From a61a3965112bb9208c715ff95a76c251b26f2ca9 Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:13:28 +0200 Subject: [PATCH 1/7] Errors moving to Nord3 in FAQ --- inst/doc/faq.md | 46 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index a965827..9319ffa 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - + 6. [Errors using a new cluster: setting Nord3](#6Errors-using-a-new-cluster-setting-nord3) ## 1. How to @@ -750,3 +750,47 @@ Aborting in file clipping.c, line 1295 ... Error in s2dverification::CDORemap(data_array, lons, lats, ...) : CDO remap failed. ``` + + +### 6.Errors using a new cluster: setting Nord3 + +When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64. + +- whether running Compute(), request password: + +``` +Password: +``` + +Check that the host name for the cluster has been include in the ´.ssh/config´. +Check also that the passwordless access has been properly set up. You can check that you can access the cluster without providing the password by using the host name ´ssh nord3´ (see more infor in the [**Practical guide**](inst/doc/practical_guide.md)). + +- alias may not be available, such as 'enas' for 'esarchive' + +In this case, the error ´No data files found for any of the specified datasets.´ will be returned. + +- repetitive prints of modules loading: + +``` +load UDUNITS/2.1.24 (PATH) +load NETCDF/4.1.3 (PATH, LD_LIBRARY_PATH, NETCDF) +load R/2.15.2 (PATH, LD_LIBRARY_PATH) +``` + +The .bashrc in your Nord 3 home must be edit with the information from [BSC ES wiki](https://earth.bsc.es/wiki/doku.php?id=computing:nord3) to load correct modules. However, if you add a line before those, the result will be the one above. + +Check your .bashrc to avoid loading modules before define the department ones. + + +- R versions: Workstation version versus remote cluster version + +Some functions depends on the R version used and they should be compatible in workstation and in the remote cluster. If the error: + +``` +cannot read workspace version 3 written by R 3.6.2; need R 3.5.0 or newer +``` + +change the R version used in your workstation to one newer. + + + -- GitLab From c0af0587e5a3f358c88437d0dfc442cef38bd492 Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:15:49 +0200 Subject: [PATCH 2/7] edits to links --- inst/doc/faq.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index 9319ffa..f9573aa 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - 6. [Errors using a new cluster: setting Nord3](#6Errors-using-a-new-cluster-setting-nord3) + 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-setting-nord3) ## 1. How to @@ -752,7 +752,7 @@ Error in s2dverification::CDORemap(data_array, lons, lats, ...) : ``` -### 6.Errors using a new cluster: setting Nord3 +### 6. Errors using a new cluster: setting Nord3 When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64. -- GitLab From 7ce9a2b7bc06145e4bc7447fad2b7ce61fe540cc Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:19:24 +0200 Subject: [PATCH 3/7] edits to links --- inst/doc/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index f9573aa..ffd0115 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-setting-nord3) + 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster:-setting-nord3) ## 1. How to -- GitLab From 279837fc7d449d3f3151bdaa270bc8df9a18472f Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:22:37 +0200 Subject: [PATCH 4/7] edits to links --- inst/doc/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index ffd0115..fdbe32f 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster:-setting-nord3) + 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-:-setting-nord3) ## 1. How to -- GitLab From 10d969413004b66613a124768e574d6c8358fecb Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:27:00 +0200 Subject: [PATCH 5/7] edits to links --- inst/doc/faq.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index fdbe32f..da8cd05 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - 6. [Errors using a new cluster: setting Nord3](#6-Errors-using-a-new-cluster-:-setting-nord3) + 6. [Errors using a new cluster (setting Nord3)](#6-Errors-using-a-new-cluster-setting-nord3) ## 1. How to @@ -752,7 +752,7 @@ Error in s2dverification::CDORemap(data_array, lons, lats, ...) : ``` -### 6. Errors using a new cluster: setting Nord3 +### 6. Errors using a new cluster (setting Nord3) When using a new cluster, some errors could happen. Here, there are some behaviours detected from issue #64. -- GitLab From 29bc63e714ed7ed093fbbb0335fa9e95eae02003 Mon Sep 17 00:00:00 2001 From: nperez Date: Thu, 18 Jun 2020 18:28:33 +0200 Subject: [PATCH 6/7] edits to links remove capitals --- inst/doc/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index da8cd05..bebf4a8 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -29,7 +29,7 @@ This document intends to be the first reference for any doubts that you may have 3. [Compute() successfully but then killed on R session](#3-compute-successfully-but-then-killed-on-r-session) 4. [My jobs work well in workstation and fatnodes but not on Power9 (or vice versa)](#4-my-jobs-work-well-in-workstation-and-fatnodes-but-not-on-power9-or-vice-versa) 5. [Errors related to wrong file formatting](#5-errors-related-to-wrong-file-formatting) - 6. [Errors using a new cluster (setting Nord3)](#6-Errors-using-a-new-cluster-setting-nord3) + 6. [Errors using a new cluster (setting Nord3)](#6-errors-using-a-new-cluster-setting-nord3) ## 1. How to -- GitLab From 8e6d8005344be947ec3aaf416fcc9452569b33f2 Mon Sep 17 00:00:00 2001 From: Andrea Date: Thu, 18 Jun 2020 19:06:26 +0200 Subject: [PATCH 7/7] Update faq.md --- inst/doc/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/doc/faq.md b/inst/doc/faq.md index bebf4a8..6f1d1ac 100644 --- a/inst/doc/faq.md +++ b/inst/doc/faq.md @@ -765,7 +765,7 @@ Password: Check that the host name for the cluster has been include in the ´.ssh/config´. Check also that the passwordless access has been properly set up. You can check that you can access the cluster without providing the password by using the host name ´ssh nord3´ (see more infor in the [**Practical guide**](inst/doc/practical_guide.md)). -- alias may not be available, such as 'enas' for 'esarchive' +- alias may not be available, such as 'esnas' for 'esarchive' In this case, the error ´No data files found for any of the specified datasets.´ will be returned. -- GitLab