From 7fc04d830d372abbebcf9ec3701e38d7b3fec4b8 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Sun, 11 Feb 2024 21:46:02 +0100 Subject: [PATCH 01/76] {2023.06}[foss/2022b] ImageMagick v7.1.0-53 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml index 9e92c79062..b8fddd02bb 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml @@ -1,3 +1,4 @@ easyconfigs: - SciPy-bundle-2023.02-gfbf-2022b.eb - GDAL-3.6.2-foss-2022b.eb + - ImageMagick-7.1.0-53-GCCcore-12.2.0.eb From 8491f9f090f5a55441904cd1d3b4c7ba5dacab4f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 15 Feb 2024 11:58:49 +0100 Subject: [PATCH 02/76] Always use LMOD_RC file, and make sure loading CUDA apps always works when building --- eessi_container.sh | 6 ++++++ init/eessi_environment_variables | 16 +++++++++------- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/eessi_container.sh b/eessi_container.sh index d6e9558202..143cbcc6c8 100755 --- a/eessi_container.sh +++ b/eessi_container.sh @@ -457,6 +457,12 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then mkdir -p ${EESSI_USR_LOCAL_CUDA} BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda" [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}" + if [[ "${NVIDIA_MODE}" == "install" ]] ; then + # We need to "trick" our LMOD_RC file to allow us to load CUDA modules even without a CUDA driver + # (this works because we build within a container and the LMOD_RC recognises that) + touch ${EESSI_TMPDIR}/libcuda.so + export SINGULARITY_CONTAINLIBS="${EESSI_TMPDIR}/libcuda.so" + fi fi fi diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index af5222e7b9..e042e8575a 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -50,6 +50,15 @@ if [ -d $EESSI_PREFIX ]; then show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory." export EESSI_SOFTWARE_PATH=$EESSI_PREFIX/software/$EESSI_OS_TYPE/$EESSI_SOFTWARE_SUBDIR + + # Configure our LMOD_RC file + export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua" + if [ -f $LMOD_RC ]; then + show_msg "Found Lmod configuration file at $LMOD_RC" + else + error "Lmod configuration file not found at $LMOD_RC" + fi + if [ ! -z $EESSI_BASIC_ENV ]; then show_msg "Only setting up basic environment, so we're done" elif [ -d $EESSI_SOFTWARE_PATH ]; then @@ -76,13 +85,6 @@ if [ -d $EESSI_PREFIX ]; then false fi - export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua" - if [ -f $LMOD_RC ]; then - show_msg "Found Lmod configuration file at $LMOD_RC" - else - error "Lmod configuration file not found at $LMOD_RC" - fi - else error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!" fi From f3f9721dac3f590768cb9dcb6fbcf26535f049d8 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 15:12:53 +0100 Subject: [PATCH 03/76] {2023.06}[foss/2023b] WSClean 3.4 + DP3 6.0 --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 4dd31dbd5d..fea9107dc0 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -8,3 +8,33 @@ easyconfigs: - matplotlib-3.8.2-gfbf-2023b.eb: options: from-pr: 19552 + - AOFlagger-3.4.0-foss-2023b.eb: + options: + from-pr: 19840 + # Exclude Lua from `filter-deps` as the compat layer version is too old for the software + filter-deps: + - Autoconf + - Automake + - Autotools + - binutils + - bzip2 + - DBus + - flex + - gettext + - gperf + - help2man + - intltool + - libreadline + - libtool + - ncurses + - M4 + - makeinfo + - util-linux + - XZ + - zlib + - DP3-6.0-foss-2023b.eb: + options: + from-pr: 19840 + - WSClean-3.4-foss-2023b.eb: + options: + from-pr: 19840 From f8cd2aa673187d6c1b346d53658932368118bd2a Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 15:41:51 +0100 Subject: [PATCH 04/76] Remove AOFlagger (Lua is no longer part of filter-deps) --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 24 ------------------- 1 file changed, 24 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index fea9107dc0..bf7e34932b 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -8,30 +8,6 @@ easyconfigs: - matplotlib-3.8.2-gfbf-2023b.eb: options: from-pr: 19552 - - AOFlagger-3.4.0-foss-2023b.eb: - options: - from-pr: 19840 - # Exclude Lua from `filter-deps` as the compat layer version is too old for the software - filter-deps: - - Autoconf - - Automake - - Autotools - - binutils - - bzip2 - - DBus - - flex - - gettext - - gperf - - help2man - - intltool - - libreadline - - libtool - - ncurses - - M4 - - makeinfo - - util-linux - - XZ - - zlib - DP3-6.0-foss-2023b.eb: options: from-pr: 19840 From eafbb6b757320ee003d678989c05bba6eb28ce2f Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 17:29:55 +0100 Subject: [PATCH 05/76] Include easyblocks from pr 3088 to fix Python path --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index bf7e34932b..e8496f371a 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -8,9 +8,27 @@ easyconfigs: - matplotlib-3.8.2-gfbf-2023b.eb: options: from-pr: 19552 + - AOFlagger-3.4.0-foss-2023b.eb: + options: + from:pr: 19840 + include-easyblocks-from-pr: 3088 + - casacore-3.5.0-foss-2023b.eb: + options: + from:pr: 19840 + include-easyblocks-from-pr: 3088 - DP3-6.0-foss-2023b.eb: options: from-pr: 19840 + include-easyblocks-from-pr: 3088 + - IDG-1.2.0-foss-2023b.eb: + options: + from-pr: 19840 + include-easyblocks-from-pr: 3088 + - EveryBeam-0.5.2-foss-2023b.eb: + options: + from-pr: 19840 + include-easyblocks-from-pr: 3088 - WSClean-3.4-foss-2023b.eb: options: from-pr: 19840 + include-easyblocks-from-pr: 3088 From df089de7c137ecb3232eca5f4266ca7d7cf577ed Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 17:42:44 +0100 Subject: [PATCH 06/76] Fix typo --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index e8496f371a..c874d7753f 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -10,11 +10,11 @@ easyconfigs: from-pr: 19552 - AOFlagger-3.4.0-foss-2023b.eb: options: - from:pr: 19840 + from-pr: 19840 include-easyblocks-from-pr: 3088 - casacore-3.5.0-foss-2023b.eb: options: - from:pr: 19840 + from-pr: 19840 include-easyblocks-from-pr: 3088 - DP3-6.0-foss-2023b.eb: options: From 2ec41e17b8e6701323e2a1a2070bc7b82c417980 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 21 Feb 2024 07:49:52 +0100 Subject: [PATCH 07/76] List dependencies first --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index c874d7753f..d89bf6b1b0 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -16,15 +16,15 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 - - DP3-6.0-foss-2023b.eb: + - IDG-1.2.e0-foss-2023b.eb: options: from-pr: 19840 include-easyblocks-from-pr: 3088 - - IDG-1.2.0-foss-2023b.eb: + - EveryBeam-0.5.2-foss-2023b.eb: options: from-pr: 19840 include-easyblocks-from-pr: 3088 - - EveryBeam-0.5.2-foss-2023b.eb: + - DP3-6.0-foss-2023b.eb: options: from-pr: 19840 include-easyblocks-from-pr: 3088 From d0ba0b724fb8ac8a4516d40731023e31fb190b02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 21 Feb 2024 09:42:52 +0100 Subject: [PATCH 08/76] fix typo in IDG version --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index d89bf6b1b0..33acff2e23 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -16,7 +16,7 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 - - IDG-1.2.e0-foss-2023b.eb: + - IDG-1.2.0-foss-2023b.eb: options: from-pr: 19840 include-easyblocks-from-pr: 3088 From 5d797a93f21bf7e898898af0e15bc063849c0bd8 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 21 Feb 2024 11:24:06 +0100 Subject: [PATCH 09/76] Include Armadillo-12.8.0-foss-2023b.eb --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 33acff2e23..7d5ce34a83 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -12,6 +12,10 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 + - Armadillo-12.8.0-foss-2023b.eb: + options: + from-pr: 19840 + include-easyblocks-from-pr: 3088 - casacore-3.5.0-foss-2023b.eb: options: from-pr: 19840 From a55826ddc0f4175e6fb94b7eb355a263d7a4b759 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 21 Feb 2024 11:24:41 +0100 Subject: [PATCH 10/76] Revert "Include Armadillo-12.8.0-foss-2023b.eb" This reverts commit b72730eecd5265829b58e8b09c7476d460bb011a. --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 7d5ce34a83..33acff2e23 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -12,10 +12,6 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 - - Armadillo-12.8.0-foss-2023b.eb: - options: - from-pr: 19840 - include-easyblocks-from-pr: 3088 - casacore-3.5.0-foss-2023b.eb: options: from-pr: 19840 From f63a4d83c0f307f7a7928f8deaab28f09f3ecf21 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 21 Feb 2024 11:24:06 +0100 Subject: [PATCH 11/76] Include Armadillo-12.8.0-foss-2023b.eb --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 33acff2e23..7d5ce34a83 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -12,6 +12,10 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 + - Armadillo-12.8.0-foss-2023b.eb: + options: + from-pr: 19840 + include-easyblocks-from-pr: 3088 - casacore-3.5.0-foss-2023b.eb: options: from-pr: 19840 From 7a0acebeb3826ba3bbb6172da344d906c60f2a1c Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 21 Feb 2024 15:35:54 +0100 Subject: [PATCH 12/76] Include arpack-ng-3.9.0-foss-2023b.eb --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 7d5ce34a83..07c2af56a7 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -12,6 +12,10 @@ easyconfigs: options: from-pr: 19840 include-easyblocks-from-pr: 3088 + - arpack-ng-3.9.0-foss-2023b.eb: + options: + from-pr: 19840 + include-easyblocks-from-pr: 3088 - Armadillo-12.8.0-foss-2023b.eb: options: from-pr: 19840 From 5c546ea8bff9692f4f6fbd68c0951bc29ff78f05 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 22 Feb 2024 18:05:46 +0100 Subject: [PATCH 13/76] Disable 'vectorize' toolchain option for casacore 3.5.0 on aarch64/neoverse_v1 with eb_hook --- eb_hooks.py | 29 ++++++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/eb_hooks.py b/eb_hooks.py index d29a837339..42f67278a8 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -21,7 +21,7 @@ CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1' -CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic' +CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic' EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs' @@ -159,6 +159,28 @@ def post_prepare_hook(self, *args, **kwargs): if self.name in POST_PREPARE_HOOKS: POST_PREPARE_HOOKS[self.name](self, *args, **kwargs) +def parse_hook_casacore_disable_vectorize(ec, eprefix): + """ + Disable 'vectorize' toolchain option for casacore 3.5.0 on aarch64/neoverse_v1 + Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023) gives an error when building for aarch64/neoverse_v1. + See also, https://github.com/EESSI/software-layer/pull/479 + """ + if ec.name == 'casacore': + tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version'] + if ( + LooseVersion(ec.version) == LooseVersion('3.5.0') and + tcname == 'foss' and tcversion == '2023b' + ): + if get_cpu_architecture() == CPU_TARGET_NEOVERSE_V1: + ec['toolchainopts']['vectorize'] = False + print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts']) + else: + print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name) + else: + print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain) + + else: + raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!") def parse_hook_cgal_toolchainopts_precise(ec, eprefix): """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER.""" @@ -327,7 +349,7 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs): if LooseVersion(self.version) <= LooseVersion('3.9.0'): self.cfg.update('preconfigopts', "sed -i 's/%s/%s/g' arch/configure_new.defaults && " % (pattern, repl)) print_msg("Using custom preconfigopts for %s: %s", self.name, self.cfg['preconfigopts']) - + if LooseVersion('4.0.0') <= LooseVersion(self.version) <= LooseVersion('4.2.1'): self.cfg.update('preconfigopts', "sed -i 's/%s/%s/g' arch/configure.defaults && " % (pattern, repl)) print_msg("Using custom preconfigopts for %s: %s", self.name, self.cfg['preconfigopts']) @@ -414,7 +436,7 @@ def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs): """ 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" + self.cfg['testopts'] = "|| echo ignoring failing tests" def pre_test_hook_increase_max_failed_tests_arm_PyTorch(self, *args, **kwargs): """ @@ -579,6 +601,7 @@ def inject_gpu_property(ec): PARSE_HOOKS = { + 'casacore': parse_hook_casacore_disable_vectorize, 'CGAL': parse_hook_cgal_toolchainopts_precise, 'fontconfig': parse_hook_fontconfig_add_fonts, 'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors, From 5b822a3e2292e80077956b0a3f7c9e453a1d25cd Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 22 Feb 2024 18:09:02 +0100 Subject: [PATCH 14/76] Remove empty line --- eb_hooks.py | 1 - 1 file changed, 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 42f67278a8..2cc9f63ad4 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -178,7 +178,6 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name) else: print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain) - else: raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!") From 889243779f41ee43c68079c2bd98133857d75e98 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 22 Feb 2024 18:11:03 +0100 Subject: [PATCH 15/76] Cleanup code --- eb_hooks.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 2cc9f63ad4..448d6fe62c 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -159,10 +159,11 @@ def post_prepare_hook(self, *args, **kwargs): if self.name in POST_PREPARE_HOOKS: POST_PREPARE_HOOKS[self.name](self, *args, **kwargs) + def parse_hook_casacore_disable_vectorize(ec, eprefix): """ Disable 'vectorize' toolchain option for casacore 3.5.0 on aarch64/neoverse_v1 - Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023) gives an error when building for aarch64/neoverse_v1. + Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023b) gives an error when building for aarch64/neoverse_v1. See also, https://github.com/EESSI/software-layer/pull/479 """ if ec.name == 'casacore': @@ -181,6 +182,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): else: raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!") + def parse_hook_cgal_toolchainopts_precise(ec, eprefix): """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER.""" if ec.name == 'CGAL': From 4e5f2db05384b43af4ebbe4bca3b787660b21875 Mon Sep 17 00:00:00 2001 From: t1mk1k <96469032+t1mk1k@users.noreply.github.com> Date: Fri, 23 Feb 2024 15:26:14 +0100 Subject: [PATCH 16/76] Retrieve cpu_target from EESSI env vars MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- eb_hooks.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 448d6fe62c..747ca5f601 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -172,7 +172,8 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): LooseVersion(ec.version) == LooseVersion('3.5.0') and tcname == 'foss' and tcversion == '2023b' ): - if get_cpu_architecture() == CPU_TARGET_NEOVERSE_V1: + cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') + if cpu_target == CPU_TARGET_NEOVERSE_V1: ec['toolchainopts']['vectorize'] = False print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts']) else: From 354407375cc65087c5850f162077b7fa22f785f2 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 23 Feb 2024 15:30:27 +0100 Subject: [PATCH 17/76] Specify print message for skipping non-neoverse_v1 --- eb_hooks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eb_hooks.py b/eb_hooks.py index 747ca5f601..15813ec354 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -177,7 +177,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): ec['toolchainopts']['vectorize'] = False print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts']) else: - print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name) + print_msg("Not changing option vectorize for %s on non-neoverse_v1", ec.name) else: print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain) else: From 0aea4b44691d237d9359e0a35991b3874b2a092b Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 26 Feb 2024 19:33:34 +0100 Subject: [PATCH 18/76] Create toolchainopts dict if it does not exist --- eb_hooks.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index 15813ec354..d93ee37067 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -174,6 +174,8 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): ): cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') if cpu_target == CPU_TARGET_NEOVERSE_V1: + if not hasattr(ec, 'toolchainopts'): + ec['toolchainopts'] = {} ec['toolchainopts']['vectorize'] = False print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts']) else: From 07296d3589587cf1090e574513185ad6e50b3d69 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 27 Feb 2024 11:17:33 +0100 Subject: [PATCH 19/76] Enable lax vector conversion for DP3 --- eb_hooks.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index d93ee37067..1478f1a508 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -186,6 +186,32 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!") +def parse_hook_dp3_enable_relaxed_vector_conversions(ec, eprefix): + """ + Enable lax vector conversion for DP3 on aarch64/neoverse_v1 + Compiling DP3 6.0 with GCC 13.2.0 (foss-2023b) gives a conversion error when building for aarch64/neoverse_v1. + See also, https://github.com/EESSI/software-layer/pull/479 + """ + if ec.name == 'DP3': + tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version'] + if ( + LooseVersion(ec.version) == LooseVersion('6.0') and + tcname == 'foss' and tcversion == '2023b' + ): + cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') + if cpu_target == CPU_TARGET_NEOVERSE_V1: + if not hasattr(ec, 'configopts'): + ec['configopts'] = "" + ec['configopts'] += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -flax-vector-conversions" ' + print_msg("Changed configopts for %s: %s", ec.name, ec['configopts']) + else: + print_msg("Not changing configopts for %s on non-neoverse_v1", ec.name) + else: + print_msg("Not changing configopts for %s %s %s", ec.name, ec.version, ec.toolchain) + else: + raise EasyBuildError("DP3-specific hook triggered for non-DP3 easyconfig?!") + + def parse_hook_cgal_toolchainopts_precise(ec, eprefix): """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER.""" if ec.name == 'CGAL': @@ -607,6 +633,7 @@ def inject_gpu_property(ec): PARSE_HOOKS = { 'casacore': parse_hook_casacore_disable_vectorize, 'CGAL': parse_hook_cgal_toolchainopts_precise, + 'DP3': parse_hook_dp3_enable_relaxed_vector_conversions, 'fontconfig': parse_hook_fontconfig_add_fonts, 'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors, 'pybind11': parse_hook_pybind11_replace_catch2, From 793e9f8ec925aa09b020f72d4acffa1ce0b400eb Mon Sep 17 00:00:00 2001 From: Richard Top Date: Wed, 28 Feb 2024 13:20:54 +0000 Subject: [PATCH 20/76] {2023.06}[foss/2023a] dask v2023.9.2 --- .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + eb_hooks.py | 14 +++++++++++++- 2 files changed, 14 insertions(+), 1 deletion(-) 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..d444b1f8ae 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 + - dask-2023.9.2-foss-2023a.eb diff --git a/eb_hooks.py b/eb_hooks.py index d29a837339..4ed72a12ac 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -204,6 +204,18 @@ def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix): raise EasyBuildError("OpenBLAS-specific hook triggered for non-OpenBLAS easyconfig?!") +def parse_hook_Pillow_SIMD_harcoded_paths(ec, eprefix): + # patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template + # (which will be empty if EasyBuild is not configured to use an alternate sysroot); + # see also https://gitlab.com/eessi/support/-/issues/9 + if ec.name == 'Pillow-SIMD': + ec.update('preinstallopts', """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """) + ec.update('preinstallopts', """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """) + print_msg("Using custom configure options for %s: %s", ec.name, ec['preinstallopts']) + else: + raise EasyBuildError("Pillow-SIMD-specific hook triggered for non-Pillow-SIMD easyconfig?!") + + def parse_hook_pybind11_replace_catch2(ec, eprefix): """ Replace Catch2 build dependency in pybind11 easyconfigs with one that doesn't use system toolchain. @@ -237,7 +249,6 @@ def parse_hook_qt5_check_qtwebengine_disable(ec, eprefix): def parse_hook_ucx_eprefix(ec, eprefix): - """Make UCX aware of compatibility layer via additional configuration options.""" if ec.name == 'UCX': ec.update('configopts', '--with-sysroot=%s' % eprefix) ec.update('configopts', '--with-rdmacm=%s' % os.path.join(eprefix, 'usr')) @@ -582,6 +593,7 @@ def inject_gpu_property(ec): 'CGAL': parse_hook_cgal_toolchainopts_precise, 'fontconfig': parse_hook_fontconfig_add_fonts, 'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors, + 'Pillow-SIMD' : parse_hook_Pillow_SIMD_harcoded_paths, 'pybind11': parse_hook_pybind11_replace_catch2, 'Qt5': parse_hook_qt5_check_qtwebengine_disable, 'UCX': parse_hook_ucx_eprefix, From 68a766fe8637c7c90b7c667aa0f738b8807f115f Mon Sep 17 00:00:00 2001 From: Richard Top Date: Wed, 28 Feb 2024 13:27:38 +0000 Subject: [PATCH 21/76] fixed info --- eb_hooks.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/eb_hooks.py b/eb_hooks.py index 4ed72a12ac..d30700267b 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -205,6 +205,7 @@ def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix): def parse_hook_Pillow_SIMD_harcoded_paths(ec, eprefix): + """Make Pillow-SIMD aware of sysroot.""" # patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template # (which will be empty if EasyBuild is not configured to use an alternate sysroot); # see also https://gitlab.com/eessi/support/-/issues/9 @@ -249,6 +250,7 @@ def parse_hook_qt5_check_qtwebengine_disable(ec, eprefix): def parse_hook_ucx_eprefix(ec, eprefix): + """Make UCX aware of compatibility layer via additional configuration options.""" if ec.name == 'UCX': ec.update('configopts', '--with-sysroot=%s' % eprefix) ec.update('configopts', '--with-rdmacm=%s' % os.path.join(eprefix, 'usr')) From 3cdf80390fa3150bcde82427537776c22bf7bb25 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Wed, 28 Feb 2024 17:33:43 +0000 Subject: [PATCH 22/76] removed the hook and added --from-pr --- .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 5 ++++- eb_hooks.py | 14 -------------- 2 files changed, 4 insertions(+), 15 deletions(-) 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 d444b1f8ae..983d59cc04 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 @@ -29,4 +29,7 @@ easyconfigs: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19554 options: from-pr: 19554 - - dask-2023.9.2-foss-2023a.eb + - dask-2023.9.2-foss-2023a.eb: + options: + from-pr: 19996 + diff --git a/eb_hooks.py b/eb_hooks.py index d30700267b..d29a837339 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -204,19 +204,6 @@ def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix): raise EasyBuildError("OpenBLAS-specific hook triggered for non-OpenBLAS easyconfig?!") -def parse_hook_Pillow_SIMD_harcoded_paths(ec, eprefix): - """Make Pillow-SIMD aware of sysroot.""" - # patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template - # (which will be empty if EasyBuild is not configured to use an alternate sysroot); - # see also https://gitlab.com/eessi/support/-/issues/9 - if ec.name == 'Pillow-SIMD': - ec.update('preinstallopts', """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """) - ec.update('preinstallopts', """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """) - print_msg("Using custom configure options for %s: %s", ec.name, ec['preinstallopts']) - else: - raise EasyBuildError("Pillow-SIMD-specific hook triggered for non-Pillow-SIMD easyconfig?!") - - def parse_hook_pybind11_replace_catch2(ec, eprefix): """ Replace Catch2 build dependency in pybind11 easyconfigs with one that doesn't use system toolchain. @@ -595,7 +582,6 @@ def inject_gpu_property(ec): 'CGAL': parse_hook_cgal_toolchainopts_precise, 'fontconfig': parse_hook_fontconfig_add_fonts, 'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors, - 'Pillow-SIMD' : parse_hook_Pillow_SIMD_harcoded_paths, 'pybind11': parse_hook_pybind11_replace_catch2, 'Qt5': parse_hook_qt5_check_qtwebengine_disable, 'UCX': parse_hook_ucx_eprefix, From 117081843c09ae69e9b25eb18ecc54f6736cc16f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 29 Feb 2024 10:01:17 +0100 Subject: [PATCH 23/76] Temporary fix for CI by pinning archspec version --- .github/workflows/tests.yml | 2 +- .github/workflows/tests_init.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 8e74a4e844..faa7eb82ff 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -22,7 +22,7 @@ jobs: - name: install Python packages run: | - pip install archspec + pip install archspec==0.2.2 - name: test eessi_software_subdir.py script run: | diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml index 38ccbbad31..053acb9730 100644 --- a/.github/workflows/tests_init.yml +++ b/.github/workflows/tests_init.yml @@ -22,7 +22,7 @@ jobs: - name: install Python packages run: | - pip install archspec pytest + pip install archspec==0.2.2 pytest - name: unit tests for eessi_software_subdir_for_host.py script run: From cf7705643865f85b0e73f5185952a400f41c95f6 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Thu, 29 Feb 2024 13:39:14 +0100 Subject: [PATCH 24/76] remove-blanks --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 - 1 file changed, 1 deletion(-) 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 983d59cc04..7d9c331fcf 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 @@ -32,4 +32,3 @@ easyconfigs: - dask-2023.9.2-foss-2023a.eb: options: from-pr: 19996 - From 887e102631ef5fbfadffef744c7724e28a01217f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 29 Feb 2024 13:50:41 +0100 Subject: [PATCH 25/76] Update easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 7d9c331fcf..d187d8e92c 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 @@ -29,6 +29,7 @@ easyconfigs: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19554 options: from-pr: 19554 - - dask-2023.9.2-foss-2023a.eb: + - Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb: options: from-pr: 19996 + - dask-2023.9.2-foss-2023a.eb From 938e52e66b529458fad9984f79bce156dc43d023 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 29 Feb 2024 14:16:17 +0100 Subject: [PATCH 26/76] Update easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + 1 file changed, 1 insertion(+) 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 d187d8e92c..0a0a625c35 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 @@ -31,5 +31,6 @@ easyconfigs: from-pr: 19554 - Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb: options: + # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19996 from-pr: 19996 - dask-2023.9.2-foss-2023a.eb From 301ab593867335700b576cc9949fe58c408325e7 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 29 Feb 2024 18:12:22 +0100 Subject: [PATCH 27/76] Make check_missing_installations.sh check against develop branch of EasyBuild --- check_missing_installations.sh | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 5ea7c5a4f5..8845adb161 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -18,6 +18,13 @@ easystack=$1 LOCAL_TMPDIR=$(mktemp -d) +# Clone the develop branch of EasyBuild and use that to search for easyconfigs +git clone -b develop https://github.com/easybuilders/easybuild-easyconfigs.git $LOCAL_TMPDIR/easyconfigs +EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs + +# All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr +grep -v from-pr ${easystack} > ${LOCAL_TMPDIR}/${easystack} + source $TOPDIR/scripts/utils.sh source $TOPDIR/configure_easybuild @@ -27,7 +34,7 @@ ${EB:-eb} --show-config echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..." eb_missing_out=$LOCAL_TMPDIR/eb_missing.out -${EB:-eb} --easystack ${easystack} --missing 2>&1 | tee ${eb_missing_out} +${EB:-eb} --easystack ${LOCAL_TMPDIR}/${easystack} --missing 2>&1 | tee ${eb_missing_out} exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." From 93d1d7df3c0659e9886bac3cd0d4c994e7a82d09 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 29 Feb 2024 18:19:46 +0100 Subject: [PATCH 28/76] Use filename rather than full path --- check_missing_installations.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 8845adb161..6c38e8e37f 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -23,7 +23,8 @@ git clone -b develop https://github.com/easybuilders/easybuild-easyconfigs.git $ EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr -grep -v from-pr ${easystack} > ${LOCAL_TMPDIR}/${easystack} +tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack}) +grep -v from-pr ${easystack} > ${tmp_easystack} source $TOPDIR/scripts/utils.sh @@ -34,7 +35,7 @@ ${EB:-eb} --show-config echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..." eb_missing_out=$LOCAL_TMPDIR/eb_missing.out -${EB:-eb} --easystack ${LOCAL_TMPDIR}/${easystack} --missing 2>&1 | tee ${eb_missing_out} +${EB:-eb} --easystack ${tmp_easystack} --missing 2>&1 | tee ${eb_missing_out} exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." From f6259dc563bcb1cad3ee962f56501872e53c0cba Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 29 Feb 2024 18:26:16 +0100 Subject: [PATCH 29/76] export envvar --- check_missing_installations.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 6c38e8e37f..c902fa8184 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -20,7 +20,7 @@ LOCAL_TMPDIR=$(mktemp -d) # Clone the develop branch of EasyBuild and use that to search for easyconfigs git clone -b develop https://github.com/easybuilders/easybuild-easyconfigs.git $LOCAL_TMPDIR/easyconfigs -EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs +export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack}) From 78ba8d8e304ec0ae4c82721e3e5fae7e25402f91 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 1 Mar 2024 12:53:07 +0100 Subject: [PATCH 30/76] Adding OSU microbenchmarks with GPU support for 2023a, and one without GPU support for 2023b --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 2 ++ 1 file changed, 2 insertions(+) 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 0a0a625c35..0d8e71e86c 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 @@ -34,3 +34,5 @@ easyconfigs: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19996 from-pr: 19996 - dask-2023.9.2-foss-2023a.eb + - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb + - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb From efbeb561740f8ef5c066e1b064c16f45087c668f Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 4 Mar 2024 16:59:00 +0100 Subject: [PATCH 31/76] Use LMOD_CONFIG_DIR instead of LMOD_RC to allow user overrides of what we specify in our RC file, see search order on https://lmod.readthedocs.io/en/latest/145_properties.html?highlight=lmod_rc#the-properties-file-lmodrc-lua . Also, prefix our hooks with eessi_ to avoid unintentional clashes in namespace between site lmod configuration and eessi lmod configuration --- create_lmodrc.py | 8 ++++---- init/eessi_environment_variables | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/create_lmodrc.py b/create_lmodrc.py index bc69dd4396..ff34906c0b 100755 --- a/create_lmodrc.py +++ b/create_lmodrc.py @@ -29,7 +29,7 @@ return content end -local function cuda_enabled_load_hook(t) +local function eessi_cuda_enabled_load_hook(t) local frameStk = require("FrameStk"):singleton() local mt = frameStk:mt() local simpleName = string.match(t.modFullName, "(.-)/") @@ -94,7 +94,7 @@ end end -local function openmpi_load_hook(t) +local function eessi_openmpi_load_hook(t) -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1, -- to work around hang/crash due to bug in OpenMPI; -- see https://gitlab.com/eessi/support/-/issues/41 @@ -114,8 +114,8 @@ end end -hook.register("load", cuda_enabled_load_hook) -hook.register("load", openmpi_load_hook) +hook.register("load", eessi_cuda_enabled_load_hook) +hook.register("load", eessi_openmpi_load_hook) """ def error(msg): diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index af5222e7b9..d3a209630e 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -76,8 +76,8 @@ if [ -d $EESSI_PREFIX ]; then false fi - export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua" - if [ -f $LMOD_RC ]; then + export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod" + if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then show_msg "Found Lmod configuration file at $LMOD_RC" else error "Lmod configuration file not found at $LMOD_RC" From 590cabd7c068a9986f0eba33792005a7b9ce883a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 5 Mar 2024 10:42:27 +0100 Subject: [PATCH 32/76] Combine functions into a single function, before registering this as a hook. Lmod only permits the registration of a single function, trying to register a second function will just overwrite the first, as can be seen from https://github.com/TACC/Lmod/blob/a97d68193a6f32ebca4b4bd70dac0f6ac8fddefe/src/Hook.lua#L87 --- create_lmodrc.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/create_lmodrc.py b/create_lmodrc.py index ff34906c0b..621c8e271a 100755 --- a/create_lmodrc.py +++ b/create_lmodrc.py @@ -114,8 +114,15 @@ end end -hook.register("load", eessi_cuda_enabled_load_hook) -hook.register("load", eessi_openmpi_load_hook) +-- Combine both functions into a single one, as we can only register one function as load hook in lmod +-- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed +function eessi_load_hook(t) + eessi_cuda_enabled_load_hook(t) + eessi_openmpi_load_hook(t) +end + + +hook.register("load", eessi_load_hook) """ def error(msg): From 0de249e32f6cb2cd1cbb694cbddf37fb93987561 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 5 Mar 2024 18:15:10 +0100 Subject: [PATCH 33/76] Look for site-specific lmodrc file in host_injections. If present, set LMOD_RC --- init/eessi_environment_variables | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index d3a209630e..1c8a68b1d5 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -82,6 +82,11 @@ if [ -d $EESSI_PREFIX ]; then else error "Lmod configuration file not found at $LMOD_RC" fi + # Allow for site-specific lmod configuration + host_lmod_rc="$EESSI_CVMFS_REPO"/host_injections/.lmod/lmodrc.lua + if [ -f $host_lmod_rc ]; then + export LMOD_RC="$host_lmod_rc" + fi else error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!" From c1840dd55f306b20e6d26201990313ad4dc18a3a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 6 Mar 2024 15:05:07 +0100 Subject: [PATCH 34/76] Next the local lmodrc within the versioned directory, e.g. /cvmfs/software.eessi.io/host_injections/2023.06/.lmod/lmodrc.lua --- init/eessi_environment_variables | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index 1c8a68b1d5..5407034191 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -83,7 +83,7 @@ if [ -d $EESSI_PREFIX ]; then error "Lmod configuration file not found at $LMOD_RC" fi # Allow for site-specific lmod configuration - host_lmod_rc="$EESSI_CVMFS_REPO"/host_injections/.lmod/lmodrc.lua + host_lmod_rc="${EESSI_PREFIX/versions/host_injections}/.lmod/lmodrc.lua if [ -f $host_lmod_rc ]; then export LMOD_RC="$host_lmod_rc" fi From df4140a74bad2f0af022c10a2d8ada12fa1627df Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 6 Mar 2024 15:54:28 +0100 Subject: [PATCH 35/76] Update init/eessi_environment_variables --- init/eessi_environment_variables | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index 5407034191..f9ca6de408 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -83,7 +83,7 @@ if [ -d $EESSI_PREFIX ]; then error "Lmod configuration file not found at $LMOD_RC" fi # Allow for site-specific lmod configuration - host_lmod_rc="${EESSI_PREFIX/versions/host_injections}/.lmod/lmodrc.lua + host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua if [ -f $host_lmod_rc ]; then export LMOD_RC="$host_lmod_rc" fi From 78e582ba2c5fd5de813836151a3d256fc6ba5c94 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 6 Mar 2024 15:59:31 +0100 Subject: [PATCH 36/76] Update init/eessi_environment_variables --- init/eessi_environment_variables | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index f9ca6de408..b41dd60924 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -78,9 +78,9 @@ if [ -d $EESSI_PREFIX ]; then export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod" if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then - show_msg "Found Lmod configuration file at $LMOD_RC" + show_msg "Found Lmod configuration file at $LMOD_CONFIG_DIR/lmodrc.lua" else - error "Lmod configuration file not found at $LMOD_RC" + error "Lmod configuration file not found at $LMOD_CONFIG_DIR/lmodrc.lua" fi # Allow for site-specific lmod configuration host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua From 77c97235f0291dff7b98f2f1958e345a7afb48ee Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 6 Mar 2024 16:00:42 +0100 Subject: [PATCH 37/76] Update init/eessi_environment_variables --- init/eessi_environment_variables | 1 + 1 file changed, 1 insertion(+) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index b41dd60924..d4c113c67a 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -85,6 +85,7 @@ if [ -d $EESSI_PREFIX ]; then # Allow for site-specific lmod configuration host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua if [ -f $host_lmod_rc ]; then + show_msg "Found site Lmod configuration file at $LMOD_RC" export LMOD_RC="$host_lmod_rc" fi From 276a64c66347e24b94ace71914547cc0abd75381 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Thu, 7 Mar 2024 07:54:23 +0000 Subject: [PATCH 38/76] {2023.06}[gompi/2023b] CDO v2.2.2 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 4dd31dbd5d..2664d8f417 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -8,3 +8,6 @@ easyconfigs: - matplotlib-3.8.2-gfbf-2023b.eb: options: from-pr: 19552 + - CDO-2.2.2-gompi-2023b.eb: + options: + from-pr: 19792 From e33938f1a8424d28966827c4a8942f82b8043bed Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 7 Mar 2024 14:52:25 +0100 Subject: [PATCH 39/76] Revert changes in eessi_environment_variables. Limit this PR to the bug fix only. We can follow up properly using SitePackage.lua instead --- init/eessi_environment_variables | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index d4c113c67a..af5222e7b9 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -76,17 +76,11 @@ if [ -d $EESSI_PREFIX ]; then false fi - export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod" - if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then - show_msg "Found Lmod configuration file at $LMOD_CONFIG_DIR/lmodrc.lua" + export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua" + if [ -f $LMOD_RC ]; then + show_msg "Found Lmod configuration file at $LMOD_RC" else - error "Lmod configuration file not found at $LMOD_CONFIG_DIR/lmodrc.lua" - fi - # Allow for site-specific lmod configuration - host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua - if [ -f $host_lmod_rc ]; then - show_msg "Found site Lmod configuration file at $LMOD_RC" - export LMOD_RC="$host_lmod_rc" + error "Lmod configuration file not found at $LMOD_RC" fi else From 45022b6b47c3046ea3e2d4033197fdd80dc63850 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 8 Mar 2024 17:30:55 +0100 Subject: [PATCH 40/76] Allow for open PRs when checking missing installations in build script --- EESSI-install-software.sh | 2 +- check_missing_installations.sh | 20 +++++++++++++++++--- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 69de9d1997..75b4f71178 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -237,7 +237,7 @@ else copy_build_log "${eb_last_log}" "${build_logs_dir}" fi - $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file} + $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file} ${TOPDIR}/${pr_diff} else fatal_error "Easystack file ${easystack_file} not found!" fi diff --git a/check_missing_installations.sh b/check_missing_installations.sh index c902fa8184..623c46c74f 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -10,8 +10,15 @@ TOPDIR=$(dirname $(realpath $0)) -if [ $# -ne 1 ]; then - echo "ERROR: Usage: $0 " >&2 +if [ "$#" -eq 1 ]; then + true +elif [ "$#" -eq 2 ]; then + echo "Using $2 to give create exceptions for PR filtering of easystack" + # Find lines that are added and use from-pr, make them unique, grab the + # PR numbers and use them to construct something we can use within awk + pr_exceptions=$(grep ^+ $2 | grep from-pr | uniq | awk '{print $3}' | xargs -i echo " || /'{}'/") +else + echo "ERROR: Usage: $0 ()" >&2 exit 1 fi easystack=$1 @@ -24,7 +31,10 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack}) -grep -v from-pr ${easystack} > ${tmp_easystack} +# Let's use awk so we can allow for exceptions if we are given a PR diff file +awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack" +awk_command=${awk_command/\\/} # Strip out the backslash we needed for ! +eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack} source $TOPDIR/scripts/utils.sh @@ -40,6 +50,10 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" +if [ "$#" -eq 1 ]; then + fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)" +fi + check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}" # the above assesses the installed software for each easyconfig provided in From 723fce82b272cccd75a1d1841ef301be419461e6 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 11:39:33 +0100 Subject: [PATCH 41/76] Check for unmerged EasyConfig output pattern --- bot/check-build.sh | 143 ++++++++++++++++++++++++++++----------------- 1 file changed, 90 insertions(+), 53 deletions(-) diff --git a/bot/check-build.sh b/bot/check-build.sh index ec1ca56bba..e737363f35 100755 --- a/bot/check-build.sh +++ b/bot/check-build.sh @@ -98,15 +98,15 @@ job_dir=${PWD} job_out="slurm-${SLURM_JOB_ID}.out" [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'" if [[ -f ${job_out} ]]; then - SLURM=1 + SLURM_OUTPUT_FOUND=1 [[ ${VERBOSE} -ne 0 ]] && echo " found slurm output file '"${job_out}"'" else - SLURM=0 + SLURM_OUTPUT_FOUND=0 [[ ${VERBOSE} -ne 0 ]] && echo " Slurm output file '"${job_out}"' NOT found" fi ERROR=-1 -if [[ ${SLURM} -eq 1 ]]; then +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then GP_error='ERROR: ' grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_error}") [[ $? -eq 0 ]] && ERROR=1 || ERROR=0 @@ -116,7 +116,7 @@ if [[ ${SLURM} -eq 1 ]]; then fi FAILED=-1 -if [[ ${SLURM} -eq 1 ]]; then +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then GP_failed='FAILED: ' grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}") [[ $? -eq 0 ]] && FAILED=1 || FAILED=0 @@ -126,7 +126,7 @@ if [[ ${SLURM} -eq 1 ]]; then fi MISSING=-1 -if [[ ${SLURM} -eq 1 ]]; then +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then GP_req_missing=' required modules missing:' grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_req_missing}") [[ $? -eq 0 ]] && MISSING=1 || MISSING=0 @@ -136,7 +136,7 @@ if [[ ${SLURM} -eq 1 ]]; then fi NO_MISSING=-1 -if [[ ${SLURM} -eq 1 ]]; then +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then GP_no_missing='No missing installations' grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_no_missing}") [[ $? -eq 0 ]] && NO_MISSING=1 || NO_MISSING=0 @@ -147,7 +147,7 @@ fi TGZ=-1 TARBALL= -if [[ ${SLURM} -eq 1 ]]; then +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then GP_tgz_created="\.tar\.gz created!" grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_tgz_created}" | sort -u) if [[ $? -eq 0 ]]; then @@ -169,9 +169,27 @@ fi [[ ${VERBOSE} -ne 0 ]] && echo " NO_MISSING.: $([[ $NO_MISSING -eq 1 ]] && echo 'yes' || echo 'no') (yes)" [[ ${VERBOSE} -ne 0 ]] && echo " TGZ_CREATED: $([[ $TGZ -eq 1 ]] && echo 'yes' || echo 'no') (yes)" +# Here, we try to do some additional analysis on the output file +# to see if we can print a more clear 'reason' for the failure +# For now, we only analyse unmerged EasyConfigs as potential cause, but we can easily add checks for other +# specific scenarios below + +# Check for the pattern being added here https://github.com/EESSI/software-layer/pull/493 to the output to +# see if EasyConfigs might have been unmerged, and that's causing a failure +UNMERGED_EASYCONFIG=-1 +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then + gp_unmerged="are you sure all PRs referenced have been merged in EasyBuild" + grep_unmerged=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${gp_unmerged}") + [[ $? -eq 0 ]] && UNMERGED_EASYCONFIG=1 || UNMERGED_EASYCONFIG=0 + # have to be careful to not add searched for pattern into slurm out file + [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${gp_unmerged}"'" + [[ ${VERBOSE} -ne 0 ]] && echo "${grep_unmerged}" +fi + job_result_file=_bot_job${SLURM_JOB_ID}.result -if [[ ${SLURM} -eq 1 ]] && \ +# Default reason: +if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]] && \ [[ ${ERROR} -eq 0 ]] && \ [[ ${FAILED} -eq 0 ]] && \ [[ ${MISSING} -eq 0 ]] && \ @@ -180,7 +198,12 @@ if [[ ${SLURM} -eq 1 ]] && \ [[ ! -z ${TARBALL} ]]; then # SUCCESS status="SUCCESS" + reason="" summary=":grin: SUCCESS" +elif [[ ${UNMERGED_EASYCONFIG} -eq 1 ]]; then + status="FAILURE" + reason="EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild?" + summary=":cry: FAILURE" else # FAILURE status="FAILURE" @@ -253,14 +276,6 @@ fi # ### -# construct and write complete PR comment details: implements third alternative -comment_template="
__SUMMARY_FMT__
__DETAILS_FMT____ARTEFACTS_FMT__
" -comment_summary_fmt="__SUMMARY__ _(click triangle for details)_" -comment_details_fmt="
_Details_
__DETAILS_LIST__
" -comment_success_item_fmt=":white_check_mark: __ITEM__" -comment_failure_item_fmt=":x: __ITEM__" -comment_artefacts_fmt="
_Artefacts_
__ARTEFACTS_LIST__
" -comment_artefact_details_fmt="
__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__
" function print_br_item() { format="${1}" @@ -332,42 +347,65 @@ echo -n "comment_description = " >> ${job_result_file} # - __DETAILS_FMT__ -> variable $comment_details # - __ARTEFACTS_FMT__ -> variable $comment_artefacts +# construct and write complete PR comment details: implements third alternative +comment_template="
__SUMMARY_FMT__
__REASON_FMT____DETAILS_FMT____ARTEFACTS_FMT__
" +comment_success_item_fmt=":white_check_mark: __ITEM__" +comment_failure_item_fmt=":x: __ITEM__" + +# Initialize comment_description +comment_description=${comment_template} + +# Now, start replacing template items one by one +# Replace the summary template (__SUMMARY_FMT__) +comment_summary_fmt="__SUMMARY__ _(click triangle for details)_" comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}" +comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}} + +# Only add if there is a reason (e.g. no reason for successful runs) +if [[ ! -z ${reason} ]]; then + comment_reason_fmt="
_Reason_
__REASONS__
" + reason_details="${comment_reason_fmt/__REASONS__/${reason}}" + comment_description=${comment_description/__REASON_FMT__/${reason_details}} +else + comment_description=${comment_description/__REASON_FMT__/""} +fi -# first construct comment_details_list, abbreviated CoDeList +# Replace the details template (__DETAILS_FMT__) +# first construct comment_details_list, abbreviated comment_details_list # then use it to set comment_details -CoDeList="" +comment_details_list="" success_msg="job output file ${job_out}" failure_msg="no job output file ${job_out}" -CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}") +comment_details_list=${comment_details_list}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}") success_msg="no message matching ${GP_error}" failure_msg="found message matching ${GP_error}" -CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}") +comment_details_list=${comment_details_list}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}") success_msg="no message matching ${GP_failed}" failure_msg="found message matching ${GP_failed}" -CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}") +comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}") success_msg="no message matching ${GP_req_missing}" failure_msg="found message matching ${GP_req_missing}" -CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}") +comment_details_list=${comment_details_list}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}") success_msg="found message(s) matching ${GP_no_missing}" failure_msg="no message matching ${GP_no_missing}" -CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}") +comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}") success_msg="found message matching ${GP_tgz_created}" failure_msg="no message matching ${GP_tgz_created}" -CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}") - -comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}" - +comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}") +# Now, do the actual repalcement of __DETAILS_FMT__ +comment_details_fmt="
_Details_
__DETAILS_LIST__
" +comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}" +comment_description=${comment_description/__DETAILS_FMT__/${comment_details}} -# first construct comment_artefacts_list, abbreviated CoArList +# first construct comment_artefacts_list # then use it to set comment_artefacts -CoArList="" +comment_artifacts_list="" # TARBALL should only contain a single tarball if [[ ! -z ${TARBALL} ]]; then @@ -427,50 +465,49 @@ if [[ ! -z ${TARBALL} ]]; then software_pkgs=$(echo "${software_entries}" | sed -e "s@${prefix}/software/@@" | awk -F/ '{if (NR >= 2) {print $1 "/" $2}}' | sort -u) artefact_summary="$(print_code_item '__ITEM__' ${TARBALL})" - CoArList="" - CoArList="${CoArList}$(print_br_item2 'size: __ITEM__ MiB (__ITEM2__ bytes)' ${size_mib} ${size})" - CoArList="${CoArList}$(print_br_item 'entries: __ITEM__' ${entries})" - CoArList="${CoArList}$(print_br_item 'modules under ___ITEM___' ${prefix}/modules/all)" - CoArList="${CoArList}
"
+    comment_artifacts_list=""
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item2 'size: __ITEM__ MiB (__ITEM2__ bytes)' ${size_mib} ${size})"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'entries: __ITEM__' ${entries})"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'modules under ___ITEM___' ${prefix}/modules/all)"
+    comment_artifacts_list="${comment_artifacts_list}
"
     if [[ ! -z ${modules} ]]; then
         while IFS= read -r mod ; do
-            CoArList="${CoArList}$(print_br_item '__ITEM__' ${mod})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' ${mod})"
         done <<< "${modules}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no module files in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no module files in tarball')"
     fi
-    CoArList="${CoArList}
"
-    CoArList="${CoArList}$(print_br_item 'software under ___ITEM___' ${prefix}/software)"
-    CoArList="${CoArList}
"
+    comment_artifacts_list="${comment_artifacts_list}
"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'software under ___ITEM___' ${prefix}/software)"
+    comment_artifacts_list="${comment_artifacts_list}
"
     if [[ ! -z ${software_pkgs} ]]; then
         while IFS= read -r sw_pkg ; do
-            CoArList="${CoArList}$(print_br_item '__ITEM__' ${sw_pkg})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' ${sw_pkg})"
         done <<< "${software_pkgs}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no software packages in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no software packages in tarball')"
     fi
-    CoArList="${CoArList}
"
-    CoArList="${CoArList}$(print_br_item 'other under ___ITEM___' ${prefix})"
-    CoArList="${CoArList}
"
+    comment_artifacts_list="${comment_artifacts_list}
"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'other under ___ITEM___' ${prefix})"
+    comment_artifacts_list="${comment_artifacts_list}
"
     if [[ ! -z ${other_shortened} ]]; then
         while IFS= read -r other ; do
-            CoArList="${CoArList}$(print_br_item '__ITEM__' ${other})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' ${other})"
         done <<< "${other_shortened}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no other files in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no other files in tarball')"
     fi
-    CoArList="${CoArList}
"
+    comment_artifacts_list="${comment_artifacts_list}
" else - CoArList="${CoArList}$(print_dd_item 'No artefacts were created or found.' '')" + comment_artifacts_list="${comment_artifacts_list}$(print_dd_item 'No artefacts were created or found.' '')" fi +comment_artefact_details_fmt="
__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__
" comment_artefacts_details="${comment_artefact_details_fmt/__ARTEFACT_SUMMARY__/${artefact_summary}}" -comment_artefacts_details="${comment_artefacts_details/__ARTEFACT_DETAILS__/${CoArList}}" -comment_artefacts="${comment_artefacts_fmt/__ARTEFACTS_LIST__/${comment_artefacts_details}}" +comment_artefacts_details="${comment_artefacts_details/__ARTEFACT_DETAILS__/${comment_artifacts_list}}" -# now put all pieces together creating comment_details from comment_template -comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}} -comment_description=${comment_description/__DETAILS_FMT__/${comment_details}} +comment_artefacts_fmt="
_Artefacts_
__ARTEFACTS_LIST__
" +comment_artefacts="${comment_artefacts_fmt/__ARTEFACTS_LIST__/${comment_artefacts_details}}" comment_description=${comment_description/__ARTEFACTS_FMT__/${comment_artefacts}} echo "${comment_description}" >> ${job_result_file} From f4f277605a17aea824f940ae1de0727b190be47d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 13:22:18 +0100 Subject: [PATCH 42/76] First, try without --from-pr. If that fails, try with --from-pr, but only for items added to the EasyStack file in _this_ PR to software-layer. If that succeeds, the reason must be that one of the EasyBuild PRs wasn't merged yet, and we can add that information to the fail_msg to make it more explicit --- check_missing_installations.sh | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 623c46c74f..fd2c0d34bb 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -31,6 +31,8 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack}) +grep -v from-pr ${easystack} > ${tmp_easystack} + # Let's use awk so we can allow for exceptions if we are given a PR diff file awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack" awk_command=${awk_command/\\/} # Strip out the backslash we needed for ! @@ -51,7 +53,25 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" if [ "$#" -eq 1 ]; then - fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)" + # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR + # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg + + # Let's use awk so we can allow for exceptions if we are given a PR diff file + awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack" + awk_command=${awk_command/\\/} # Strip out the backslash we needed for ! + eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack} + + msg=">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}," + msg="${msg} allowing for --from-pr's that were added in this PR..." + echo ${msg} + eb_missing_out=$LOCAL_TMPDIR/eb_missing_with_from_pr.out + ${EB:-eb} --easystack ${tmp_easystack} --missing 2>&1 | tee ${eb_missing_out} + exit_code=${PIPESTATUS[0]} + + # If now we succeeded, the reason must be that we originally stripped the --from-pr's + if [ "$#" -eq 0 ]; then + fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)" + fi fi check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}" From b7891087072ab05b50d93295b0f8990e27b50edf Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 13:24:08 +0100 Subject: [PATCH 43/76] Add CFITSIO as a test example, see if we can get a clear error message printed on a build failure here --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 2664d8f417..51e96f1fac 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -10,4 +10,7 @@ easyconfigs: from-pr: 19552 - CDO-2.2.2-gompi-2023b.eb: options: - from-pr: 19792 + from-pr: 19792 + - CFITSIO-4.3.1-GCCcore-13.2.0.eb: + options: + from-pr: 19840 From d178a8f14d6e16f5bcddcd7af0bb7978f647d823 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 13:34:33 +0100 Subject: [PATCH 44/76] Added clarifying comment --- bot/check-build.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bot/check-build.sh b/bot/check-build.sh index e737363f35..24c608b04a 100755 --- a/bot/check-build.sh +++ b/bot/check-build.sh @@ -207,6 +207,8 @@ elif [[ ${UNMERGED_EASYCONFIG} -eq 1 ]]; then else # FAILURE status="FAILURE" + # General failure, we don't know a more specific reason + reason="" summary=":cry: FAILURE" fi From 9123c9c8f483cf5f6b1e931cfe5a4484fc978faa Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 13:37:08 +0100 Subject: [PATCH 45/76] Correct mistake: I meant to _move_ the awk part, not duplicate it --- check_missing_installations.sh | 5 ----- 1 file changed, 5 deletions(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index fd2c0d34bb..4781ecc72a 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -33,11 +33,6 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack}) grep -v from-pr ${easystack} > ${tmp_easystack} -# Let's use awk so we can allow for exceptions if we are given a PR diff file -awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack" -awk_command=${awk_command/\\/} # Strip out the backslash we needed for ! -eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack} - source $TOPDIR/scripts/utils.sh source $TOPDIR/configure_easybuild From 7e4422335f1c2f3ad682362a060906866b9b90f4 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 13:54:07 +0100 Subject: [PATCH 46/76] Now actually check against the exit code of the pipe... --- check_missing_installations.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 4781ecc72a..51a328b50c 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" -if [ "$#" -eq 1 ]; then +if [ "$exit_code" -eq 1 ]; then # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg From da749a111320720773d648d4a55caa2ba1a826e3 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Sat, 9 Mar 2024 14:08:27 +0100 Subject: [PATCH 47/76] Make seperate exit code for the run that allows --from-pr --- check_missing_installations.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 51a328b50c..6d84384fd7 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -61,10 +61,10 @@ if [ "$exit_code" -eq 1 ]; then echo ${msg} eb_missing_out=$LOCAL_TMPDIR/eb_missing_with_from_pr.out ${EB:-eb} --easystack ${tmp_easystack} --missing 2>&1 | tee ${eb_missing_out} - exit_code=${PIPESTATUS[0]} + exit_code_with_from_pr=${PIPESTATUS[0]} # If now we succeeded, the reason must be that we originally stripped the --from-pr's - if [ "$#" -eq 0 ]; then + if [ "$exit_code_with_from_pr" -eq 0 ]; then fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)" fi fi From 86d8a36c52a9a3dfe9af25662bc6c95968804024 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 11:46:32 +0100 Subject: [PATCH 48/76] Remove ineffective DP3 hook --- eb_hooks.py | 27 --------------------------- 1 file changed, 27 deletions(-) diff --git a/eb_hooks.py b/eb_hooks.py index 1478f1a508..d93ee37067 100644 --- a/eb_hooks.py +++ b/eb_hooks.py @@ -186,32 +186,6 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix): raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!") -def parse_hook_dp3_enable_relaxed_vector_conversions(ec, eprefix): - """ - Enable lax vector conversion for DP3 on aarch64/neoverse_v1 - Compiling DP3 6.0 with GCC 13.2.0 (foss-2023b) gives a conversion error when building for aarch64/neoverse_v1. - See also, https://github.com/EESSI/software-layer/pull/479 - """ - if ec.name == 'DP3': - tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version'] - if ( - LooseVersion(ec.version) == LooseVersion('6.0') and - tcname == 'foss' and tcversion == '2023b' - ): - cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR') - if cpu_target == CPU_TARGET_NEOVERSE_V1: - if not hasattr(ec, 'configopts'): - ec['configopts'] = "" - ec['configopts'] += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -flax-vector-conversions" ' - print_msg("Changed configopts for %s: %s", ec.name, ec['configopts']) - else: - print_msg("Not changing configopts for %s on non-neoverse_v1", ec.name) - else: - print_msg("Not changing configopts for %s %s %s", ec.name, ec.version, ec.toolchain) - else: - raise EasyBuildError("DP3-specific hook triggered for non-DP3 easyconfig?!") - - def parse_hook_cgal_toolchainopts_precise(ec, eprefix): """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER.""" if ec.name == 'CGAL': @@ -633,7 +607,6 @@ def inject_gpu_property(ec): PARSE_HOOKS = { 'casacore': parse_hook_casacore_disable_vectorize, 'CGAL': parse_hook_cgal_toolchainopts_precise, - 'DP3': parse_hook_dp3_enable_relaxed_vector_conversions, 'fontconfig': parse_hook_fontconfig_add_fonts, 'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors, 'pybind11': parse_hook_pybind11_replace_catch2, From f8816acf3c0c0022bbba3e123f6d0239469728d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Mar 2024 14:19:15 +0100 Subject: [PATCH 49/76] {2023.06}[2023a] JupyterNotebook v7.0.2 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + 1 file changed, 1 insertion(+) 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 0d8e71e86c..cb207e50ea 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 @@ -36,3 +36,4 @@ easyconfigs: - dask-2023.9.2-foss-2023a.eb - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb + - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb From 310e1e3a36df67c5d51b9bb0dbe80fc97abf1fa7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 Mar 2024 15:34:50 +0100 Subject: [PATCH 50/76] Initial attempt at splitting off the LMOD hooks into a seperate SitePackage.lua file --- EESSI-install-software.sh | 15 +++- create_lmodrc.py | 108 ----------------------- create_lmodsitepackage.py | 141 +++++++++++++++++++++++++++++++ init/eessi_environment_variables | 17 +++- 4 files changed, 166 insertions(+), 115 deletions(-) create mode 100755 create_lmodsitepackage.py diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 69de9d1997..ed137c522d 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -248,11 +248,20 @@ fi ### add packages here echo ">> Creating/updating Lmod cache..." -export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua" +export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod" +lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua" lmodrc_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodrc.py$' > /dev/null; echo $?) -if [ ! -f $LMOD_RC ] || [ ${lmodrc_changed} == '0' ]; then +if [ ! -f $lmod_rc_file ] || [ ${lmodrc_changed} == '0' ]; then python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH} - check_exit_code $? "$LMOD_RC created" "Failed to create $LMOD_RC" + check_exit_code $? "$lmod_rc_file created" "Failed to create $lmod_rc_file" +fi + +echo ">> Creating/updating Lmod SitePackage.lua ..." +export LMOD_PACKAGE_PATH=${EASYBUILD_INSTALLPATH}/.lmod" +lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" +if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then + python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH} + check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file" fi $TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH} diff --git a/create_lmodrc.py b/create_lmodrc.py index 621c8e271a..ae65153a20 100755 --- a/create_lmodrc.py +++ b/create_lmodrc.py @@ -17,113 +17,6 @@ } """ -GPU_LMOD_RC ="""require("strict") -local hook = require("Hook") -local open = io.open - -local function read_file(path) - local file = open(path, "rb") -- r read mode and b binary mode - if not file then return nil end - local content = file:read "*a" -- *a or *all reads the whole file - file:close() - return content -end - -local function eessi_cuda_enabled_load_hook(t) - local frameStk = require("FrameStk"):singleton() - local mt = frameStk:mt() - local simpleName = string.match(t.modFullName, "(.-)/") - -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections. - -- This is required for end users to build additional CUDA software. If the full SDK isn't present, refuse - -- to load the CUDA module and print an informative message on how to set up GPU support for EESSI - local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n" - if simpleName == 'CUDA' then - -- get the full host_injections path - local hostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections') - -- build final path where the CUDA software should be installed - local cudaEasyBuildDir = hostInjections .. "/software/" .. t.modFullName .. "/easybuild" - local cudaDirExists = isDir(cudaEasyBuildDir) - if not cudaDirExists then - local advice = "but while the module file exists, the actual software is not entirely shipped with EESSI " - advice = advice .. "due to licencing. You will need to install a full copy of the CUDA SDK where EESSI " - advice = advice .. "can find it.\\n" - advice = advice .. refer_to_docs - LmodError("\\nYou requested to load ", simpleName, " ", advice) - end - end - -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker, - -- otherwise, refuse to load the requested module and print error message - local haveGpu = mt:haveProperty(simpleName,"arch","gpu") - if haveGpu then - local arch = os.getenv("EESSI_CPU_FAMILY") or "" - local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt" - local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so" - local cudaDriverExists = isFile(cudaDriverFile) - local singularityCudaExists = isFile("/.singularity.d/libs/libcuda.so") - if not (cudaDriverExists or singularityCudaExists) then - local advice = "which relies on the CUDA runtime environment and driver libraries. " - advice = advice .. "In order to be able to use the module, you will need " - advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n" - advice = advice .. refer_to_docs - LmodError("\\nYou requested to load ", simpleName, " ", advice) - else - -- CUDA driver exists, now we check its version to see if an update is needed - if cudaDriverExists then - local cudaVersion = read_file(cudaVersionFile) - local cudaVersion_req = os.getenv("EESSICUDAVERSION") - -- driver CUDA versions don't give a patch version for CUDA - local major, minor = string.match(cudaVersion, "(%d+)%.(%d+)") - local major_req, minor_req, patch_req = string.match(cudaVersion_req, "(%d+)%.(%d+)%.(%d+)") - local driver_libs_need_update = false - if major < major_req then - driver_libs_need_update = true - elseif major == major_req then - if minor < minor_req then - driver_libs_need_update = true - end - end - if driver_libs_need_update == true then - local advice = "but the module you want to load requires CUDA " .. cudaVersion_req .. ". " - advice = advice .. "Please update your CUDA driver libraries and then " - advice = advice .. "let EESSI know about the update.\\n" - advice = advice .. refer_to_docs - LmodError("\\nYour driver CUDA version is ", cudaVersion, " ", advice) - end - end - end - end -end - -local function eessi_openmpi_load_hook(t) - -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1, - -- to work around hang/crash due to bug in OpenMPI; - -- see https://gitlab.com/eessi/support/-/issues/41 - local frameStk = require("FrameStk"):singleton() - local mt = frameStk:mt() - local moduleName = string.match(t.modFullName, "(.-)/") - local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or "" - if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then - local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI" - LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)") - local ompiMcaBtl = os.getenv("OMPI_MCA_btl") - if ompiMcaBtl == nil then - setenv("OMPI_MCA_btl", "^smcuda") - else - setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda") - end - end -end - --- Combine both functions into a single one, as we can only register one function as load hook in lmod --- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed -function eessi_load_hook(t) - eessi_cuda_enabled_load_hook(t) - eessi_openmpi_load_hook(t) -end - - -hook.register("load", eessi_load_hook) -""" def error(msg): sys.stderr.write("ERROR: %s\n" % msg) @@ -143,7 +36,6 @@ def error(msg): 'dot_lmod': DOT_LMOD, 'prefix': prefix, } -lmodrc_txt += '\n' + GPU_LMOD_RC try: os.makedirs(os.path.dirname(lmodrc_path), exist_ok=True) with open(lmodrc_path, 'w') as fp: diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py new file mode 100755 index 0000000000..9e77eafecf --- /dev/null +++ b/create_lmodsitepackage.py @@ -0,0 +1,141 @@ +#!/usr/bin/env python3 +# +# Create SitePackage.lua configuration file for Lmod. +# +import os +import sys + +DOT_LMOD = '.lmod' + +hook_txt ="""require("strict") +local hook = require("Hook") +local open = io.open + +local function read_file(path) + local file = open(path, "rb") -- r read mode and b binary mode + if not file then return nil end + local content = file:read "*a" -- *a or *all reads the whole file + file:close() + return content +end + +local function eessi_cuda_enabled_load_hook(t) + local frameStk = require("FrameStk"):singleton() + local mt = frameStk:mt() + local simpleName = string.match(t.modFullName, "(.-)/") + -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections. + -- This is required for end users to build additional CUDA software. If the full SDK isn't present, refuse + -- to load the CUDA module and print an informative message on how to set up GPU support for EESSI + local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n" + if simpleName == 'CUDA' then + -- get the full host_injections path + local hostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections') + -- build final path where the CUDA software should be installed + local cudaEasyBuildDir = hostInjections .. "/software/" .. t.modFullName .. "/easybuild" + local cudaDirExists = isDir(cudaEasyBuildDir) + if not cudaDirExists then + local advice = "but while the module file exists, the actual software is not entirely shipped with EESSI " + advice = advice .. "due to licencing. You will need to install a full copy of the CUDA SDK where EESSI " + advice = advice .. "can find it.\\n" + advice = advice .. refer_to_docs + LmodError("\\nYou requested to load ", simpleName, " ", advice) + end + end + -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker, + -- otherwise, refuse to load the requested module and print error message + local haveGpu = mt:haveProperty(simpleName,"arch","gpu") + if haveGpu then + local arch = os.getenv("EESSI_CPU_FAMILY") or "" + local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt" + local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so" + local cudaDriverExists = isFile(cudaDriverFile) + local singularityCudaExists = isFile("/.singularity.d/libs/libcuda.so") + if not (cudaDriverExists or singularityCudaExists) then + local advice = "which relies on the CUDA runtime environment and driver libraries. " + advice = advice .. "In order to be able to use the module, you will need " + advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n" + advice = advice .. refer_to_docs + LmodError("\\nYou requested to load ", simpleName, " ", advice) + else + -- CUDA driver exists, now we check its version to see if an update is needed + if cudaDriverExists then + local cudaVersion = read_file(cudaVersionFile) + local cudaVersion_req = os.getenv("EESSICUDAVERSION") + -- driver CUDA versions don't give a patch version for CUDA + local major, minor = string.match(cudaVersion, "(%d+)%.(%d+)") + local major_req, minor_req, patch_req = string.match(cudaVersion_req, "(%d+)%.(%d+)%.(%d+)") + local driver_libs_need_update = false + if major < major_req then + driver_libs_need_update = true + elseif major == major_req then + if minor < minor_req then + driver_libs_need_update = true + end + end + if driver_libs_need_update == true then + local advice = "but the module you want to load requires CUDA " .. cudaVersion_req .. ". " + advice = advice .. "Please update your CUDA driver libraries and then " + advice = advice .. "let EESSI know about the update.\\n" + advice = advice .. refer_to_docs + LmodError("\\nYour driver CUDA version is ", cudaVersion, " ", advice) + end + end + end + end +end + +local function eessi_openmpi_load_hook(t) + -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1, + -- to work around hang/crash due to bug in OpenMPI; + -- see https://gitlab.com/eessi/support/-/issues/41 + local frameStk = require("FrameStk"):singleton() + local mt = frameStk:mt() + local moduleName = string.match(t.modFullName, "(.-)/") + local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or "" + if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then + local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI" + LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)") + local ompiMcaBtl = os.getenv("OMPI_MCA_btl") + if ompiMcaBtl == nil then + setenv("OMPI_MCA_btl", "^smcuda") + else + setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda") + end + end +end + +-- Combine both functions into a single one, as we can only register one function as load hook in lmod +-- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed +function eessi_load_hook(t) + eessi_cuda_enabled_load_hook(t) + eessi_openmpi_load_hook(t) +end + + +hook.register("load", eessi_load_hook) +""" + +def error(msg): + sys.stderr.write("ERROR: %s\n" % msg) + sys.exit(1) + + +if len(sys.argv) != 2: + error("Usage: %s " % sys.argv[0]) + +prefix = sys.argv[1] + +if not os.path.exists(prefix): + error("Prefix directory %s does not exist!" % prefix) + +sitepackage_path = os.path.join(prefix, DOT_LMOD, 'SitePackage.lua') +sitepackage_txt += hook_txt +try: + os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True) + with open(sitepackage_path, 'w') as fp: + fp.write(sitepackage_txt) + +except (IOError, OSError) as err: + error("Failed to create %s: %s" % (sitepackage_path, err)) + +print(sitepackage_path) diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables index af5222e7b9..78f01b1921 100644 --- a/init/eessi_environment_variables +++ b/init/eessi_environment_variables @@ -76,11 +76,20 @@ if [ -d $EESSI_PREFIX ]; then false fi - export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua" - if [ -f $LMOD_RC ]; then - show_msg "Found Lmod configuration file at $LMOD_RC" + export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod" + lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua" + if [ -f $lmod_rc_file ]; then + show_msg "Found Lmod configuration file at $lmod_rc_file" else - error "Lmod configuration file not found at $LMOD_RC" + error "Lmod configuration file not found at $lmod_rc_file" + fi + + export LMOD_PACKAGE_PATH="$EESSI_SOFTWARE_PATH/.lmod" + lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" + if [ -f $lmod_sitepackage_file ]; then + show_msg "Found Lmod SitePackage.lua file at $lmod_sitepackage_file" + else + error "Lmod SitePackage.lua file not found at $lmod_sitepackage_file" fi else From a8c2883f0c73af0537a834221c3ae439f44c1b2f Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 11 Mar 2024 15:59:32 +0100 Subject: [PATCH 51/76] Correct typo Co-authored-by: ocaisa --- bot/check-build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bot/check-build.sh b/bot/check-build.sh index 24c608b04a..10b1ed6a11 100755 --- a/bot/check-build.sh +++ b/bot/check-build.sh @@ -400,7 +400,7 @@ comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${succ success_msg="found message matching ${GP_tgz_created}" failure_msg="no message matching ${GP_tgz_created}" comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}") -# Now, do the actual repalcement of __DETAILS_FMT__ +# Now, do the actual replacement of __DETAILS_FMT__ comment_details_fmt="
_Details_
__DETAILS_LIST__
" comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}" comment_description=${comment_description/__DETAILS_FMT__/${comment_details}} From 6553e294163fb9e117803a2433acba3c14e135f2 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 Mar 2024 16:05:16 +0100 Subject: [PATCH 52/76] Skip the if-condition also if pr_exceptions is empty. There is no point in running the eb --missing again in that case, since there were no --from-pr's in this PR to begin with, so unmerged PRs cannot be the reason for failing --- check_missing_installations.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 6d84384fd7..0ee6ec4385 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -47,9 +47,11 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" -if [ "$exit_code" -eq 1 ]; then +if [ "$exit_code" -eq 1 ] && [ ! -z $pr_exceptions ]; then # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg + # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as + # well skip this check - unmerged PRs can not be the reason for the non-zero exit code in that scenario # Let's use awk so we can allow for exceptions if we are given a PR diff file awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack" From 27a12bd2e4a88c486f3dd5b5be57ac16eefd2650 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 Mar 2024 16:09:46 +0100 Subject: [PATCH 53/76] Added missing quote --- EESSI-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index ed137c522d..219fa8680a 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -257,7 +257,7 @@ if [ ! -f $lmod_rc_file ] || [ ${lmodrc_changed} == '0' ]; then fi echo ">> Creating/updating Lmod SitePackage.lua ..." -export LMOD_PACKAGE_PATH=${EASYBUILD_INSTALLPATH}/.lmod" +export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod" lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH} From 81e544f15333b3d3b3ed70f4954f414f262ba6cd Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 11 Mar 2024 16:11:31 +0100 Subject: [PATCH 54/76] Cant add to a variable that doesnt exist... We don't need this intermediate assignment anyway --- create_lmodsitepackage.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py index 9e77eafecf..9a4a232863 100755 --- a/create_lmodsitepackage.py +++ b/create_lmodsitepackage.py @@ -129,11 +129,10 @@ def error(msg): error("Prefix directory %s does not exist!" % prefix) sitepackage_path = os.path.join(prefix, DOT_LMOD, 'SitePackage.lua') -sitepackage_txt += hook_txt try: os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True) with open(sitepackage_path, 'w') as fp: - fp.write(sitepackage_txt) + fp.write(hook_txt) except (IOError, OSError) as err: error("Failed to create %s: %s" % (sitepackage_path, err)) From 0343684cc8e7b73fc25e160007dc458c2c54e6d0 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 12 Mar 2024 10:19:33 +0100 Subject: [PATCH 55/76] {2023.06}[foss/2023b] python-casacore 3.5.2 + libspatialindex 1.9.3 --- .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 54011c262e..186f4f86b3 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -43,3 +43,9 @@ easyconfigs: - CDO-2.2.2-gompi-2023b.eb: options: from-pr: 19792 + - python-casacore-3.5.2-foss-2023b.eb: + options: + from-pr: 20084 + - libspatialindex-1.9.3-GCCcore-13.2.0.eb: + options: + from-pr: 19922 From 3e43b061314bdde685b585804a047802cb95f81a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 12 Mar 2024 14:00:38 +0100 Subject: [PATCH 56/76] add ImageMagick-7.1.1-15-GCCcore-12.3.0.eb --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++ 1 file changed, 3 insertions(+) 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 cb207e50ea..8165755865 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 @@ -37,3 +37,6 @@ easyconfigs: - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb + - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb: + options: + from-pr: 20086 From 02955711c5600305d8feedece3e85978626ff962 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 12 Mar 2024 18:33:07 +0100 Subject: [PATCH 57/76] Use PR that sets LD_LIBRARY_PATH for python-casacore --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 186f4f86b3..e2d35276df 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -45,7 +45,7 @@ easyconfigs: from-pr: 19792 - python-casacore-3.5.2-foss-2023b.eb: options: - from-pr: 20084 + from-pr: 20089 - libspatialindex-1.9.3-GCCcore-13.2.0.eb: options: from-pr: 19922 From dab1ac0f66c6164c9ea9bc3798be7a0673465ac5 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:12:15 +0100 Subject: [PATCH 58/76] Create generic function to compare (and if needed copy) files based on an explicit list from one dir to another. Use that generic function to replace the existing code copying the scripts dir, and the scripts/gpu_support/nvidia dir. Add to that a copy of the init dir and the current subdirs, again listing the files to copy explicitely for safety. --- install_scripts.sh | 80 +++++++++++++++++++++++++++++++++------------- 1 file changed, 57 insertions(+), 23 deletions(-) diff --git a/install_scripts.sh b/install_scripts.sh index 6e6cd825ac..ac1741428e 100755 --- a/install_scripts.sh +++ b/install_scripts.sh @@ -25,6 +25,35 @@ compare_and_copy() { fi } +copy_files_by_list() { +# Compares and copies listed files from a source to a target directory + if [ "$#" -ne 3 ]; then + echo "Usage of function: copy_files_by_list " + echo "Here, file_list is an (expanded) bash array" + echo "Example:" + echo "my_files=(file1 file2)" + echo 'copy_files_by_list /my/source /my/target "${my_files[@]}"' + return 1 + fi + source_dir="$1" + target_dir="$2" + # Need to shift all arguments to the left twice. Then, rebuild the array with the rest of the arguments + shift + shift + file_list=("$@") + + # Create target dir + mkdir -p ${target_dir} + + # Copy from source to target + echo "Copying files: ${file_list[@]}" + echo "From directory: ${source_dir}" + echo "To directory: ${target_dir}" + + for file in ${file_list[@]}; do + compare_and_copy ${source_dir}/${file} ${target_dir}/${file} + done +} POSITIONAL_ARGS=() @@ -54,28 +83,33 @@ set -- "${POSITIONAL_ARGS[@]}" TOPDIR=$(dirname $(realpath $0)) -# Subdirs for generic scripts -SCRIPTS_DIR_SOURCE=${TOPDIR}/scripts # Source dir -SCRIPTS_DIR_TARGET=${INSTALL_PREFIX}/scripts # Target dir +# Copy for init directory +init_files=( + bash eessi_archdetect.sh eessi_defaults eessi_environment_variables eessi_software_subdir_for_host.py + minimal_eessi_env README.md test.py +) +copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}" -# Create target dir -mkdir -p ${SCRIPTS_DIR_TARGET} +# Copy for the init/arch_specs directory +arch_specs_files=( + eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_x86.spec +) +copy_files_by_list ${TOPDIR}/init/arch_specs ${INSTALL_PREFIX}/init/arch_specs "${arch_specs_files[@]}" -# Copy scripts into this prefix -echo "copying scripts from ${SCRIPTS_DIR_SOURCE} to ${SCRIPTS_DIR_TARGET}" -for file in utils.sh; do - compare_and_copy ${SCRIPTS_DIR_SOURCE}/${file} ${SCRIPTS_DIR_TARGET}/${file} -done -# Subdirs for GPU support -NVIDIA_GPU_SUPPORT_DIR_SOURCE=${SCRIPTS_DIR_SOURCE}/gpu_support/nvidia # Source dir -NVIDIA_GPU_SUPPORT_DIR_TARGET=${SCRIPTS_DIR_TARGET}/gpu_support/nvidia # Target dir - -# Create target dir -mkdir -p ${NVIDIA_GPU_SUPPORT_DIR_TARGET} - -# Copy files from this directory into the prefix -# To be on the safe side, we dont do recursive copies, but we are explicitely copying each individual file we want to add -echo "copying scripts from ${NVIDIA_GPU_SUPPORT_DIR_SOURCE} to ${NVIDIA_GPU_SUPPORT_DIR_TARGET}" -for file in install_cuda_host_injections.sh link_nvidia_host_libraries.sh; do - compare_and_copy ${NVIDIA_GPU_SUPPORT_DIR_SOURCE}/${file} ${NVIDIA_GPU_SUPPORT_DIR_TARGET}/${file} -done +# Copy for init/Magic_castle directory +mc_files=( + bash eessi_python3 +) +copy_files_by_list ${TOPDIR}/init/Magic_Castle ${INSTALL_PREFIX}/init/Magic_Castle "${mc_files[@]}" + +# Copy for the scripts directory +script_files=( + utils.sh +) +copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@]}" + +# Copy files for the scripts/gpu_support/nvidia directory +nvidia_files=( + install_cuda_host_injections.sh link_nvidia_host_libraries.sh +) +copy_files_by_list ${TOPDIR}/gpu_support/nvidia ${INSTALL_PREFIX}/gpu_support/nvidia "${nvidia_files[@]}" From 0abedef29ffceb22a5cafa88869bf48b38f3fbb3 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:17:47 +0100 Subject: [PATCH 59/76] An expanded bash array counts as extra arguments. Thus, we cannot check for three arguments, it can be anything greater than 2 --- install_scripts.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install_scripts.sh b/install_scripts.sh index ac1741428e..e8077aa242 100755 --- a/install_scripts.sh +++ b/install_scripts.sh @@ -27,7 +27,7 @@ compare_and_copy() { copy_files_by_list() { # Compares and copies listed files from a source to a target directory - if [ "$#" -ne 3 ]; then + if [ ! "$#" -ge 3 ]; then echo "Usage of function: copy_files_by_list " echo "Here, file_list is an (expanded) bash array" echo "Example:" From 11c7525e03069c0a5aa85d36a9cca5a1aeaff381 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:21:06 +0100 Subject: [PATCH 60/76] Forgot to check the diff if the create_lmodsitepackage.py actually changed --- EESSI-install-software.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 219fa8680a..2d5912736b 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -259,6 +259,7 @@ fi echo ">> Creating/updating Lmod SitePackage.lua ..." export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod" lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" +sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?) if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH} check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file" From a07b8a8accc23666be71f36ce0d09e82e9ffdc30 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:22:01 +0100 Subject: [PATCH 61/76] Is quoting the problem --- EESSI-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 2d5912736b..c51459967d 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -260,7 +260,7 @@ echo ">> Creating/updating Lmod SitePackage.lua ..." export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod" lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?) -if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then +if [ ! -f $lmod_sitepackage_file ] || [ "${sitepackage_changed}" == '0' ]; then python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH} check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file" fi From 90b3ce068aa787715d82a20656c99f656f561a44 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:23:57 +0100 Subject: [PATCH 62/76] Try quoting --- EESSI-install-software.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index c51459967d..2a4f7182cd 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -260,7 +260,7 @@ echo ">> Creating/updating Lmod SitePackage.lua ..." export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod" lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua" sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?) -if [ ! -f $lmod_sitepackage_file ] || [ "${sitepackage_changed}" == '0' ]; then +if [ ! -f "$lmod_sitepackage_file" ] || [ "${sitepackage_changed}" == '0' ]; then python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH} check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file" fi From 9c707e4a69ad385474067f2adee599632ffda882 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Mar 2024 19:25:30 +0100 Subject: [PATCH 63/76] Correct prefix for the gpu_support scripts --- install_scripts.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install_scripts.sh b/install_scripts.sh index e8077aa242..508735975c 100755 --- a/install_scripts.sh +++ b/install_scripts.sh @@ -112,4 +112,4 @@ copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@ nvidia_files=( install_cuda_host_injections.sh link_nvidia_host_libraries.sh ) -copy_files_by_list ${TOPDIR}/gpu_support/nvidia ${INSTALL_PREFIX}/gpu_support/nvidia "${nvidia_files[@]}" +copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}" From c08831ee060d153bb1da466cfaa00e4103c37e31 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 13 Mar 2024 15:46:24 +0100 Subject: [PATCH 64/76] Update bot/check-build.sh Co-authored-by: Kenneth Hoste --- bot/check-build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bot/check-build.sh b/bot/check-build.sh index 10b1ed6a11..e075518421 100755 --- a/bot/check-build.sh +++ b/bot/check-build.sh @@ -174,7 +174,7 @@ fi # For now, we only analyse unmerged EasyConfigs as potential cause, but we can easily add checks for other # specific scenarios below -# Check for the pattern being added here https://github.com/EESSI/software-layer/pull/493 to the output to +# Check for the pattern being added here by check_missing_installations.sh to the output to # see if EasyConfigs might have been unmerged, and that's causing a failure UNMERGED_EASYCONFIG=-1 if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then From 992b11dc782d391899862f80033f08b1efba4634 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 13 Mar 2024 15:47:37 +0100 Subject: [PATCH 65/76] Remove PR to trigger comment Co-authored-by: Kenneth Hoste --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 2b5844289d..e2d35276df 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -49,6 +49,3 @@ easyconfigs: - libspatialindex-1.9.3-GCCcore-13.2.0.eb: options: from-pr: 19922 - - CFITSIO-4.3.1-GCCcore-13.2.0.eb: - options: - from-pr: 19840 From 8d6493ea05422ee443f10bc9230c3ff3884af998 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 13 Mar 2024 15:48:08 +0100 Subject: [PATCH 66/76] Trigger on any non-zero exit code Co-authored-by: Kenneth Hoste --- check_missing_installations.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 0ee6ec4385..7c29228416 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" -if [ "$exit_code" -eq 1 ] && [ ! -z $pr_exceptions ]; then +if [ "$exit_code" -ne 0 ] && [ ! -z $pr_exceptions ]; then # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as From 54bb3ec1cdd6cae823068a67cdfdb5d443d4e69b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 14 Mar 2024 09:38:29 +0100 Subject: [PATCH 67/76] Make sure the changed init scripts also end up in the tarball --- create_tarball.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/create_tarball.sh b/create_tarball.sh index a619df9439..5bd8eeb110 100755 --- a/create_tarball.sh +++ b/create_tarball.sh @@ -51,6 +51,13 @@ if [ -d ${eessi_version}/scripts ]; then find ${eessi_version}/scripts -type f | grep -v '/\.wh\.' >> ${files_list} fi +# also include init, which is also copied by install_scripts.sh +if [ -d ${eessi_version}/init ]; then + find ${eessi_version}/init -type f | grep -v '/\.wh\.' >> ${files_list} +fi + + + if [ -d ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules ]; then # module files find ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list} From 0fdbd3a3be714c116b76f72c694406ea03e513fe Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Mar 2024 11:35:35 +0100 Subject: [PATCH 68/76] Add Z3 with new module name Via https://github.com/easybuilders/easybuild-easyconfigs/pull/20050 , the different Z3 easyconfigs have been consolidated. This means the version used as a dependency for PyTorch has been "corrected" so we need to dance around that for our CI purposes --- .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 6 ++++++ 1 file changed, 6 insertions(+) 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 8165755865..5a46cf5fb2 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 @@ -40,3 +40,9 @@ easyconfigs: - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb: options: from-pr: 20086 + - Z3-4.12.2-GCCcore-12.3.0.eb: + options: + # The Z3 dependency of PyTorch had it's versionsuffix removed + # and we need to workaround the problem this creates, + # see https://github.com/EESSI/software-layer/pull/501 for details + from-pr: 20050 From 5a6bfd149bd59894e51adec5b2e8e9dc00873977 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 14 Mar 2024 17:47:18 +0100 Subject: [PATCH 69/76] Remove whitspace --- create_tarball.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/create_tarball.sh b/create_tarball.sh index 5bd8eeb110..2d77acfc43 100755 --- a/create_tarball.sh +++ b/create_tarball.sh @@ -56,8 +56,6 @@ if [ -d ${eessi_version}/init ]; then find ${eessi_version}/init -type f | grep -v '/\.wh\.' >> ${files_list} fi - - if [ -d ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules ]; then # module files find ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list} From d097189aa07f2d323779212e4451a2df2466193d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 22:55:43 +0100 Subject: [PATCH 70/76] {2023.06}[2023a] PyOpenGL 3.1.7 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + 1 file changed, 1 insertion(+) 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 5a46cf5fb2..1d3119e5c2 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 @@ -46,3 +46,4 @@ easyconfigs: # and we need to workaround the problem this creates, # see https://github.com/EESSI/software-layer/pull/501 for details from-pr: 20050 + - PyOpenGL-3.1.7-GCCcore-12.3.0.eb From 8245aff4b7f4dd178924cd42eda76c21eed146fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 15 Mar 2024 00:02:09 +0100 Subject: [PATCH 71/76] add from-pr=20007 --- .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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 1d3119e5c2..65b4265ff7 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 @@ -46,4 +46,6 @@ easyconfigs: # and we need to workaround the problem this creates, # see https://github.com/EESSI/software-layer/pull/501 for details from-pr: 20050 - - PyOpenGL-3.1.7-GCCcore-12.3.0.eb + - PyOpenGL-3.1.7-GCCcore-12.3.0.eb: + options: + from-pr: 20007 From af58e1a5fc00ab311eab185a91302d0c735c8978 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2024 20:48:12 +0100 Subject: [PATCH 72/76] {2023.06}[2023a] ipympl 0.9.3 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++ 1 file changed, 3 insertions(+) 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 65b4265ff7..384aa04a9c 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 @@ -49,3 +49,6 @@ easyconfigs: - PyOpenGL-3.1.7-GCCcore-12.3.0.eb: options: from-pr: 20007 + - ipympl-0.9.3-foss-2023a.eb: + options: + from-pr: 20126 From a12b9a340e17953a8e6fe741245663c69ece813b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2024 21:13:32 +0100 Subject: [PATCH 73/76] fix check_missing_installations.sh when unmerged PR is used --- check_missing_installations.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 7c29228416..d8135ea3cb 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]} ok_msg="Command 'eb --missing ...' succeeded, analysing output..." fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" -if [ "$exit_code" -ne 0 ] && [ ! -z $pr_exceptions ]; then +if [ "$exit_code" -ne 0 ] && [ ! -z "$pr_exceptions" ]; then # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as From bef38bafea82a15300e6c9ded9d2dd2843c3dadf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2024 10:55:57 +0100 Subject: [PATCH 74/76] {2023.06}[2023a] OpenJPEG 2.5.0 --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 1 + 1 file changed, 1 insertion(+) 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 384aa04a9c..0a1343295e 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 @@ -52,3 +52,4 @@ easyconfigs: - ipympl-0.9.3-foss-2023a.eb: options: from-pr: 20126 + - OpenJPEG-2.5.0-GCCcore-12.3.0.eb From 56e4b87d1c0de54f374ca77d7c316be173d8bb9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 26 Mar 2024 14:56:15 +0100 Subject: [PATCH 75/76] add LittleCMS, giflib, OpenJPEG to fix check_missing CI --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index e2d35276df..380c0107c6 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -49,3 +49,6 @@ easyconfigs: - libspatialindex-1.9.3-GCCcore-13.2.0.eb: options: from-pr: 19922 + - LittleCMS-2.15-GCCcore-13.2.0.eb + - giflib-5.2.1-GCCcore-13.2.0.eb + - OpenJPEG-2.5.0-GCCcore-13.2.0.eb From 32f04020a1b3e3c7061107d221dc4faf155c7fb0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 26 Mar 2024 15:38:05 +0100 Subject: [PATCH 76/76] also add libwebp-1.3.2-GCCcore-13.2.0.eb --- .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml index 380c0107c6..25cdde27e6 100644 --- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml +++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml @@ -52,3 +52,5 @@ easyconfigs: - LittleCMS-2.15-GCCcore-13.2.0.eb - giflib-5.2.1-GCCcore-13.2.0.eb - OpenJPEG-2.5.0-GCCcore-13.2.0.eb + - libwebp-1.3.2-GCCcore-13.2.0.eb +