{2023.06}[2023a] cutadapt 4.9 (testing staging bundles)

.github/workflows/test-software.eessi.io.yml

@@ -8,30 +8,41 @@ on:
 permissions:
   contents: read # to fetch code (actions/checkout)
 env:
+  EESSI_VERSION: '2023.06'
   EESSI_ACCELERATOR_TARGETS: |
     x86_64/amd/zen2:
       - nvidia/cc80
     x86_64/amd/zen3:
       - nvidia/cc80
 jobs:
   check_missing:
-    runs-on: ubuntu-24.04
     strategy:
       fail-fast: false
       matrix:
-        EESSI_VERSION:
-        - 2023.06
-        EESSI_SOFTWARE_SUBDIR_OVERRIDE:
-        - aarch64/generic
-        - aarch64/neoverse_n1
-        - aarch64/neoverse_v1
-        - x86_64/amd/zen2
-        - x86_64/amd/zen3
-        - x86_64/amd/zen4
-        - x86_64/intel/haswell
-        - x86_64/intel/sapphirerapids
-        - x86_64/intel/skylake_avx512
-        - x86_64/generic
+        include:
+          # Arm CPU targets
+          - runs_on: ubuntu-24.04-arm
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/generic
+          - runs_on: ubuntu-24.04-arm
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_n1
+          - runs_on: ubuntu-24.04-arm
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_v1
+          # x86_64 CPU targets
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen2
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen3
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen4
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/haswell
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/sapphirerapids
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/skylake_avx512
+          - runs_on: ubuntu-24.04
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/generic
+    runs-on: ${{ matrix.runs_on }}
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
@@ -46,20 +57,20 @@ jobs:
         - name: Test check_missing_installations.sh script
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
               # set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash),
               # to prevent issues with checks in the Easybuild configuration that use this variable
               export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*}
               module load EasyBuild
               which eb
               eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${EESSI_VERSION}
               export EESSI_OS_TYPE=linux
               env | grep ^EESSI | sort
 
               # first check the CPU-only builds for this CPU target
-              echo "just run check_missing_installations.sh (should use easystacks/software.eessi.io/${{matrix.EESSI_VERSION}}/eessi-${{matrix.EESSI_VERSION}}-*.yml with latest EasyBuild release)"
-              for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} .github/workflows/scripts/only_latest_easystacks.sh); do
+              echo "just run check_missing_installations.sh (should use easystacks/software.eessi.io/${EESSI_VERSION}/eessi-${EESSI_VERSION}-*.yml with latest EasyBuild release)"
+              for easystack_file in $(EESSI_VERSION=${EESSI_VERSION} .github/workflows/scripts/only_latest_easystacks.sh); do
                   echo "check missing installations for ${easystack_file}..."
                   ./check_missing_installations.sh ${easystack_file}
                   ec=$?
@@ -74,7 +85,7 @@ jobs:
                   for accel in ${accelerators}; do
                       module use ${EESSI_SOFTWARE_PATH}/accel/${accel}/modules/all
                       echo "checking missing installations for accelerator ${accel} using modulepath: ${MODULEPATH}"
-                      for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
+                      for easystack_file in $(EESSI_VERSION=${EESSI_VERSION} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
                           echo "check missing installations for ${easystack_file}..."
                           ./check_missing_installations.sh ${easystack_file}
                           ec=$?
@@ -87,14 +98,14 @@ jobs:
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
               # set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash),
               # to prevent issues with checks in the Easybuild configuration that use this variable
               export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*}
               module load EasyBuild
               which eb
               eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${EESSI_VERSION}
               export EESSI_OS_TYPE=linux
               env | grep ^EESSI | sort
               # create dummy easystack file with a single entry (something that is not installed in EESSI)

EESSI-install-software.sh

@@ -354,7 +354,7 @@ else
         echo -e "Processing easystack file ${easystack_file}...\n\n"
 
         # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
 
         # load EasyBuild module (will be installed if it's not available yet)
         source ${TOPDIR}/load_easybuild_module.sh ${eb_version}

EESSI-remove-software.sh

@@ -108,7 +108,7 @@ if [ $EUID -eq 0 ]; then
     else
         for easystack_file in ${changed_easystacks_rebuilds}; do
             # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-            eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+            eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
 
             # load EasyBuild module (will be installed if it's not available yet)
             source ${TOPDIR}/load_easybuild_module.sh ${eb_version}

create_lmodsitepackage.py

@@ -231,73 +231,6 @@
     end
 end
 
-local function using_eessi_accel_stack ()
-    local modulepath = os.getenv("MODULEPATH") or ""
-    local accel_stack_in_modulepath = false
-
-    -- Check if we are using an EESSI version 2023 accelerator stack by checking if the $MODULEPATH contains
-    -- a path that starts with /cvmfs/software.eessi.io and contains accel/nvidia/ccNN
-    for path in string.gmatch(modulepath, '(.-):') do
-        if string.sub(path, 1, 41) == "/cvmfs/software.eessi.io/versions/2023.06" then
-            if string.find(path, "accel/nvidia/cc%d%d") then
-                accel_stack_in_modulepath = true
-                break
-            end
-        end
-    end
-    return accel_stack_in_modulepath
-end
-
-local function eessi_removed_module_warning_startup_hook(usrCmd)
-    if usrCmd == 'load' and not os.getenv("EESSI_SKIP_REMOVED_MODULES_CHECK") then
-        local CUDA_RELOCATION_MSG = [[All CUDA installations and modules depending on CUDA have been relocated to GPU-specific stacks.
-        Please see https://www.eessi.io/docs/site_specific_config/gpu/ for more information.]]
-
-        local RELOCATED_CUDA_MODULES = {
-            ['NCCL'] = CUDA_RELOCATION_MSG,
-            ['NCCL/2.18.3-GCCcore-12.3.0-CUDA-12.1.1'] = CUDA_RELOCATION_MSG,
-            ['UCX-CUDA'] = CUDA_RELOCATION_MSG,
-            ['UCX-CUDA/1.14.1-GCCcore-12.3.0-CUDA-12.1.1'] = CUDA_RELOCATION_MSG,
-            -- we also have non-CUDA versions of OSU Micro Benchmarks, so only match the CUDA version
-            ['OSU-Micro-Benchmarks/7.2-gompi-2023a-CUDA-12.1.1'] = CUDA_RELOCATION_MSG,
-            ['UCC-CUDA'] = CUDA_RELOCATION_MSG,
-            ['UCC-CUDA/1.2.0-GCCcore-12.3.0-CUDA-12.1.1'] = CUDA_RELOCATION_MSG,
-            ['CUDA'] = CUDA_RELOCATION_MSG,
-            ['CUDA/12.1.1'] = CUDA_RELOCATION_MSG,
-            ['CUDA-Samples'] = CUDA_RELOCATION_MSG,
-            ['CUDA-Samples/12.1-GCC-12.3.0-CUDA-12.1.1'] = CUDA_RELOCATION_MSG,
-        }
-
-        local REMOVED_MODULES = {
-            ['ipympl/0.9.3-foss-2023a'] = 'This module has been replaced by ipympl/0.9.3-gfbf-2023a',
-        }
-
-        local masterTbl = masterTbl()
-        local error_msg = ""
-        -- The CUDA messages should only be shown if the accelerator stack is NOT being used
-        if not using_eessi_accel_stack() then
-            for _, module in pairs(masterTbl.pargs) do
-                if RELOCATED_CUDA_MODULES[module] ~= nil then
-                    error_msg = error_msg .. module .. ': ' .. RELOCATED_CUDA_MODULES[module] .. '\\n\\n'
-                end
-            end
-        end
-        for _, module in pairs(masterTbl.pargs) do
-            if REMOVED_MODULES[module] ~= nil then
-                error_msg = error_msg .. module .. ': ' .. REMOVED_MODULES[module] .. '\\n\\n'
-            end
-        end
-        if error_msg ~= "" then
-            LmodError('\\n' .. error_msg .. 'If you know what you are doing and you want to ignore this check for removed/relocated modules, set $EESSI_SKIP_REMOVED_MODULES_CHECK to any value.')
-        end
-    end
-end
-
-function eessi_startup_hook(usrCmd)
-    eessi_removed_module_warning_startup_hook(usrCmd)
-end
-
-hook.register("startup", eessi_startup_hook)
 hook.register("load", eessi_load_hook)
 
 """
@@ -320,7 +253,7 @@
                   modT.fullName:match("GCC%-([0-9]*.[0-9]*.[0-9]*)") or
                   modT.fullName:match("GCCcore%-([0-9]*.[0-9]*.[0-9]*)")
 
-    -- if nothing matches, return              
+    -- if nothing matches, return
     if tcver == nil then return end
 
     -- if we have matches, check if the toolchain version is either 2022b or 12.2.0

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.4-2023a.yml

@@ -59,3 +59,4 @@ easyconfigs:
       # without any from-commit this will use a version from April 6, 2024
       # https://github.com/easybuilders/easybuild-easyconfigs/blob/88f6f9c7439c535e62461e6e71b1961c7be118b8/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb
       # EB 5.0.0 has a few changes to that
+  - cutadapt-4.9-GCCcore-12.3.0.eb

easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.0.0-2023a.yml

@@ -4,3 +4,13 @@ easyconfigs:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22292
         # and https://github.com/easybuilders/easybuild-easyconfigs/pull/22646
         from-commit: b212c00fdc3983678037429719f1b210cb978b42
+  - MUSCLE-5.1.0-GCCcore-12.3.0.eb:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyconfigs/pull/22780
+        from-commit: ff159780fbaa881fb442b0ee1b37cd9e3d981ca9
+  - bcgTree-1.2.1-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22707
+        # and https://github.com/easybuilders/easybuild-easyconfigs/pull/22540
+        # and https://github.com/easybuilders/easybuild-easyconfigs/pull/22781
+        from-commit: 720c5b5b8280bf342d827617ee14738f3d231097

easystacks/software.eessi.io/2023.06/grace/eessi-2023.06-eb-4.9.0-2023a.yml

@@ -0,0 +1,4 @@
+easyconfigs:
+#This is an outdated version of the Z3-4.12.2-GCCcore-12.3.0 easyconfig, adding it to keep sync with the other stacks
+#see https://github.com/easybuilders/easybuild-easyconfigs/pull/20050
+  - Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb

easystacks/software.eessi.io/2023.06/icelake_cclake/001-eb-4.9.4.yml

@@ -0,0 +1,16 @@
+easyconfigs:
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.8.2/easybuild/reprod/EasyBuild-4.8.2.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.8.2/easybuild/reprod/easyblocks/*.py
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.0/easybuild/reprod/EasyBuild-4.9.0.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.0/easybuild/reprod/easyblocks/*.py
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.1/easybuild/reprod/EasyBuild-4.9.1.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.1/easybuild/reprod/easyblocks/*.py
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/5.0.0/easybuild/reprod/EasyBuild-5.0.0.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/5.0.0/easybuild/reprod/easyblocks/*.py
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.4/easybuild/reprod/EasyBuild-4.9.4.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.4/easybuild/reprod/easyblocks/*.py

easystacks/software.eessi.io/2023.06/icelake_cclake/002-eb-4.9.1.yml

@@ -0,0 +1,4 @@
+easyconfigs:
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.2/easybuild/reprod/EasyBuild-4.9.2.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.2/easybuild/reprod/easyblocks/*.py

easystacks/software.eessi.io/2023.06/icelake_cclake/003-eb-4.9.2.yml

@@ -0,0 +1,4 @@
+easyconfigs:
+  - /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.3/easybuild/reprod/EasyBuild-4.9.3.eb:
+      options:
+        include-easyblocks: /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/intel/haswell/software/EasyBuild/4.9.3/easybuild/reprod/easyblocks/*.py

eb_hooks.py

@@ -373,40 +373,6 @@ def parse_hook_freeimage_aarch64(ec, *args, **kwargs):
             print_msg("Changed toolchainopts for %s: %s", ec.name, ec['toolchainopts']) 
 
 
-def parse_hook_lammps_remove_deps_for_aarch64(ec, *args, **kwargs):
-    """
-    Remove x86_64 specific dependencies for the CI and missing installations to pass on aarch64
-    """
-    if ec.name == 'LAMMPS':
-        if ec.version in ('2Aug2023_update2', '29Aug2024'):
-            if os.getenv('EESSI_CPU_FAMILY') == 'aarch64':
-                # ScaFaCoS and tbb are not compatible with aarch64/* CPU targets,
-                # so remove them as dependencies for LAMMPS (they're optional);
-                # see also https://github.com/easybuilders/easybuild-easyconfigs/pull/19164 +
-                # https://github.com/easybuilders/easybuild-easyconfigs/pull/19000;
-                # we need this hook because we check for missing installations for all CPU targets
-                # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
-                ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('ScaFaCoS', 'tbb',)]
-    else:
-        raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
-
-
-def parse_hook_CP2K_remove_deps_for_aarch64(ec, *args, **kwargs):
-    """
-    Remove x86_64 specific dependencies for the CI and missing installations to pass on aarch64
-    """
-    if ec.name == 'CP2K' and ec.version in ('2023.1',):
-        if os.getenv('EESSI_CPU_FAMILY') == 'aarch64':
-            # LIBXSMM is not supported on ARM with GCC 12.2.0 and 12.3.0
-            # See https://www.cp2k.org/dev:compiler_support
-            # See https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
-            # we need this hook because we check for missing installations for all CPU targets
-            # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
-            ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('libxsmm',)]
-    else:
-        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")
-
-
 def parse_hook_zen4_module_only(ec, eprefix):
     """
     Use --force --module-only if building a foss-2022b-based EasyConfig for Zen4.
@@ -1192,8 +1158,6 @@ def post_module_hook(self, *args, **kwargs):
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'FreeImage': parse_hook_freeimage_aarch64,
     'grpcio': parse_hook_grpcio_zlib,
-    'LAMMPS': parse_hook_lammps_remove_deps_for_aarch64,
-    'CP2K': parse_hook_CP2K_remove_deps_for_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,

scripts/gpu_support/nvidia/install_cuda_and_libraries.sh

@@ -96,7 +96,7 @@ for EASYSTACK_FILE in ${TOPDIR}/easystacks/eessi-*CUDA*.yml; do
     echo -e "Processing easystack file ${easystack_file}...\n\n"
 
     # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-    eb_version=$(echo ${EASYSTACK_FILE} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+    eb_version=$(echo ${EASYSTACK_FILE} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
 
     # Load EasyBuild version for this easystack file _before_ loading EESSI-extend
     module_avail_out=${tmpdir}/ml.out