From 515c0ad8896ca68d87d7eb84c796c33cd3003281 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 11 Sep 2023 14:13:09 +0200 Subject: [PATCH 1/8] Add espresso with GCC/11.3.0 and without CUDA to EESSI pilot 2023.06 --- eessi-2023.06-eb-4.7.2-2022a.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/eessi-2023.06-eb-4.7.2-2022a.yml b/eessi-2023.06-eb-4.7.2-2022a.yml index d40ddff261..f690d49192 100644 --- a/eessi-2023.06-eb-4.7.2-2022a.yml +++ b/eessi-2023.06-eb-4.7.2-2022a.yml @@ -1,3 +1,6 @@ easyconfigs: - GCC-11.3.0 - OpenMPI-4.1.4-GCC-11.3.0.eb + - ESPResSo-4.2.1-foss-2022a.eb: + options: + from-pr: 18486 From 2333240285bdd82c95a69bf2f0126b43958aa2c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 13:57:40 +0200 Subject: [PATCH 2/8] install ESPResSo-4.2.1-foss-2022a with EasyBuild v4.8.1 --- eessi-2023.06-eb-4.7.2-2022a.yml | 3 --- eessi-2023.06-eb-4.8.1-2022a.yml | 1 + 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/eessi-2023.06-eb-4.7.2-2022a.yml b/eessi-2023.06-eb-4.7.2-2022a.yml index f690d49192..d40ddff261 100644 --- a/eessi-2023.06-eb-4.7.2-2022a.yml +++ b/eessi-2023.06-eb-4.7.2-2022a.yml @@ -1,6 +1,3 @@ easyconfigs: - GCC-11.3.0 - OpenMPI-4.1.4-GCC-11.3.0.eb - - ESPResSo-4.2.1-foss-2022a.eb: - options: - from-pr: 18486 diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 8de4c6169d..c05316bcf7 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -5,3 +5,4 @@ easyconfigs: options: from-pr: 18870 - foss-2022a + - ESPResSo-4.2.1-foss-2022a From afcd92dff998e039ad8a2d7e5682604f6b1f7ad2 Mon Sep 17 00:00:00 2001 From: Maxim Date: Tue, 10 Oct 2023 11:40:26 +0200 Subject: [PATCH 3/8] Update eessi-2023.06-eb-4.8.1-2022a.yml --- eessi-2023.06-eb-4.8.1-2022a.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index c05316bcf7..646f28533d 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -6,3 +6,5 @@ easyconfigs: from-pr: 18870 - foss-2022a - ESPResSo-4.2.1-foss-2022a + options: + from-pr: 18963 From d877d7076790e2bd671604df36f2016ac86cbe09 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 10 Oct 2023 11:53:12 +0200 Subject: [PATCH 4/8] Add missing colon --- eessi-2023.06-eb-4.8.1-2022a.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 3c27495cd1..c9a249872b 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -5,7 +5,7 @@ easyconfigs: options: from-pr: 18870 - foss-2022a - - ESPResSo-4.2.1-foss-2022a + - ESPResSo-4.2.1-foss-2022a: options: from-pr: 18963 - SciPy-bundle-2022.05-foss-2022a From f8b4f42baa9451a2f5fa50d28fdc009e875d414b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Oct 2023 16:47:56 +0200 Subject: [PATCH 5/8] add ESPResSo to end of easystack file to preserve installation order --- eessi-2023.06-eb-4.8.1-2022a.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index c9a249872b..8317a40b7a 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -5,8 +5,8 @@ easyconfigs: options: from-pr: 18870 - foss-2022a + - SciPy-bundle-2022.05-foss-2022a + - BAMM-2.5.0-foss-2022a.eb - ESPResSo-4.2.1-foss-2022a: options: from-pr: 18963 - - SciPy-bundle-2022.05-foss-2022a - - BAMM-2.5.0-foss-2022a.eb From eae083ff82f540f056c4e7a3a732133d8813314c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Oct 2023 08:58:40 +0200 Subject: [PATCH 6/8] add hook to ignore failing tests in ESPResSo v4.2.1 + add corresponding tracker issue to list of known issues --- eb_hooks.py | 35 +++++++++++++++++++++++----------- eessi-2023.06-known-issues.yml | 24 +++++++++++++++-------- 2 files changed, 40 insertions(+), 19 deletions(-) diff --git a/eb_hooks.py b/eb_hooks.py index dbb8415541..31f2b9588d 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -247,6 +247,7 @@ def pre_configure_hook_metabat_filtered_zlib_dep(self, *args, **kwargs): else: raise EasyBuildError("MetaBAT-specific hook triggered for non-MetaBAT easyconfig?!") + def pre_configure_hook_wrf_aarch64(self, *args, **kwargs): """ Pre-configure hook for WRF: @@ -266,11 +267,32 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs): else: raise EasyBuildError("WRF-specific hook triggered for non-WRF easyconfig?!") + def pre_test_hook(self,*args, **kwargs): """Main pre-test hook: trigger custom functions based on software name.""" if self.name in PRE_TEST_HOOKS: PRE_TEST_HOOKS[self.name](self, *args, **kwargs) + +def pre_test_hook_ignore_failing_tests_ESPResSo(self, *args, **kwargs): + """ + Pre-test hook for ESPResSo: skip failing tests, tests frequently timeout due to known bugs in ESPResSo v4.2.1 + cfr. https://github.com/EESSI/software-layer/issues/363 + """ + if self.name == 'ESPResSo' and self.version == '4.2.1': + self.cfg['testopts'] = "|| echo 'ignoring failing tests (probably due to timeouts)'" + + +def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs): + """ + Pre-test hook for FFTW.MPI: skip failing tests for FFTW.MPI 3.3.10 on neoverse_v1 + cfr. https://github.com/EESSI/software-layer/issues/325 + """ + cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') + if self.name == 'FFTW.MPI' and self.version == '3.3.10' and cpu_target == CPU_TARGET_NEOVERSE_V1: + self.cfg['testopts'] = "|| echo ignoring failing tests" + + def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs): """ Pre-test hook for SciPy-bundle: skip failing tests for SciPy-bundle 2021.10 (currently the only version that is failing). @@ -307,16 +329,6 @@ def pre_single_extension_isoband(ext, *args, **kwargs): ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' src/testthat/vendor/catch.h && " -def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs): - """ - Pre-test hook for FFTW.MPI: skip failing tests for FFTW.MPI 3.3.10 on neoverse_v1 - cfr. https://github.com/EESSI/software-layer/issues/325 - """ - cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') - if self.name == 'FFTW.MPI' and self.version == '3.3.10' and cpu_target == CPU_TARGET_NEOVERSE_V1: - self.cfg['testopts'] = "|| echo ignoring failing tests" - - PARSE_HOOKS = { 'CGAL': parse_hook_cgal_toolchainopts_precise, 'fontconfig': parse_hook_fontconfig_add_fonts, @@ -337,8 +349,9 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs): } PRE_TEST_HOOKS = { - 'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle, + '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, } PRE_SINGLE_EXTENSION_HOOKS = { diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml index f2f96aee34..846e862983 100644 --- a/eessi-2023.06-known-issues.yml +++ b/eessi-2023.06-known-issues.yml @@ -1,22 +1,30 @@ +- x86_64/*: + - ESPResSo-4.2.1-foss-2022a: + - issue: https://github.com/EESSI/software-layer/issues/363 + - info: "Failing tests in ESPResSo v4.2.1 due to timeouts" +- aarch64/*: + - ESPResSo-4.2.1-foss-2022a: + - issue: https://github.com/EESSI/software-layer/issues/363 + - info: "Failing tests in ESPResSo v4.2.1 due to timeouts" - aarch64/neoverse_v1: - - FFTW/3.3.10-GCC-11.3.0: + - FFTW-3.3.10-GCC-11.3.0: - issue: https://github.com/EESSI/software-layer/issues/325 - info: "Flaky FFTW tests, random failures" - - FFTW/3.3.10-gompi-2021b: + - FFTW-3.3.10-gompi-2021b: - issue: https://github.com/EESSI/software-layer/issues/325 - info: "Flaky FFTW tests, random failures" - - OpenBLAS/0.3.18-GCC-11.2.0: + - OpenBLAS-0.3.18-GCC-11.2.0: - issue: https://github.com/EESSI/software-layer/issues/314 - info: "Increased number of non-numerical failures in OpenBLAS test suite (238 vs max. 150 on x86_64/*)" - - OpenBLAS/0.3.20-GCC-11.3.0: + - OpenBLAS-0.3.20-GCC-11.3.0: - issue: https://github.com/EESSI/software-layer/issues/314 - info: "Increased number of non-numerical failures in OpenBLAS test suite (238 vs max. 150 on x86_64/*)" - - OpenBLAS/0.3.21-GCC-12.2.0: + - OpenBLAS-0.3.21-GCC-12.2.0: - issue: https://github.com/EESSI/software-layer/issues/314 - info: "Increased number of non-numerical failures in OpenBLAS test suite (344 vs max. 150 on x86_64/*)" - - SciPy-bundle/2021.05-foss-2021a: + - SciPy-bundle-2021.05-foss-2021a: - issue: https://github.com/EESSI/software-layer/issues/318 - info: "2 failing tests (vs 30554 passed) in scipy test suite" - - SciPy-bundle/2021.10-foss-2021b: + - SciPy-bundle-2021.10-foss-2021b: - issue: https://github.com/EESSI/software-layer/issues/318 - - info: "20 failing tests (vs 14429 passed) in numpy test suite + 55 failing tests (vs 32438 passed) in scipy test suite" + - info: "20 ailing tests (vs 14429 passed) in numpy test suite + 55 failing tests (vs 32438 passed) in scipy test suite" From 8779e8b350bf2379a36b7671d150fce5f2f8a262 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Oct 2023 12:44:30 +0200 Subject: [PATCH 7/8] filter out YAML files that are used to keep track of known issues and missing installations --- EESSI-pilot-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index c6c51e7abc..9586abde1d 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -190,7 +190,7 @@ fi pr_diff=$(ls [0-9]*.diff | head -1) # use PR patch file to determine in which easystack files stuff was added -for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$'); do +for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$' | egrep -v 'known-issues|missing'); do echo -e "Processing easystack file ${easystack_file}...\n\n" From cd5cea918c26e67174f278df80a43ef9a2cff045 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Oct 2023 16:30:53 +0200 Subject: [PATCH 8/8] fix missing latter in info message in list of known issues --- eessi-2023.06-known-issues.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml index 846e862983..6cb464cd20 100644 --- a/eessi-2023.06-known-issues.yml +++ b/eessi-2023.06-known-issues.yml @@ -27,4 +27,4 @@ - info: "2 failing tests (vs 30554 passed) in scipy test suite" - SciPy-bundle-2021.10-foss-2021b: - issue: https://github.com/EESSI/software-layer/issues/318 - - info: "20 ailing tests (vs 14429 passed) in numpy test suite + 55 failing tests (vs 32438 passed) in scipy test suite" + - info: "20 failing tests (vs 14429 passed) in numpy test suite + 55 failing tests (vs 32438 passed) in scipy test suite"