From ab2c260e4d9b9a1b70b7246b10977437ad0fcd15 Mon Sep 17 00:00:00 2001 From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com> Date: Wed, 29 Nov 2023 10:38:57 +0100 Subject: [PATCH 01/11] {2023.06}[foss/2023a] OpenFOAM v10 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index e685785f16..b67e894825 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -12,3 +12,4 @@ easyconfigs: options: from-pr: 19270 - SciPy-bundle-2023.07-gfbf-2023a.eb + - OpenFOAM-10-foss-2023a.eb From 3439e8b07981dff466b9efb1af4215bedb603351 Mon Sep 17 00:00:00 2001 From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com> Date: Fri, 1 Dec 2023 12:06:39 +0100 Subject: [PATCH 02/11] Include gnuplot fix from PR easybuilders/easyconfigs#19261 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index 4a302c409b..514ed0b86e 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -22,4 +22,7 @@ easyconfigs: options: from-pr: 19339 - Qt5-5.15.10-GCCcore-12.3.0.eb + - gnuplot-5.4.8-GCCcore-12.3.0.eb: + options: + from-pr: 19261 - OpenFOAM-10-foss-2023a.eb From 10751d25858239fe78465a5e523fc0077ac4b487 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 15 Dec 2023 15:15:14 +0100 Subject: [PATCH 03/11] Add pre test hook to skip netCDF tests --- eb_hooks.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index 6fe92c7f7b..2081bfedab 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -366,6 +366,18 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs): if self.name == 'SciPy-bundle' and self.version in ['2021.10', '2023.07'] and cpu_target == CPU_TARGET_NEOVERSE_V1: self.cfg['testopts'] = "|| echo ignoring failing tests" +def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs): + """ + Pre-test hook for SciPy-bundle: skip failing tests for selected netCDF versions on neoverse_v1 + cfr. https://github.com/EESSI/software-layer/issues/325 + The following tests are problematic: + 163 - nc_test4_run_par_test (Timeout) + 190 - h5_test_run_par_tests (Timeout) + A few other tests are skipped in the easyconfig and patches for similar issues, see above issue for details. + """ + cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') + if self.name == 'netCDF' and self.version == '4.9.2' and cpu_target == CPU_TARGET_NEOVERSE_V1: + self.cfg['testopts'] = "|| echo ignoring failing tests" def pre_single_extension_hook(ext, *args, **kwargs): """Main pre-configure hook: trigger custom functions based on software name.""" From 94206acbcc02da084ba4d5d85219d9ae92f885ac Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 15 Dec 2023 15:16:05 +0100 Subject: [PATCH 04/11] Add correct issue reference in hook --- eb_hooks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 2081bfedab..3074eb8ee3 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -369,7 +369,7 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs): def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs): """ Pre-test hook for SciPy-bundle: skip failing tests for selected netCDF versions on neoverse_v1 - cfr. https://github.com/EESSI/software-layer/issues/325 + cfr. https://github.com/EESSI/software-layer/issues/425 The following tests are problematic: 163 - nc_test4_run_par_test (Timeout) 190 - h5_test_run_par_tests (Timeout) From db150f4838c47d25e7a683ae239c44b25dd88a6d Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 15 Dec 2023 16:34:42 +0100 Subject: [PATCH 05/11] Fix hook --- eb_hooks.py | 1 + 1 file changed, 1 insertion(+) diff --git a/eb_hooks.py b/eb_hooks.py index 3074eb8ee3..bf5da0cc64 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -430,6 +430,7 @@ def pre_single_extension_isoband(ext, *args, **kwargs): 'ESPResSo': pre_test_hook_ignore_failing_tests_ESPResSo, 'FFTW.MPI': pre_test_hook_ignore_failing_tests_FFTWMPI, 'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle, + 'netCDF': pre_test_hook_ignore_failing_tests_netCDF, } PRE_SINGLE_EXTENSION_HOOKS = { From 98b51a90fa62e65ab9d87b096246b4744e8b96ab Mon Sep 17 00:00:00 2001 From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com> Date: Wed, 3 Jan 2024 19:16:34 +0100 Subject: [PATCH 06/11] Use only half the cores to build OpenFOAM --- eb_hooks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 8e29d2c103..edff46221a 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -79,7 +79,7 @@ def post_ready_hook(self, *args, **kwargs): # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores. # here we reduce parallellism to only use half of that for selected software, # to avoid failing builds/tests due to out-of-memory problems - if self.name in ['TensorFlow']: + if self.name in ['TensorFlow'] or self.name in ['OpenFOAM']: parallel = self.cfg['parallel'] if parallel > 1: self.cfg['parallel'] = parallel // 2 From 9c0ca0d408304ece1cdeed0aeabb42b9403bfd94 Mon Sep 17 00:00:00 2001 From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com> Date: Mon, 8 Jan 2024 11:31:46 +0100 Subject: [PATCH 07/11] Revert to using all cores in OpenFOAM tests Reducing in half did not solve issue with hanging/crashing in sanity checks --- eb_hooks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 3b52b54e9e..00aee51816 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -80,7 +80,7 @@ def post_ready_hook(self, *args, **kwargs): # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores. # here we reduce parallellism to only use half of that for selected software, # to avoid failing builds/tests due to out-of-memory problems - if self.name in ['TensorFlow'] or self.name in ['OpenFOAM']: + if self.name in ['TensorFlow']: parallel = self.cfg['parallel'] if parallel > 1: self.cfg['parallel'] = parallel // 2 From 9bae7f590a6bfe34e48fe20bc0be066ee407fb25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 15:26:18 +0100 Subject: [PATCH 08/11] add OpenMPI from PR 19940 (and rebuild: True) --- .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index 75dc86c31a..70fb5bfbe0 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -22,10 +22,6 @@ easyconfigs: options: from-pr: 19339 - Qt5-5.15.10-GCCcore-12.3.0.eb - - gnuplot-5.4.8-GCCcore-12.3.0.eb: - options: - from-pr: 19261 - - OpenFOAM-10-foss-2023a.eb - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb - LHAPDF-6.5.4-GCC-12.3.0.eb: options: @@ -56,3 +52,11 @@ easyconfigs: - BWA-0.7.17-20220923-GCCcore-12.3.0.eb: options: from-pr: 19820 + - gnuplot-5.4.8-GCCcore-12.3.0.eb: + options: + from-pr: 19261 + - OpenMPI-4.1.5-GCC-12.3.0.eb: + options: + from-pr: 19940 + rebuild: True + - OpenFOAM-10-foss-2023a.eb From d3c1f654371126a5187d3a9e07b6def690f8725d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 15:41:24 +0100 Subject: [PATCH 09/11] fix indentation --- .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index 70fb5bfbe0..b971c5adad 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -57,6 +57,6 @@ easyconfigs: from-pr: 19261 - OpenMPI-4.1.5-GCC-12.3.0.eb: options: - from-pr: 19940 - rebuild: True + from-pr: 19940 + rebuild: True - OpenFOAM-10-foss-2023a.eb From f2844fb210aa865155989811c88d85b7d8b3c1a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 26 Mar 2024 17:09:49 +0100 Subject: [PATCH 10/11] remove OpenMPI, which has been rebuilt in #488 --- .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index b971c5adad..1c3ea8fd78 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -55,8 +55,4 @@ easyconfigs: - gnuplot-5.4.8-GCCcore-12.3.0.eb: options: from-pr: 19261 - - OpenMPI-4.1.5-GCC-12.3.0.eb: - options: - from-pr: 19940 - rebuild: True - OpenFOAM-10-foss-2023a.eb From 5a43f9ef8d8d66dfa2bd0226f28a8bdf7521892b Mon Sep 17 00:00:00 2001 From: Neves-P Date: Tue, 26 Mar 2024 19:16:00 +0100 Subject: [PATCH 11/11] Don't need gnuplot, install with EasyBuild 4.9.0 --- .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 4 ---- .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml index 1c3ea8fd78..7244219dc3 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml @@ -52,7 +52,3 @@ easyconfigs: - BWA-0.7.17-20220923-GCCcore-12.3.0.eb: options: from-pr: 19820 - - gnuplot-5.4.8-GCCcore-12.3.0.eb: - options: - from-pr: 19261 - - OpenFOAM-10-foss-2023a.eb diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml index 157a47a49e..13d7ebdc02 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml @@ -29,3 +29,4 @@ easyconfigs: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19554 options: from-pr: 19554 + - OpenFOAM-10-foss-2023a.eb