .../e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb | 42 +++++++++++++++++++ .../e/eXpress/eXpress-1.5.1-libbamtools.patch | 11 +++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-libbamtools.patch diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..2c714d52d5 --- /dev/null +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb @@ -0,0 +1,42 @@ +# 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 = "eXpress" +version = "1.5.1" + +easyblock = "CMakeMake" + +homepage = 'http://bio.math.berkeley.edu/eXpress/index.html' +description = """ eXpress is a streaming tool for quantifying the abundances of a set + of target sequences from sampled subsequences. Example applications include transcript-level + RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), + transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.""" + +toolchain = {'version': '1.4.10', 'name': 'goolf'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/'] + +builddependencies = [ + ('CMake', '2.8.12'), + ('BamTools', '2.2.3') +] + +dependencies = [ + ('Boost', '1.51.0'), # Boost-1.53.0 not working? + ('gperftools', '2.1'), + ('protobuf', '2.5.0') +] + +separate_build_dir = True + +patches = ['eXpress-1.5.1-libbamtools.patch'] + +sanity_check_paths = { + 'files': ["bin/express"], + 'dirs': [""] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-libbamtools.patch b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-libbamtools.patch new file mode 100644 index 0000000000..4c807adfec --- /dev/null +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-libbamtools.patch @@ -0,0 +1,11 @@ +--- express-1.5.1-src.orig/src/CMakeLists.txt 2013-12-08 20:09:18.000000000 +0100 ++++ express-1.5.1-src/src/CMakeLists.txt 2014-03-27 23:09:17.014311307 +0100 +@@ -16,7 +16,7 @@ + if(WIN32) + set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") + else(WIN32) +- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") ++ set(LIBRARIES ${LIBRARIES} "$ENV{EBROOTBAMTOOLS}/lib/libbamtools.a" "pthread") + endif(WIN32) + + if (PROTOBUF_FOUND) -- GitLab From 7f44e15d59104926ea96473e095ebbd9bc7dbd1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 16:04:18 +0100 Subject: [PATCH 503/566] add easyconfig file for GCC multilib build --- .../easyconfigs/g/GCC/GCC-4.8.2-multilib.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb new file mode 100644 index 0000000000..509d5e27ca --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -0,0 +1,31 @@ +name = "GCC" +version = '4.8.2' +versionsuffix = '-multilib' + +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-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', +] + +languages = ['c', 'c++', 'fortran', 'lto'] + +multilib = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From d4aa4bce578662daaa026ea74973ff0a85c9b4a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 16:11:07 +0100 Subject: [PATCH 504/566] add easyconfig file for LIBSVM --- .../l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb new file mode 100644 index 0000000000..ced7e71f8c --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.17' + +homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'ictce', 'version': '4.1.13'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Qt', '4.8.4')] + +makeopts = ' && cd svm-toy/qt && make MOC=$EBROOTQT/bin/moc ' +makeopts += 'CFLAGS="$CFLAGS -I$EBROOTQT/include -I$EBROOTQT/include/QtGui -lQtGui -lQtCore" && cd -' + +files_to_copy = [(['svm-*'], 'bin'), 'tools'] + +# make sure the gzip, gunzip and compress binaries are available after installation +sanity_check_paths = { + 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'toy', 'train']], + 'dirs': ['tools'], +} + +moduleclass = 'lib' -- GitLab From 7b01b528a41689d9ab5d7f245289e25a8e1a7480 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 16:12:14 +0100 Subject: [PATCH 505/566] remove comment --- easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb index ced7e71f8c..c033ab0207 100644 --- a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb @@ -18,7 +18,6 @@ makeopts += 'CFLAGS="$CFLAGS -I$EBROOTQT/include -I$EBROOTQT/include/QtGui -lQtG files_to_copy = [(['svm-*'], 'bin'), 'tools'] -# make sure the gzip, gunzip and compress binaries are available after installation sanity_check_paths = { 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'toy', 'train']], 'dirs': ['tools'], -- GitLab From 7e1a623683d46e441577925e8acebdf8a37ece18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 17:04:33 +0100 Subject: [PATCH 506/566] add GCC v4.8.2 CLooG easyconfigs, both with and without multilib --- .../g/GCC/GCC-4.8.2-CLooG-multilib.eb | 39 +++++++++++++++++++ .../easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb 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 new file mode 100644 index 0000000000..2d3d0d9732 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -0,0 +1,39 @@ +name = "GCC" +version = '4.8.2' +versionsuffix = "-CLooG-multilib" + +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 + 'http://www.bastoul.net/cloog/pages/download/', # CLooG official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', + 'cloog-0.18.2.tar.gz', +] + +languages = ['c', 'c++', 'fortran', 'lto'] + +withcloog = True + +clooguseisl = True + +multilib = 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/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb new file mode 100644 index 0000000000..b56bf2cda9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.8.2' +versionsuffix = "-CLooG" + +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 + 'http://www.bastoul.net/cloog/pages/download/', # CLooG official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', + 'cloog-0.18.2.tar.gz', +] + +languages = ['c', 'c++', 'fortran', 'lto'] + +withcloog = True + +clooguseisl = True + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' -- GitLab From 989d2ee570d9521548ef39e8dd96449ebd2bfad0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 17:24:22 +0100 Subject: [PATCH 507/566] use CLooG v0.18.1 with GCC v4.8.2 --- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 2d3d0d9732..546001ab6b 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 @@ -22,7 +22,7 @@ sources = [ 'gmp-5.1.3.tar.bz2', 'mpfr-3.1.2.tar.gz', 'mpc-1.0.1.tar.gz', - 'cloog-0.18.2.tar.gz', + 'cloog-0.18.1.tar.gz', ] languages = ['c', 'c++', 'fortran', 'lto'] 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 b56bf2cda9..f3c7e6b745 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.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-0.18.2.tar.gz', + 'cloog-0.18.1.tar.gz', ] languages = ['c', 'c++', 'fortran', 'lto'] -- GitLab From f15aa551d21e477af6625f8405fc8b610c2746da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Mar 2014 22:22:23 +0100 Subject: [PATCH 508/566] fix description --- easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb index c033ab0207..515dc5d0ab 100644 --- a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb @@ -4,7 +4,8 @@ name = 'LIBSVM' version = '3.17' homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' -description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -- GitLab From 4844518f6a34d69e319868bb3f6b4b3ad1621a3d Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 11:27:41 +0100 Subject: [PATCH 509/566] move easyblock to first line --- easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb index 2c714d52d5..2a9c740dd3 100644 --- a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb @@ -3,11 +3,11 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = "CMakeMake" + name = "eXpress" version = "1.5.1" -easyblock = "CMakeMake" - homepage = 'http://bio.math.berkeley.edu/eXpress/index.html' description = """ eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level -- GitLab From d5550daff335bc566e6031c17978ba9597de3924 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 11:29:38 +0100 Subject: [PATCH 510/566] updated source_url to more generic one --- easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb index 2a9c740dd3..eb6680d2d6 100644 --- a/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/eXpress/eXpress-1.5.1-goolf-1.4.10.eb @@ -17,7 +17,7 @@ description = """ eXpress is a streaming tool for quantifying the abundances of toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = ['%(namelower)s-%(version)s-src.tgz'] -source_urls = ['http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/'] +source_urls = ['http://bio.math.berkeley.edu/eXpress/downloads/%(namelower)s-%(version)s/'] builddependencies = [ ('CMake', '2.8.12'), -- GitLab From 33ed3e2de627ba8911be5ecbd060f1c1a318640a Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 12:21:42 +0100 Subject: [PATCH 511/566] CEM-0.9.1-goolf-1.4.10.eb --- .../c/CEM/CEM-0.9.1-goolf-1.4.10.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..6709e17801 --- /dev/null +++ b/easybuild/easyconfigs/c/CEM/CEM-0.9.1-goolf-1.4.10.eb @@ -0,0 +1,36 @@ +# 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 = "CEM" +version = "0.9.1" + +homepage = 'http://alumni.cs.ucr.edu/~liw/cem.html' +description = """ CEM: Transcriptome Assembly and Isoform Expression Level Estimation + from Biased RNA-Seq Reads. CEM is an algorithm to assemble transcripts and estimate + their expression levels from RNA-Seq reads. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://alumni.cs.ucr.edu/~liw/'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('GSL', '1.16') +] + +start_dir = "src" + +files_to_copy = ["../bin", "../demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['bed2sam', 'bed2gtf', 'comparegtf', + 'gtf2pred', 'isolassocem', 'pred2gtf', + 'processsam', 'sortgtf']], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 250f2d3a159299880d1ab41f5bb2c8519cab3f65 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 15:37:15 +0100 Subject: [PATCH 512/566] BitSeq-0.7.0-goolf-1.4.10.eb --- .../b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..82b02fc155 --- /dev/null +++ b/easybuild/easyconfigs/b/BitSeq/BitSeq-0.7.0-goolf-1.4.10.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 +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = "BitSeq" +version = "0.7.0" + +homepage = 'https://code.google.com/p/bitseq/' +description = """ BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an + application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) + data and estimating differential expression (DE) between conditions. An advantage of this + approach is the ability to account for both technical uncertainty and intrinsic biological + variance in order to avoid false DE calls. The technical contribution to the uncertainty comes + both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bitseq.googlecode.com/files/'] +sources = [SOURCE_TAR_GZ] + +# put here the list of generated executables when compiling +list_of_executables = ["convertSamples", "estimateDE", "estimateExpression", "estimateHyperPar", + "estimateVBExpression", "extractSamples", "getFoldChange", "getGeneExpression", + "getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment", + "transposeLargeFile", "getCounts.py", "extractTranscriptInfo.py"] + +# this is the real EasyBuild line to copy all the executables to "bin" +files_to_copy = [(list_of_executables, "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in list_of_executables], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From fbcab9046ba3bb88c64724b68de1339234d53e12 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 17:07:08 +0100 Subject: [PATCH 513/566] segemehl-0.1.7-goolf-1.4.10.eb --- .../s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.eb new file mode 100644 index 0000000000..f5e2b9d7dd --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.1.7-goolf-1.4.10.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 + +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.1.7" + +homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """ segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/'] +sources = ['%s_%s.tar.gz' % (name, version.replace('.','_'))] + +files_to_copy = [(["haarz.x", "lack.x", "segemehl.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "lack.x" , "segemehl.x"]], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 3b1a66ffb2c7d46bc62fa110f67c65f95be4f3e1 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 17:56:59 +0100 Subject: [PATCH 514/566] SRA-Toolkit-2.3.5-centos_linux64.eb --- .../SRA-Toolkit-2.3.5-centos_linux64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb new file mode 100644 index 0000000000..b77fce9377 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb @@ -0,0 +1,26 @@ +# 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 = 'Tarball' + +name = 'SRA-Toolkit' +version = '2.3.5' +versionsuffix = '-centos_linux64' + +homepage = 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std' +description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing files + from the SRA database and writing (loading) files into the .sra format """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['%s.%s%s.tar.gz' % (name.lower().replace('-',''), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["sra-stat", "sra-sort", "srapath", "bam-load"]], + 'dirs': ["example", "schema"], +} + +moduleclass = 'bio' -- GitLab From 4040aef2f77e754376fb03f4d589d5db5a759154 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sat, 29 Mar 2014 22:43:19 +0100 Subject: [PATCH 515/566] MMSEQ-1.0.8-linux64-static.eb --- .../m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb diff --git a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb new file mode 100644 index 0000000000..e59bc43670 --- /dev/null +++ b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb @@ -0,0 +1,26 @@ +# 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 = "Tarball" + +name = 'MMSEQ' +version = '1.0.8' +versionsuffix = '-linux64-static' + +homepage = 'https://github.com/eturro/mmseq' +description = """ The MMSEQ package contains a collection of statistical tools + for analysing RNA-seq expression data. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/eturro/mmseq/archive/'] +sources = ['%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/mmseq-linux", "bin/bam2hits-linux", "bin/extract_transcripts-linux" ], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 98536323a2800b07afd8e06be1d7b2c7f0b787a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Apr 2014 16:27:57 +0200 Subject: [PATCH 516/566] enable -fPIC for libreadline, so it can be linked into shared libs (e.g. libpython2.x.so) --- .../libreadline-6.2-cgmpolf-1.1.6.eb | 1 + .../libreadline-6.2-cgmvolf-1.1.12rc1.eb | 1 + .../libreadline-6.2-cgmvolf-1.2.7.eb | 1 + .../libreadline/libreadline-6.2-cgoolf-1.1.7.eb | 1 + .../libreadline/libreadline-6.2-gmpolf-1.4.8.eb | 1 + .../libreadline-6.2-gmvolf-1.7.12.eb | 1 + .../libreadline-6.2-gmvolf-1.7.12rc1.eb | 1 + .../libreadline-6.2-goalf-1.1.0-no-OFED.eb | 1 + .../libreadline-6.2-goalf-1.5.12-no-OFED.eb | 1 + .../libreadline-6.2-gompi-1.4.12-no-OFED.eb | 1 + .../libreadline/libreadline-6.2-goolf-1.4.10.eb | 1 + .../libreadline/libreadline-6.2-ictce-4.0.10.eb | 1 + .../libreadline/libreadline-6.2-ictce-4.0.6.eb | 1 + .../libreadline/libreadline-6.2-ictce-4.1.13.eb | 1 + .../libreadline/libreadline-6.2-ictce-5.2.0.eb | 17 ++++++++++------- .../libreadline/libreadline-6.2-ictce-5.3.0.eb | 1 + .../libreadline/libreadline-6.2-ictce-5.5.0.eb | 1 + .../libreadline/libreadline-6.2-iomkl-4.6.13.eb | 1 + .../libreadline/libreadline-6.2-iqacml-3.7.3.eb | 1 + .../libreadline-6.2-iqacml-4.4.13.eb | 1 + 20 files changed, 29 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb index b104105924..ea86f44110 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb index 08386dbd84..845fa3e7fa 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb index 5bc7206321..49c0baecf1 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb @@ -8,6 +8,7 @@ additional functions to maintain a list of previously-entered command lines, to and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb index ce9ce7a0dc..07ea263092 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'cgoolf', 'version': '1.1.7'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb index 4b179d3cea..aaa76f5f77 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmpolf', 'version': '1.4.8'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb index 4a3a76f70d..fcb196f792 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb @@ -8,6 +8,7 @@ additional functions to maintain a list of previously-entered command lines, to and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb index 04dfce7349..e0e2d5c7fa 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb index adb8107354..066765bca3 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb index 6829e60dce..146a8e9944 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb index 9a72756a88..db9397866d 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb index 91a1a3db51..e835cd63d6 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goolf-1.4.10.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb index ebff1e197f..7a1a0c8b8b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version': '4.0.10'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb index ec7c6dfb60..7cbbcd5ae7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb index 3edea96b6d..af015cd665 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb index e77b116c77..169a857dc2 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.2.0.eb @@ -8,15 +8,18 @@ The Readline library includes additional functions to maintain a list of previou to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version' : '5.2.0'} +toolchainopts = {'pic': True} -sources = ['readline-%s.tar.gz' % version] +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' : [] - } + '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/libreadline/libreadline-6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb index 96c57993e7..af7f561821 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb index 309a843372..1c9a199f1b 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb index 7ca5bdbcd1..ac364c1247 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'iomkl', 'version': '4.6.13'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb index f197ec170b..446d0f52d7 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'iqacml', 'version': '3.7.3'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb index e8897e4b13..4833ff1469 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb @@ -8,6 +8,7 @@ description = """The GNU Readline library provides a set of functions for use by to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" toolchain = {'name': 'iqacml', 'version': '4.4.13'} +toolchainopts = {'pic': True} sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] -- GitLab From 68732aacc185a4c50b1ef25b34afb29bc5afe9cc Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 3 Apr 2014 00:21:10 +0200 Subject: [PATCH 517/566] MUSTANG-3.2.1-goolf-1.4.10.eb --- .../m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb | 30 +++++++++++++++++++ .../MUSTANG-3.2.1-missing-include.patch | 10 +++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-missing-include.patch diff --git a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000..237097a644 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +# 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 = "MUSTANG" +version = "3.2.1" + +homepage = 'http://www.csse.monash.edu.au/~karun/Site/mustang.html' +description = """ MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment + of multiple protein structures. Given a set of protein structures, the program constructs + a multiple alignment using the spatial information of the Cα atoms in the set. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.csse.monash.edu.au/~karun/mustang/'] +sources = ['%(namelower)s_v%(version)s.tgz'] + +patches = ['MUSTANG-3.2.1-missing-include.patch'] + +files_to_copy = ["bin", "data", "man", "README"] + +sanity_check_paths = { + 'files': ["bin/mustang-3.2.1"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-missing-include.patch b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-missing-include.patch new file mode 100644 index 0000000000..2fe2e06a4f --- /dev/null +++ b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-missing-include.patch @@ -0,0 +1,10 @@ +--- MUSTANG_v3.2.1.orig/src/superpose_on_core_2.cpp 2009-04-18 10:30:17.000000000 +0200 ++++ MUSTANG_v3.2.1/src/superpose_on_core_2.cpp 2014-04-02 23:44:58.668808458 +0200 +@@ -54,6 +54,7 @@ + #include "read_structures.h" + #include "multiple_superposition.h" + #include "3D_manip_functions.h" ++#include "unistd.h" + + int **core_columns ; + int *core_columns_2 , NCORE = 0 ; -- GitLab From 97543c68d25b0bbf1c8adada9b05a0dbee08c9e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Apr 2014 09:59:17 +0200 Subject: [PATCH 518/566] enable -fPIC in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others --- easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index fb1f4e9935..ee127c7a3c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -7,6 +7,7 @@ and more. It uses Terminfo format, supports pads and color and multiple highligh function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'ictce', 'version': '5.2.0'} +toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -- GitLab From 7a02b8df0f9b3dae0f1acac41bd53622e9aba74a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Apr 2014 22:40:38 +0200 Subject: [PATCH 519/566] bump version to v1.12.0.0, update release notes --- RELEASE_NOTES | 25 +++++++++++++++++++++---- setup.py | 2 +- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 48872f366f..ab1bbd745c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -1,15 +1,32 @@ This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package. For more detailed information, please see the git log. -The latest version of easybuild-easyconfig provides 2,319 easyconfig files, for 444 different software packages -and 29 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 2,372 easyconfig files, for 451 different software packages +and 28 different (compiler) toolchains. -v1.11.1 (February 28th 2013) +v1.12.0 (April 4th 2014) +------------------------ + +feature + bugfix release +- added example easyconfig files for 6 new software packages: + CLooG (#653), ELPA (#738), LIBSVM (#788), netaddr (#753), netifcas (#753), slalib-c (#750) +- added easyconfigs for new toolchains: + ClangGCC/1.3.0 (#653), goolf/1.4.10-no-OFED (#749), goolf/1.5.14(-no-OFED) (#764, #767), ictce/6.2.5 (#726), iomkl (#747) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... +- various enhancements, including: + - tweak BOINC easyconfig to make use of glob support available for files_to_copy (#781) + - enable -fPIC for libreadline, so it can be linked into shared libs (e.g. libpython2.x.so) (#798) +- various bug fixes, including: + - fix Qt source_urls (#756) + - enable -fPIC in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others (#801) + - fix unit tests after changes to framework (#763, #766, #769) + +v1.11.1 (February 28th 2014) ---------------------------- (no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework -v1.11.0 (February 16th 2013) +v1.11.0 (February 16th 2014) ---------------------------- feature + bugfix release diff --git a/setup.py b/setup.py index d090434633..3a1621d82a 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 = "1.12.0.0dev" +VERSION = "1.12.0.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 81b43d379bcdd637dca3b476415dcec77df38be4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Apr 2014 09:53:14 +0200 Subject: [PATCH 520/566] bump version to v1.13.0.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3a1621d82a..8c07948b75 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 = "1.12.0.0" +VERSION = "1.13.0.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 0a17eb68bb25cd885e0ae640f4f76eceded51213 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Apr 2014 09:54:29 +0200 Subject: [PATCH 521/566] bump version to v1.12.1.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3a1621d82a..1216c5c322 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 = "1.12.0.0" +VERSION = "1.12.1.0dev" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From da53b48be86cc37d63d6a3c97f3f3aa26bb994a5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Mon, 14 Apr 2014 00:37:58 +0200 Subject: [PATCH 522/566] add 5.3 & 5.4 versions of Lmod Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb | 24 +++++++++++++++++++ .../easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb new file mode 100644 index 0000000000..8a7e354fe8 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb @@ -0,0 +1,24 @@ +name = "Lmod" +version = "5.3" + +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")] + +configopts = ' --with-mpathSearch=yes ' # for backward compatibility + +sanity_check_paths = { + 'files': ["lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb new file mode 100644 index 0000000000..cd5ef76ead --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb @@ -0,0 +1,24 @@ +name = "Lmod" +version = "5.4" + +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")] + +configopts = ' --with-mpathSearch=yes ' # for backward compatibility + +sanity_check_paths = { + 'files': ["lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" -- GitLab From 5ee8e38749f5b5f9d7e69961d32c4a82a72367f2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 14 Apr 2014 12:20:55 +0200 Subject: [PATCH 523/566] added SOAPdenovo2 --- .../SOAPdenovo2-r240-goolf-1.4.10.eb | 30 +++++++++++++++++++ .../s/SOAPdenovo2/SOAPdenovo2_inistd.patch | 10 +++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb new file mode 100644 index 0000000000..bd1892711d --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +name = 'SOAPdenovo2' +version = 'r240' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """ +SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The + program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the + successor of SOAPdenovo. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sourcename = '%s-src-%s' % (name, version) +sources = [sourcename + '.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +# only a make step, no configure and install, so build in install dir +buildininstalldir = True +skipsteps = ['configure', 'install'] +patches = ['SOAPdenovo2_inistd.patch'] + +modextrapaths = {'PATH': 'sourcename'} +sanity_check_paths = { + 'files': [sourcename + '/SOAPdenovo-127mer', sourcename + '/SOAPdenovo-63mer'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch new file mode 100644 index 0000000000..b5d76889db --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch @@ -0,0 +1,10 @@ +--- SOAPdenovo2-src-r240.orig/sparsePregraph/inc/stdinc.h 2013-07-09 05:46:52.000000000 +0200 ++++ SOAPdenovo2-src-r240/sparsePregraph/inc/stdinc.h 2014-04-14 10:07:31.009191162 +0200 +@@ -32,6 +32,7 @@ + #include + #include + #include ++#include + using namespace std; + + -- GitLab From 4b1267e433672086f7b8a419f6e18b216fbd7e00 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 14 Apr 2014 13:49:39 +0200 Subject: [PATCH 524/566] no parallel make + added ictce .eb --- .../SOAPdenovo2-r240-goolf-1.4.10.eb | 2 ++ .../SOAPdenovo2-r240-ictce-5.5.0.eb | 32 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb index bd1892711d..054a0a5072 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -20,6 +20,8 @@ source_urls = [SOURCEFORGE_SOURCE] buildininstalldir = True skipsteps = ['configure', 'install'] patches = ['SOAPdenovo2_inistd.patch'] +# parallel make seems to fail +parallel = 1 modextrapaths = {'PATH': 'sourcename'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb new file mode 100644 index 0000000000..d34aa5befd --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb @@ -0,0 +1,32 @@ +name = 'SOAPdenovo2' +version = 'r240' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """ +SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The + program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the + successor of SOAPdenovo. +""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sourcename = '%s-src-%s' % (name, version) +sources = [sourcename + '.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +# only a make step, no configure and install, so build in install dir +buildininstalldir = True +skipsteps = ['configure', 'install'] +patches = ['SOAPdenovo2_inistd.patch'] +# parallel build seems to fail +parallel = 1 + +modextrapaths = {'PATH': 'sourcename'} +sanity_check_paths = { + 'files': [sourcename + '/SOAPdenovo-127mer', sourcename + '/SOAPdenovo-63mer'], + 'dirs': [], +} + +moduleclass = 'bio' -- GitLab From 65b61b9be7fe13a8e13062fa5818aa87bb59a90c Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 15 Apr 2014 02:20:25 +0200 Subject: [PATCH 525/566] update bits for Lmod/5.4 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/README.TXT | 10 +++++----- easybuild/easyconfigs/l/Lmod/sourceme | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/README.TXT b/easybuild/easyconfigs/l/Lmod/README.TXT index 6e4cf47e00..4c094b773e 100644 --- a/easybuild/easyconfigs/l/Lmod/README.TXT +++ b/easybuild/easyconfigs/l/Lmod/README.TXT @@ -9,7 +9,7 @@ Howto: Assuming you have successfully used the bootstrap procedure of EasyBuild, you should be able to initiate a recursive build of the following bits: -l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb +l/Lmod/Lmod-5.4-GCC-4.8.2.eb ### just aim for this one, with "-r" l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb n/ncurses/ncurses-5.9-GCC-4.8.2.eb g/GCC/GCC-4.8.2.eb @@ -17,17 +17,17 @@ g/GCC/GCC-4.8.2.eb This set is expected to be the needed substrate to launch you towards Lmod, which gets activated with the `sourceme` script sitting in the same directory: -`source sourceme` # N.B. it does direct assignments on environment variables; that's very intentional +`source sourceme` # N.B. it does direct assignments on environment variables; that's intentional Then try: `ml av` # ie. the Lmod equivalent to `module avail` ; it should work -If so, you implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html +If so, you just implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html Lmod's caching can help to work with *buildsets*; ref. https://fosdem.org/2014/schedule/event/hpc_devroom_hpcbios/ -You should now be able to try alternative Lmod/Lua versions, such as 3.x variety, toggle cache, and so forth. +You should now be able to try alternative Lmod/Lua versions, toggle cache, and so forth. enjoy, Fotis -2014-03-13 +2014-04-15 diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 3f7c86e156..b87c81208d 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -13,7 +13,7 @@ EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" -VERSIONLMOD="5.2.5" +VERSIONLMOD="5.4" PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD -- GitLab From 29f833c5e2431fc035f0768bdcac6533884dc75b Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 26 Apr 2013 13:21:42 +0200 Subject: [PATCH 526/566] add CP2K-ictce-5.3.0 Signed-off-by: Fotis Georgatos --- .../c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb new file mode 100644 index 0000000000..fed3d4e9ee --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb @@ -0,0 +1,33 @@ +name = 'CP2K' +version = '20111205' + +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': 'ictce', 'version': '5.3.0'} + +sources = ['CP2K-%s.tar.gz' % version] + +patches = [ + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch' + ] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5') + ] + +dependencies = [('Libint', '1.1.4')] + +# 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 (120/2196 tests fail with segfault) +ignore_regtest_fails = True + +moduleclass = 'chem' -- GitLab From b0d8faced1cc7863b184962cc777d0d294079112 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:14:45 +0200 Subject: [PATCH 527/566] improve style on CP2K-20111205-ictce-5.3.0.u3.eb and rename to CP2K-20111205-ictce-5.3.0.eb Signed-off-by: Fotis Georgatos --- .../c/CP2K/CP2K-20111205-ictce-5.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.eb new file mode 100644 index 0000000000..3e863ab079 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.eb @@ -0,0 +1,33 @@ +name = 'CP2K' +version = '20111205' + +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': 'ictce', 'version': '5.3.0'} + +sources = [SOURCE_TAR_GZ] + +patches = [ + 'fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +builddependencies = [ + ('flex', '2.5.35'), + ('Bison', '2.5'), +] + +dependencies = [('Libint', '1.1.4')] + +# 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 (120/2196 tests fail with segfault) +ignore_regtest_fails = True + +moduleclass = 'chem' -- GitLab From 292fa80d8e119689d42fd4cb8ae009eb1bd4ad02 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:30:59 +0200 Subject: [PATCH 528/566] really delete old CP2K still hanging around Signed-off-by: Fotis Georgatos --- .../c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb deleted file mode 100644 index fed3d4e9ee..0000000000 --- a/easybuild/easyconfigs/c/CP2K/CP2K-20111205-ictce-5.3.0.u3.eb +++ /dev/null @@ -1,33 +0,0 @@ -name = 'CP2K' -version = '20111205' - -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': 'ictce', 'version': '5.3.0'} - -sources = ['CP2K-%s.tar.gz' % version] - -patches = [ - 'fix_compile_date_lastcvs.patch', - 'do_regtest_nocompile.patch' - ] - -builddependencies = [ - ('flex', '2.5.35'), - ('Bison', '2.5') - ] - -dependencies = [('Libint', '1.1.4')] - -# 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 (120/2196 tests fail with segfault) -ignore_regtest_fails = True - -moduleclass = 'chem' -- GitLab From 31e269f7ca96322e8b37141587fe5cd74ed81d13 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:48:58 +0200 Subject: [PATCH 529/566] address remarks for 5.3, 5.4 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb | 7 +++++-- easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb | 7 +++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb index 8a7e354fe8..05c978e0f9 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb @@ -10,14 +10,17 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo 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'] +source_urls = [ + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] dependencies = [("Lua", "5.1.4-8")] configopts = ' --with-mpathSearch=yes ' # for backward compatibility sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb index cd5ef76ead..b126ae6a13 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb @@ -10,14 +10,17 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo 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'] +source_urls = [ + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] dependencies = [("Lua", "5.1.4-8")] configopts = ' --with-mpathSearch=yes ' # for backward compatibility sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } -- GitLab From 2e17b7f58c1b50a4d14ae00268852780c2b297e7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:49:56 +0200 Subject: [PATCH 530/566] address remarks for 5.2* Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb | 2 +- easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb | 2 +- easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb | 7 +++++-- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb index 769d793890..988d710727 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.7.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb index 78f3f1e26b..4d0d5e01bc 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-GCC-4.8.2.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb index f386c53edb..8b641dfb5f 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ source_urls = ['http://sourceforge.net/projects/lmod/files/'] dependencies = [("Lua", "5.1.4-5")] sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb index 14c2d00848..898aff188b 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.2.5-GCC-4.8.2.eb @@ -10,12 +10,15 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo 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'] +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/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } -- GitLab From 967b66e3344495c4dbbbd760aac5c5f7691a6fa9 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:50:32 +0200 Subject: [PATCH 531/566] drop customization of mpathsearch Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb | 2 -- easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb index 05c978e0f9..0331bf0116 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.3-GCC-4.8.2.eb @@ -17,8 +17,6 @@ source_urls = [ dependencies = [("Lua", "5.1.4-8")] -configopts = ' --with-mpathSearch=yes ' # for backward compatibility - sanity_check_paths = { 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb index b126ae6a13..48d4c46271 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4-GCC-4.8.2.eb @@ -17,8 +17,6 @@ source_urls = [ dependencies = [("Lua", "5.1.4-8")] -configopts = ' --with-mpathSearch=yes ' # for backward compatibility - sanity_check_paths = { 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] -- GitLab From d1dd2d2f035ed6e8a16ab9faaebeaad3ec7bc0b4 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 16:53:47 +0200 Subject: [PATCH 532/566] add export LMOD_MPATH_AVAIL=yes Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/sourceme | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index b87c81208d..05de173d32 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -19,6 +19,7 @@ PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH +export LMOD_MPATH_AVAIL=yes # most sites with life science audience would expect this source $PREFIXLMOD/init/profile export PAGER=cat # Keep it simple, for a start -- GitLab From 3d3d627577b1d1a4e4e34f7f25d59dcee85fc5cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Apr 2014 17:03:02 +0200 Subject: [PATCH 533/566] add easyconfig for Lmod v5.4.1 --- .../l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..5f11d572b5 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb @@ -0,0 +1,24 @@ +name = "Lmod" +version = "5.4.1" + +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")] + +configopts = ' --with-mpathSearch=yes ' # for backward compatibility + +sanity_check_paths = { + 'files': ["lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" -- GitLab From fe17f2e1ac1d056122a87115e41aa18c7ab8d71d Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 17:32:16 +0200 Subject: [PATCH 534/566] rephrase a comment Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/sourceme | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 05de173d32..7d0716eb75 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -9,7 +9,6 @@ ## Remember to change the following, as per individual case EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} -#EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"/opt/apps/HPCBIOS.20131224"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" @@ -19,7 +18,7 @@ PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD export PATH=$PREFIXLUA/bin:$PREFIXLUA/libexec:$PATH -export LMOD_MPATH_AVAIL=yes # most sites with life science audience would expect this +export LMOD_MPATH_AVAIL=yes # `module avail` now also searches the pathnames of modulefiles source $PREFIXLMOD/init/profile export PAGER=cat # Keep it simple, for a start -- GitLab From 5b7decb2e41d487c8809ae94e71c341aaa5bb7ca Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Thu, 17 Apr 2014 23:01:11 +0200 Subject: [PATCH 535/566] promote lmod to v5.4.1 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/sourceme | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 7d0716eb75..4bbb358f9c 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -12,7 +12,7 @@ EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" -VERSIONLMOD="5.4" +VERSIONLMOD="5.4.1" PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD -- GitLab From cf4683de1fabeed90d9288269bd3b96cdb1cbda7 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 18 Apr 2014 00:11:50 +0200 Subject: [PATCH 536/566] promote lmod to v5.4.2 Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/sourceme | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 4bbb358f9c..3030d30fab 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -12,7 +12,7 @@ EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" -VERSIONLMOD="5.4.1" +VERSIONLMOD="5.4.2" PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD -- GitLab From 5fb7bb46f0922bb298a98946d6a4feb577ba7812 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 18 Apr 2014 00:15:10 +0200 Subject: [PATCH 537/566] promote to Lmod/5.4.2 Signed-off-by: Fotis Georgatos --- .../l/Lmod/{Lmod-5.4.1-GCC-4.8.2.eb => Lmod-5.4.2-GCC-4.8.2.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/Lmod/{Lmod-5.4.1-GCC-4.8.2.eb => Lmod-5.4.2-GCC-4.8.2.eb} (97%) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb similarity index 97% rename from easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb rename to easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb index 5f11d572b5..1420889489 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.4.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb @@ -1,5 +1,5 @@ name = "Lmod" -version = "5.4.1" +version = "5.4.2" homepage = "http://sourceforge.net/projects/lmod/" description = """Lmod is a Lua based module system. Modules allow for dynamic modification -- GitLab From 8fce30e72400607c2a5003259d74e1a1e1a84201 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 18 Apr 2014 00:19:19 +0200 Subject: [PATCH 538/566] style & fixes Signed-off-by: Fotis Georgatos --- easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb index 1420889489..bf79635a7b 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.4.2-GCC-4.8.2.eb @@ -10,14 +10,15 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo 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'] +source_urls = [ + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] dependencies = [("Lua", "5.1.4-8")] -configopts = ' --with-mpathSearch=yes ' # for backward compatibility - sanity_check_paths = { - 'files': ["lmod/%(version)s/init/profile"], + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], 'dirs': [] } -- GitLab From e3207ef125f7c85192db2b19018bdc5f363b3734 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Apr 2014 18:48:09 +0200 Subject: [PATCH 539/566] add easyconfigs for older GCC versions --- easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb | 25 ++++++++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb | 25 ++++++++++++++++++++++ easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb | 25 ++++++++++++++++++++++ easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb | 20 +++++++++++++++++ easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb | 22 +++++++++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb new file mode 100644 index 0000000000..6379dea586 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb @@ -0,0 +1,25 @@ +name = "GCC" +version = '4.2.4' + +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': ''} # empty version to ensure that dependencies are loaded + +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GMP', '4.3.2'), + ('MPFR', '2.4.2'), +] + +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' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb new file mode 100644 index 0000000000..9b19f80ad1 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb @@ -0,0 +1,25 @@ +name = "GCC" +version = '4.3.6' + +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': ''} # empty version to ensure that dependencies are loaded + +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GMP', '4.3.2'), + ('MPFR', '2.4.2'), +] + +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' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb new file mode 100644 index 0000000000..1593b8223d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb @@ -0,0 +1,25 @@ +name = "GCC" +version = '4.4.7' + +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': ''} # empty version to ensure that dependencies are loaded + +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GMP', '4.3.2'), + ('MPFR', '2.4.2'), +] + +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' diff --git a/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb b/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb new file mode 100644 index 0000000000..873b3ab746 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb @@ -0,0 +1,20 @@ +name = 'GMP' +version = '4.3.2' + +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': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.so', 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb b/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb new file mode 100644 index 0000000000..51ed7bde5f --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb @@ -0,0 +1,22 @@ +name = 'MPFR' +version = '2.4.2' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision +floating-point computations with correct rounding.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '4.3.2')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.so', 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' -- GitLab From d77cc1159a35b33bb47db2e3e1395343df8ecb49 Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 25 Apr 2014 16:40:12 +0200 Subject: [PATCH 540/566] added Bowtie2-2.2.2-goolf-1.4.10.eb --- .../b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb new file mode 100644 index 0000000000..10fbc1b97d --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -0,0 +1,36 @@ +# 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 = 'Bowtie2' +version = '2.2.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%s-%s-source.zip' % (name.lower(), version)] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' -- GitLab From d5073bfb1241ecbabb74463b562effa2cc8d0b2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Apr 2014 17:40:20 +0200 Subject: [PATCH 541/566] bump version to v1.12.1.0, update release notes --- RELEASE_NOTES | 7 ++++++- setup.py | 2 +- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index ab1bbd745c..585eb113b2 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -4,6 +4,11 @@ For more detailed information, please see the git log. The latest version of easybuild-easyconfig provides 2,372 easyconfig files, for 451 different software packages and 28 different (compiler) toolchains. +v1.12.1 (April 25th 2014) +-------------------------- + +(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework) + v1.12.0 (April 4th 2014) ------------------------ @@ -24,7 +29,7 @@ feature + bugfix release v1.11.1 (February 28th 2014) ---------------------------- -(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework +(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework) v1.11.0 (February 16th 2014) ---------------------------- diff --git a/setup.py b/setup.py index 1216c5c322..d068b5214a 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 = "1.12.1.0dev" +VERSION = "1.12.1.0" API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) -- GitLab From 771ed5e8ddc4a6ee39f49e96591c81d4a9c78de5 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Tue, 29 Apr 2014 15:11:21 +0200 Subject: [PATCH 542/566] bring-in Lmod/5.5 related bits Signed-off-by: Fotis Georgatos --- .../easyconfigs/l/Lmod/Lmod-5.5-GCC-4.8.2.eb | 25 +++++++++++++++++++ easybuild/easyconfigs/l/Lmod/README.TXT | 8 +++--- easybuild/easyconfigs/l/Lmod/sourceme | 4 +-- 3 files changed, 32 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.5-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.5-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.5-GCC-4.8.2.eb new file mode 100644 index 0000000000..2c8f284bdd --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.5-GCC-4.8.2.eb @@ -0,0 +1,25 @@ +name = "Lmod" +version = "5.5" + +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/README.TXT b/easybuild/easyconfigs/l/Lmod/README.TXT index 4c094b773e..a19f3e4986 100644 --- a/easybuild/easyconfigs/l/Lmod/README.TXT +++ b/easybuild/easyconfigs/l/Lmod/README.TXT @@ -9,7 +9,9 @@ Howto: Assuming you have successfully used the bootstrap procedure of EasyBuild, you should be able to initiate a recursive build of the following bits: -l/Lmod/Lmod-5.4-GCC-4.8.2.eb ### just aim for this one, with "-r" + `time eb Lmod-5.5-GCC-4.8.2.eb -r` + +l/Lmod/Lmod-5.5-GCC-4.8.2.eb ### so, you just aim for this one, with "-r" l/Lua/Lua-5.1.4-8-GCC-4.8.2.eb n/ncurses/ncurses-5.9-GCC-4.8.2.eb g/GCC/GCC-4.8.2.eb @@ -23,11 +25,11 @@ Then try: `ml av` # ie. the Lmod equivalent to `module avail` ; it should work -If so, you just implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html +If so, now you implemented the better instance of: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html Lmod's caching can help to work with *buildsets*; ref. https://fosdem.org/2014/schedule/event/hpc_devroom_hpcbios/ You should now be able to try alternative Lmod/Lua versions, toggle cache, and so forth. enjoy, Fotis -2014-04-15 +2014-04-29 diff --git a/easybuild/easyconfigs/l/Lmod/sourceme b/easybuild/easyconfigs/l/Lmod/sourceme index 3030d30fab..147c82fe86 100644 --- a/easybuild/easyconfigs/l/Lmod/sourceme +++ b/easybuild/easyconfigs/l/Lmod/sourceme @@ -2,7 +2,7 @@ # # This script helps to implement policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-17.html # -# prereq: Lmod/5.2.5-GCC-4.8.2 +# prereq: Lmod/5.5-GCC-4.8.2 # prereq: Lua/5.1.4-8-GCC-4.8.2 # # build prereqs, take a note: GCC/4.8.2 & ncurses/5.9 @@ -12,7 +12,7 @@ EASYBUILD_PREFIX=${EASYBUILD_PREFIX:-"$HOME/.local/easybuild"} TOOLCHAIN="GCC-4.8.2" VERSIONLUA="5.1.4-8" -VERSIONLMOD="5.4.2" +VERSIONLMOD="5.5" PREFIXLUA=$EASYBUILD_PREFIX/software/Lua/$VERSIONLUA-$TOOLCHAIN PREFIXLMOD=$EASYBUILD_PREFIX/software/Lmod/$VERSIONLMOD-$TOOLCHAIN/lmod/$VERSIONLMOD -- GitLab From d39f33f3347351fa56372ccf65a61e96560184c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Apr 2014 13:28:01 +0200 Subject: [PATCH 543/566] add configure options for GMP/MPFR --- easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb | 2 ++ easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb | 2 ++ easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb index 6379dea586..3ccecb918f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb @@ -17,6 +17,8 @@ dependencies = [ languages = ['c', 'c++', 'fortran'] +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR" + # 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-4.3.6.eb b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb index 9b19f80ad1..b182cdcc48 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb @@ -17,6 +17,8 @@ dependencies = [ languages = ['c', 'c++', 'fortran'] +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR" + # 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-4.4.7.eb b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb index 1593b8223d..b33b83ca23 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb @@ -17,6 +17,8 @@ dependencies = [ languages = ['c', 'c++', 'fortran'] +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR" + # building GCC sometimes fails if make parallelism is too high, so let's limit it maxparallel = 4 -- GitLab From 9eda8016315edd633d8c8bc0a83ef5280f8cffaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Apr 2014 14:16:58 +0200 Subject: [PATCH 544/566] add easyconfig for GCC v4.1.2 --- easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb | 30 ++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb new file mode 100644 index 0000000000..42a1d25324 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb @@ -0,0 +1,30 @@ +name = "GCC" +version = '4.1.2' + +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': ''} # empty version to ensure that dependencies are loaded + +source_urls = ['http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GMP', '4.3.2'), + ('MPFR', '2.4.2'), +] + +# building GCC v4.1.2 requires an old GCC version, so don't rely on system compiler +builddependencies = [('GCC', '4.2.4')] + +languages = ['c', 'c++', 'fortran'] + +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR" + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' -- GitLab From bebfbac6a1fd2ceba48173380a400948d54e8e97 Mon Sep 17 00:00:00 2001 From: pescobar Date: Mon, 5 May 2014 13:54:08 +0200 Subject: [PATCH 545/566] moved easyblock line to top --- .../v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb index 0d59c2f0e7..26093f8c38 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.12-goolf-1.4.10-Perl-5.16.3.eb @@ -3,11 +3,11 @@ # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +easyblock = 'MakeCp' + name = 'VCFtools' version = '0.1.12' -easyblock = 'MakeCp' - homepage = "http://vcftools.sourceforge.net/" description = """The aim of VCFtools is to provide methods for working with VCF files: validating, -- GitLab From 1c75c914652ac0728cd21fe7aea1fb07bb8819f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2014 09:57:05 +0200 Subject: [PATCH 546/566] add easyconfig file for Lmod 5.5.1 --- .../l/Lmod/Lmod-5.5.1-GCC-4.8.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lmod/Lmod-5.5.1-GCC-4.8.2.eb diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-5.5.1-GCC-4.8.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-5.5.1-GCC-4.8.2.eb new file mode 100644 index 0000000000..90c9e48256 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-5.5.1-GCC-4.8.2.eb @@ -0,0 +1,25 @@ +name = "Lmod" +version = "5.5.1" + +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" -- GitLab From 4eb1e9fcc8746339d3018e83cf9e6e862fc6f6b3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Thu, 8 May 2014 11:09:19 +0200 Subject: [PATCH 547/566] Jellyfish-2.1.3-goolf-1.4.10.eb --- .../Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000..65d9262c6c --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +# 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 = 'Jellyfish' +version = '2.1.3' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +runtest = "check" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' -- GitLab From 8de04d4357fdac4285edebfc0dcac7b3fe32498e Mon Sep 17 00:00:00 2001 From: pescobar Date: Fri, 9 May 2014 18:25:02 +0200 Subject: [PATCH 548/566] RSEQtools-0.6-goolf-1.4.10.eb --- .../r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb 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 new file mode 100644 index 0000000000..13fe7b28ad --- /dev/null +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -0,0 +1,62 @@ +# 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 = 'RSEQtools' +version = '0.6' + +homepage = 'http://rseqtools.gersteinlab.org' +description = """ A modular framework to analyze RNA-Seq data using compact + and anonymized data summaries.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.gersteinlab.org/proj/rnaseq/rseqtools/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('BLAT', '3.5'), + ('GSL', '1.16'), +] + +# this apps is tricky to compile so we will do everything in premakeopts +# +# firt define required environment variables +premakeopts = 'export BIOINFOGSLDIR=$EBROOTGSL && export BIOINFOCONFDIR=conf && ' +# now move to "bios" folder and run "make && make prod". Then come back to root folder +premakeopts += 'cd bios && make && make prod && cd - && ' +# now move to "mrf" folder, re-export the needed env var and run make +premakeopts += 'cd mrf && export BIOINFOCONFDIR=../bios/conf/ && make && ' +# this final echo prevents the latest make from MakeCp block to be executed. +# I know, it's a dirty hack but it works :) +premakeopts += 'echo "compilation done"' + +parallel = 1 + +# these are all the binaries compiled in "mrf" folder +binary_files = ["psl2mrf", "bowtie2mrf", "singleExport2mrf", "mrfSubsetByTargetName", + "mrfQuantifier", "mrfAnnotationCoverage", "mrf2wig", "mrf2gff", "mrfSampler", + "mrf2bgr", "wigSegmenter", "mrfMappingBias", "mrfSelectRegion", "mrfSelectSpliced", + "mrfSelectAnnotated", "createSpliceJunctionLibrary", "gff2interval", "export2fastq", + "mergeTranscripts", "interval2gff", "interval2sequences", "bed2interval", + "interval2bed", "mrf2sam", "sam2mrf", "mrfValidate", "bgrQuantifier", + "bgrSegmenter", "mrfCountRegion"] + +files_to_copy = [ + (['mrf/%s' % x for x in binary_files], "bin"), + "LICENSE", "README", "bios", "mrf", "test" +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binary_files], + 'dirs': [] +} + +modextravars = { + 'BIOINFOCONFDIR': '$root/bios/conf', +} + +moduleclass = 'bio' -- GitLab From af9e8c77a72a659bf5366b94aaca9684b9d494d6 Mon Sep 17 00:00:00 2001 From: Aaron Zauner Date: Wed, 14 May 2014 19:12:41 +0200 Subject: [PATCH 549/566] added Ruby 2.1.0 for goolf 1.4.10 --- .../r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..520edc5c97 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# 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 = '2.1.0' + +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': 'goolf', 'version': '1.4.10'} + +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 e016373d7de1adba2ff4ec2ae4dd61025603c0f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 May 2014 21:04:36 +0200 Subject: [PATCH 550/566] merge PRs #691 and #823 --- .../SOAPdenovo2-2.40-goolf-1.4.10.eb | 41 ------------------ ... => SOAPdenovo2-fix-unistd-includes.patch} | 0 .../SOAPdenovo2-r240-goolf-1.4.10.eb | 42 +++++++++++-------- ...3.0.eb => SOAPdenovo2-r240-ictce-5.3.0.eb} | 25 +++++------ .../SOAPdenovo2-r240-ictce-5.5.0.eb | 42 +++++++++++-------- .../s/SOAPdenovo2/fix-unistd-includes.patch | 40 ------------------ 6 files changed, 59 insertions(+), 131 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb rename easybuild/easyconfigs/s/SOAPdenovo2/{SOAPdenovo2_inistd.patch => SOAPdenovo2-fix-unistd-includes.patch} (100%) rename easybuild/easyconfigs/s/SOAPdenovo2/{SOAPdenovo2-2.40-ictce-5.3.0.eb => SOAPdenovo2-r240-ictce-5.3.0.eb} (50%) delete mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb deleted file mode 100644 index f5c3b3a3ef..0000000000 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-goolf-1.4.10.eb +++ /dev/null @@ -1,41 +0,0 @@ -# With <3 for EasyBuild -# -# EasyConfig for SOAPdenovo2: -# ---------------------------------------------------------------------------- -# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH -# License: MIT -# Authors: Petar Forai -# ---------------------------------------------------------------------------- - -easyblock = "MakeCp" - -name = 'SOAPdenovo2' -version = '240' - -homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' -description = """SOAPdenovo is a novel short-read assembly method that can build a -de novo draft assembly for human-sized genomes. The program is specially designed to -assemble Illumina short reads. It creates new opportunities for building reference -sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. -SOAPdenovo2 is the successor of SOAPdenovo.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} - -patches = ['fix-unistd-includes.patch'] - -# like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz -sources = ['%(name)s-src-r%(version)s.tgz'] -source_urls = [SOURCEFORGE_SOURCE] - -# parallel build is broken -maxparallel = 1 - -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] - -sanity_check_paths = { - 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-fix-unistd-includes.patch similarity index 100% rename from easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2_inistd.patch rename to easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-fix-unistd-includes.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb index 054a0a5072..2d5dc632a2 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -1,32 +1,38 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + name = 'SOAPdenovo2' version = 'r240' homepage = 'http://soap.genomics.org.cn/index.html' -description = """ -SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The - program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference - sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the - successor of SOAPdenovo. -""" +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -sourcename = '%s-src-%s' % (name, version) -sources = [sourcename + '.tgz'] source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2_fix-unistd-includes.patch'] -# only a make step, no configure and install, so build in install dir -buildininstalldir = True -skipsteps = ['configure', 'install'] -patches = ['SOAPdenovo2_inistd.patch'] -# parallel make seems to fail -parallel = 1 +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] -modextrapaths = {'PATH': 'sourcename'} sanity_check_paths = { - 'files': [sourcename + '/SOAPdenovo-127mer', sourcename + '/SOAPdenovo-63mer'], + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], 'dirs': [], } - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb similarity index 50% rename from easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb rename to easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb index 32ca2a4913..ac1946eada 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-2.40-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb @@ -10,32 +10,29 @@ easyblock = "MakeCp" name = 'SOAPdenovo2' -version = '240' +version = 'r240' -homepage = 'http://www.gigasciencejournal.com/content/1/1/18/' +homepage = 'http://soap.genomics.org.cn/index.html' description = """SOAPdenovo is a novel short-read assembly method that can build a -de novo draft assembly for human-sized genomes. The program is specially designed to -assemble Illumina short reads. It creates new opportunities for building reference -sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. -SOAPdenovo2 is the successor of SOAPdenovo.""" + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -patches = ['fix-unistd-includes.patch'] - -# like http://downloads.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz -sources = ['%(name)s-src-r%(version)s.tgz'] source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2_fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'],'bin')] +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] sanity_check_paths = { - 'files': ['bin/SOAPdenovo-63mer','bin/SOAPdenovo-127mer'], + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], 'dirs': [], } - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb index d34aa5befd..a5d9d3eb8f 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb @@ -1,32 +1,38 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + name = 'SOAPdenovo2' version = 'r240' homepage = 'http://soap.genomics.org.cn/index.html' -description = """ -SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The - program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference - sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the - successor of SOAPdenovo. -""" +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -sourcename = '%s-src-%s' % (name, version) -sources = [sourcename + '.tgz'] source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2_fix-unistd-includes.patch'] -# only a make step, no configure and install, so build in install dir -buildininstalldir = True -skipsteps = ['configure', 'install'] -patches = ['SOAPdenovo2_inistd.patch'] -# parallel build seems to fail -parallel = 1 +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] -modextrapaths = {'PATH': 'sourcename'} sanity_check_paths = { - 'files': [sourcename + '/SOAPdenovo-127mer', sourcename + '/SOAPdenovo-63mer'], + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], 'dirs': [], } - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch b/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch deleted file mode 100644 index 5813a42d62..0000000000 --- a/easybuild/easyconfigs/s/SOAPdenovo2/fix-unistd-includes.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/build_preArc.cpp SOAPdenovo2-src-r240/sparsePregraph/build_preArc.cpp ---- SOAPdenovo2-src-r240.orig/sparsePregraph/build_preArc.cpp 2013-11-11 11:03:42.236283000 +0100 -+++ SOAPdenovo2-src-r240/sparsePregraph/build_preArc.cpp 2013-11-11 11:12:22.841393000 +0100 -@@ -21,12 +21,14 @@ - */ - - -+#include - #include "stdinc.h" - #include "build_preArc.h" - #include "seq_util.h" - #include "global.h" - #include "multi_threads.h" - -+ - #include - #include "bam.h" - #include "faidx.h" -diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/multi_threads.cpp SOAPdenovo2-src-r240/sparsePregraph/multi_threads.cpp ---- SOAPdenovo2-src-r240.orig/sparsePregraph/multi_threads.cpp 2013-11-11 11:03:41.749247000 +0100 -+++ SOAPdenovo2-src-r240/sparsePregraph/multi_threads.cpp 2013-11-11 11:10:04.695845000 +0100 -@@ -20,6 +20,7 @@ - * - */ - -+#include - #include "multi_threads.h" - #include "global.h" - #include "build_graph.h" -diff -r -w -u SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp ---- SOAPdenovo2-src-r240.orig/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:03:42.243266000 +0100 -+++ SOAPdenovo2-src-r240/sparsePregraph/pregraph_sparse.cpp 2013-11-11 11:10:30.945711000 +0100 -@@ -20,6 +20,7 @@ - * - */ - -+#include - #include "global.h" - #include "stdinc.h" - #include "core.h" -- GitLab From 83d0c57cef4397728a892cae87511338020c7163 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 May 2014 21:07:16 +0200 Subject: [PATCH 551/566] correct location of Ruby easyconfig file --- .../r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb new file mode 100644 index 0000000000..520edc5c97 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.0-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# 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 = '2.1.0' + +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': 'goolf', 'version': '1.4.10'} + +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 09b0cbc67e25600226e5d4df6aebd6349ec11424 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 May 2014 21:26:39 +0200 Subject: [PATCH 552/566] fix name of SOAPdenovo2 patch file --- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb | 2 +- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb | 2 +- .../easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb index 2d5dc632a2..f630ed6839 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-goolf-1.4.10.eb @@ -25,7 +25,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tgz'] -patches = ['SOAPdenovo2_fix-unistd-includes.patch'] +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb index ac1946eada..05c5b5cfbb 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.3.0.eb @@ -25,7 +25,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tgz'] -patches = ['SOAPdenovo2_fix-unistd-includes.patch'] +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb index a5d9d3eb8f..897f658237 100644 --- a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-ictce-5.5.0.eb @@ -25,7 +25,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-src-%(version)s.tgz'] -patches = ['SOAPdenovo2_fix-unistd-includes.patch'] +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] # parallel build is broken maxparallel = 1 -- GitLab From d0c4925f2c5f409361610f59b783c0c1a5e75307 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 May 2014 09:00:14 +0200 Subject: [PATCH 553/566] clean up Ruby easyconfig in wrong location --- .../r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb deleted file mode 100644 index 520edc5c97..0000000000 --- a/easybuild/easyconfigs/r/Ruby/2.1.0/Ruby-2.1.0-goolf-1.4.10.eb +++ /dev/null @@ -1,31 +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 = '2.1.0' - -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': 'goolf', 'version': '1.4.10'} - -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 e9750d0b4522bfb82c67ddb630f57f585e83432a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 May 2014 10:12:33 +0200 Subject: [PATCH 554/566] minor style fix in Bowtie2 easyconfig --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb index 879efdd95f..56b7f26201 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-ictce-5.5.0.eb @@ -21,8 +21,8 @@ description = """Bowtie 2 is an ultrafast and memory-efficient tool toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -sources = ['%s-%s-source.zip' % (name.lower(), version)] +# note: SOURCEFORGE_SOURCE constant doesn't work here because of bowtie-bio used in URL source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -# N.B. the download option above -> required for sourceforge +sources = ['%(namelower)s-%(version)s-source.zip'] moduleclass = 'bio' -- GitLab From d52db0ed8e59e54e1be1fdd327ff06e4edc95c5c Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 15:22:34 +0200 Subject: [PATCH 555/566] zlib dependency and required easyconfig --- .../p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 2 ++ .../z/zlib/zlib-1.2.8-ictce-6.2.5.eb | 22 +++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index 9206fbc286..e23da6eff6 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -21,6 +21,8 @@ toolchain = {'name': 'ictce', 'version': '6.2.5'} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +dependencies = [('zlib', '1.2.8')] + # plink makefile is a little bit tricky so we pass every options as arguments # review plink original makefile for details # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes 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 new file mode 100644 index 0000000000..c01d1b4c1f --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-6.2.5.eb @@ -0,0 +1,22 @@ +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': 'ictce', 'version': '6.2.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] + +preconfigopts = 'LDSHARED="$CC -shared"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' -- GitLab From 4f9e4b95122e32f8843a1db5cc2f98ad044bbf8e Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 15:25:04 +0200 Subject: [PATCH 556/566] changed CXX_UNIX and added openmp toolchainopt --- easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index e23da6eff6..496ac96c60 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -17,6 +17,7 @@ description = """ PLINK is a free, open-source whole genome association analysis annotation and storage of results. """ toolchain = {'name': 'ictce', 'version': '6.2.5'} +toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] @@ -27,7 +28,7 @@ dependencies = [('zlib', '1.2.8')] # review plink original makefile for details # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes # have no internet access better leave it as is -makeopts = ' CXX_UNIX="icpc -fopenmp" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' +makeopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' makeopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBVARBLAS_LAPACK_LIB_DIR/libmkl_lapack.a' files_to_copy = [ -- GitLab From c22a28590813ac478a83a09e6496b5094fbc9c02 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 15:26:04 +0200 Subject: [PATCH 557/566] switched to $BLAS_LAPACK_LIB_DIR --- easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb index 496ac96c60..dbef660517 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-6.2.5.eb @@ -29,7 +29,7 @@ dependencies = [('zlib', '1.2.8')] # if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes # have no internet access better leave it as is makeopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' -makeopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBVARBLAS_LAPACK_LIB_DIR/libmkl_lapack.a' +makeopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$BLAS_LAPACK_LIB_DIR/libmkl_lapack.a' files_to_copy = [ (["plink", "gPLINK.jar"], 'bin'), -- GitLab From da941a6f9db8728877c3c2d54e34dbd2a49ec33b Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:03:55 +0200 Subject: [PATCH 558/566] fixed source_urls --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb | 2 +- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb index 57283b6361..ae75b8cebd 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.5-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb index 401552dfac..640a7f6d83 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.6-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb index 8686bbb43c..93890f908f 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.1.0-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align", "bowtie2-build", "bowtie2-inspect"], 'bin'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb index 1ae7dd0f5e..6dbb873164 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.0-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb index 10fbc1b97d..83794c9d53 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.2-goolf-1.4.10.eb @@ -18,7 +18,7 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = ['%s-%s-source.zip' % (name.lower(), version)] -source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%s/%s' % (name.lower(), version), 'download')] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] files_to_copy = [ (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", -- GitLab From 7d543ade024e1a96af2fac2d8b3c140c7a06bbc9 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:12:08 +0200 Subject: [PATCH 559/566] changed sources --- .../s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb index b77fce9377..2921c1a627 100644 --- a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb @@ -16,7 +16,7 @@ description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing f toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] -sources = ['%s.%s%s.tar.gz' % (name.lower().replace('-',''), version, versionsuffix)] +sources = ['sra.toolkit.%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["sra-stat", "sra-sort", "srapath", "bam-load"]], -- GitLab From 853ad7b8f1c456fc33eb5d8771ea7949ec674d5f Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:29:16 +0200 Subject: [PATCH 560/566] removed dirty hack --- .../easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) 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 13fe7b28ad..d796288d70 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 @@ -29,10 +29,7 @@ premakeopts = 'export BIOINFOGSLDIR=$EBROOTGSL && export BIOINFOCONFDIR=conf && # now move to "bios" folder and run "make && make prod". Then come back to root folder premakeopts += 'cd bios && make && make prod && cd - && ' # now move to "mrf" folder, re-export the needed env var and run make -premakeopts += 'cd mrf && export BIOINFOCONFDIR=../bios/conf/ && make && ' -# this final echo prevents the latest make from MakeCp block to be executed. -# I know, it's a dirty hack but it works :) -premakeopts += 'echo "compilation done"' +premakeopts += 'cd mrf && export BIOINFOCONFDIR=../bios/conf/ && ' parallel = 1 -- GitLab From 3551fc6dc215d63cfc2afa477c2a8b518972dabe Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:31:14 +0200 Subject: [PATCH 561/566] added version suffix and use templates in sources --- .../b/BayesTraits/BayesTraits-2.0-beta-linux64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb index 940dfe4dc2..c6a2da24d4 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb @@ -6,7 +6,8 @@ easyblock = "Tarball" name = 'BayesTraits' -version = '2.0-Beta-Linux64' +version = '2.0' +versionsuffix = '-Beta-Linux64' homepage = 'http://www.evolution.reading.ac.uk/BayesTraitsV1.html' description = """ BayesTraits is a computer package for performing analyses of trait @@ -20,7 +21,7 @@ description = """ BayesTraits is a computer package for performing analyses of t toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.evolution.reading.ac.uk/Files/'] -sources = ['BayesTraitsV2-Beta-Linux64.tar.gz'] +sources = ['%(name)sV%(versionmajor)s-%(versionsuffix)s'] sanity_check_paths = { 'files': ['BayesTraits', 'Primates.trees', 'Mammal.trees'], -- GitLab From 034d9d03da1f1d77846eecf88638d18910f13e83 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:33:05 +0200 Subject: [PATCH 562/566] typo fixed --- .../s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb index 2921c1a627..fc325c12fd 100644 --- a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.3.5-centos_linux64.eb @@ -16,7 +16,7 @@ description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing f toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] -sources = ['sra.toolkit.%(version)s%(versionsuffix)s.tar.gz'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["sra-stat", "sra-sort", "srapath", "bam-load"]], -- GitLab From 90c1fe3ebdc03665c2ef5151d0eb39aa182b0996 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:52:18 +0200 Subject: [PATCH 563/566] use templates in sanity checking --- easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb index 237097a644..9ce401d07a 100644 --- a/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/MUSTANG/MUSTANG-3.2.1-goolf-1.4.10.eb @@ -23,7 +23,7 @@ patches = ['MUSTANG-3.2.1-missing-include.patch'] files_to_copy = ["bin", "data", "man", "README"] sanity_check_paths = { - 'files': ["bin/mustang-3.2.1"], + 'files': ["bin/mustang-%(version)s"], 'dirs': [] } -- GitLab From 52d676575a669cc46308e5b40896a5b91c394ef3 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 16:57:16 +0200 Subject: [PATCH 564/566] fixed typo in source --- .../easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb index c6a2da24d4..e43eef29d7 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb @@ -21,7 +21,7 @@ description = """ BayesTraits is a computer package for performing analyses of t toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.evolution.reading.ac.uk/Files/'] -sources = ['%(name)sV%(versionmajor)s-%(versionsuffix)s'] +sources = ['%(name)sV%(versionmajor)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ['BayesTraits', 'Primates.trees', 'Mammal.trees'], -- GitLab From 8af1f7b0f770c9d12f49967f14a49a53812bb795 Mon Sep 17 00:00:00 2001 From: pescobar Date: Sun, 18 May 2014 21:32:12 +0200 Subject: [PATCH 565/566] fixed typo --- .../easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb index e43eef29d7..159ed9b248 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-beta-linux64.eb @@ -21,7 +21,7 @@ description = """ BayesTraits is a computer package for performing analyses of t toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://www.evolution.reading.ac.uk/Files/'] -sources = ['%(name)sV%(versionmajor)s%(versionsuffix)s.tar.gz'] +sources = ['%(name)sV%(version_major)s%(versionsuffix)s.tar.gz'] sanity_check_paths = { 'files': ['BayesTraits', 'Primates.trees', 'Mammal.trees'], -- GitLab From 7777c0969a0277ae0a9886e1046f52edec4741b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 May 2014 21:56:11 +0200 Subject: [PATCH 566/566] add zlib dep for PLINK and use proper makeopts --- .../easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb | 6 ++++++ easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb index e943acb2ba..270600b7a4 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-goalf-1.1.0-no-OFED.eb @@ -15,10 +15,16 @@ homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' description = "plink-1.07-src: Whole-genome association analysis toolset" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +dependencies = [('zlib', '1.2.7')] + +makeopts = 'CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 FORCE_DYNAMIC=1' +makeopts += ' WITH_LAPACK=1 LIB_LAPACK="-L$BLAS_LAPACK_LIB_DIR -llapack -lf77blas -latlas -lgfortran"' + files_to_copy = [ (["plink", "gPLINK.jar"], 'bin'), "test.map", diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb index d9aca19bc6..378457546f 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-ictce-5.3.0.eb @@ -15,10 +15,16 @@ homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' description = "plink-1.07-src: Whole-genome association analysis toolset" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'openmp': True} sources = ['%(namelower)s-%(version)s-src.zip'] source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] +dependencies = [('zlib', '1.2.7')] + +makeopts = 'CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1' +makeopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$BLAS_LAPACK_LIB_DIR/libmkl_lapack.a' + files_to_copy = [ (["plink", "gPLINK.jar"], 'bin'), "test.map", -- GitLab