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Merge branch 'EESSI:main' into main
2 parents 1837764 + 00b1be2 commit f8a32c6

11 files changed

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

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@@ -8,7 +8,6 @@ on:
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permissions:
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contents: read # to fetch code (actions/checkout)
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env:
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EESSI_VERSION: '2023.06'
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EESSI_ACCELERATOR_TARGETS: |
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x86_64/amd/zen2:
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- nvidia/cc80
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fail-fast: false
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matrix:
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include:
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# Arm CPU targets
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# Arm CPU targets (EESSI 2023.06)
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/generic
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_n1
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_v1
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/nvidia/grace
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# x86_64 CPU targets
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# Arm CPU targets (EESSI 2025.06)
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/a64fx
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/generic
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_n1
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_v1
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- runs_on: ubuntu-24.04-arm
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/nvidia/grace
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# x86_64 CPU targets (EESSI 2023.06)
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen2
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen3
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen4
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/haswell
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/sapphirerapids
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/skylake_avx512
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/icelake
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/cascadelake
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2023.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/generic
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# x86_64 CPU targets (EESSI 2025.06)
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen2
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen3
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen4
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/haswell
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/sapphirerapids
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/skylake_avx512
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/icelake
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/cascadelake
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- runs_on: ubuntu-24.04
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EESSI_VERSION: 2025.06
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EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/generic
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runs-on: ${{ matrix.runs_on }}
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steps:
@@ -77,17 +133,17 @@ jobs:
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- name: Check for missing installlations
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run: |
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export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
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source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
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source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
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# set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash),
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# to prevent issues with checks in the Easybuild configuration that use this variable
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export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*}
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export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${EESSI_VERSION}
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export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
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export EESSI_OS_TYPE=linux
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env | grep ^EESSI | sort
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# first check the CPU-only builds for this CPU target
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echo "first run check_missing_installations.sh for CPU-only builds"
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for easystack_file in $(EESSI_VERSION=${EESSI_VERSION} .github/workflows/scripts/only_latest_easystacks.sh); do
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for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} .github/workflows/scripts/only_latest_easystacks.sh); do
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eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
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echo "check missing installations for ${easystack_file} with EasyBuild ${eb_version}..."
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module purge
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for accel in ${accelerators}; do
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module use ${EESSI_SOFTWARE_PATH}/accel/${accel}/modules/all
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echo "checking missing installations for accelerator ${accel} using modulepath: ${MODULEPATH}"
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for easystack_file in $(EESSI_VERSION=${EESSI_VERSION} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
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for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
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eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
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echo "check missing installations for ${easystack_file} with EasyBuild ${eb_version}..."
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module purge
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- name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
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run: |
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export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
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source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
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source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
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# set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash),
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# to prevent issues with checks in the Easybuild configuration that use this variable
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export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*}
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module load EasyBuild
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which eb
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eb --version
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export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${EESSI_VERSION}
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export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
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export EESSI_OS_TYPE=linux
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env | grep ^EESSI | sort
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# create dummy easystack file with a single entry (something that is not installed in EESSI)

‎.github/workflows/test_compare_stacks.yml‎

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matrix:
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EESSI_VERSION:
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- 2023.06
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- 2025.06
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COMPARISON_ARCH:
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- aarch64/a64fx
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- aarch64/neoverse_n1
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- aarch64/neoverse_v1
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- aarch64/nvidia/grace
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- x86_64/intel/sapphirerapids
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- x86_64/intel/icelake
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- x86_64/intel/cascadelake
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exclude:
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- EESSI_VERSION: 2023.06
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COMPARISON_ARCH: aarch64/a64fx
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steps:
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- name: Check out software-layer repository
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

‎bot/build.sh‎

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# symlink everything, except for:
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# - common files like LICENSE and README.md
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# - 'bot' subdirectory, there we need to be a bit more careful (see below)
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for file in $(ls software-layer-scripts | egrep -v 'LICENSE|README.md|^bot'); do
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for file in $(ls software-layer-scripts | egrep -v 'easystacks|LICENSE|README.md|^bot'); do
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ln -s software-layer-scripts/${file}
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done
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‎easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml‎

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- BLAST+-2.14.1-gompi-2023a.eb
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- Valgrind-3.21.0-gompi-2023a.eb
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- OrthoFinder-2.5.5-foss-2023a.eb
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- BWA-0.7.18-GCCcore-12.3.0.eb
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- lit-18.1.2-GCCcore-12.3.0.eb
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# needed due to changed/new dependencies for R-bundle-CRAN-2023.12-foss-2023a.eb
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# without any from-commit this will use a version from April 6, 2024
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# https://github.com/easybuilders/easybuild-easyconfigs/blob/88f6f9c7439c535e62461e6e71b1961c7be118b8/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb
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# EB 5.0.0 has a few changes to that

‎easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023b.yml‎

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# options:
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# from-pr: 20792
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- Valgrind-3.23.0-gompi-2023b.eb
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# recipes taken from https://github.com/EESSI/software-layer/pull/996
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- lit-18.1.7-GCCcore-13.2.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/20902
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from-commit: 79f4cf21490f7f5b187af889be5426c1332a497d
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- astropy-7.0.0-gfbf-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/22469
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from-commit: fc22841fef99cbb2a221c18029b15e692e78c27c
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- PDT-3.25.2-GCCcore-13.2.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/22523
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from-commit: 0044f08898e12cfd31177bfce0747ef2172226d1
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# from here on easyconfigs were originally built with EB 4.9.3
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# originally built with EB 4.9.3, PR 21436 was merged into develop before EB
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# 4.9.4 was released, but maybe it wasn't included in EB 4.9.4, to be on the safe
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# side we just use the commit, PR 3569 was targetting Sapphire Rapids, so likely
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# that is not needed here, however we keep it to stay in sync with what was used
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# for Sapphire Rapids
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- LAMMPS-29Aug2024-foss-2023b-kokkos.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21436
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from-commit: 9dc24e57880a8adb06ae10557c5315e66671a533
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/3569
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include-easyblocks-from-commit: 362b4679193612e04abe336fa041e2a34d183991
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# included for gracehopper on https://github.com/EESSI/software-layer/pull/993
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- SIONlib-1.7.7-GCCcore-13.2.0-tools.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21752
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# NOTE, commit is the last one before the merge commit for PR 21752
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from-commit: 6b8b53493a1188a5baa56a133574daac239730e7
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- Score-P-8.4-gompi-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/3496
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# NOTE, commit is the last one before the merge commit for PR 3496
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include-easyblocks-from-commit: 60633b0acfd41a0732992d9e16800dae71a056eb
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- Cython-3.0.10-GCCcore-13.2.0.eb
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- Mustache-1.3.3-foss-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21783
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# NOTE, commit is the last one before the merge commit for PR 21783
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from-commit: 5fa3db9eb36f91cba3fbf351549f8ba2849abc33
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- GDRCopy-2.4-GCCcore-13.2.0.eb
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# - GROMACS-2024.4-foss-2023b.eb:
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# options:
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# # https://github.com/easybuilders/easybuild-easyconfigs/pull/21851
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# # NOTE, below commit is the merge commit for PR 21851
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# from-commit: f0fa64b440deaf5fb0a6d26ff1bb3e9f36626c8a
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# Disable Gromacs build, there is an error with a test that require a further analysis
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- SlurmViewer-1.0.1-GCCcore-13.2.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21899
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# NOTE, below commit is the merge commit for PR 21899
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from-commit: 0bdeb23c9ea5a3caefd353ecd936919424c1bba4
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- wxWidgets-3.2.6-GCC-13.2.0.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21915
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# NOTE, below commit is the merge commit for PR 21915
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from-commit: 58f16c0caf8c5494c68e9eda8cbf19e9145d3cfa
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- DP3-6.2-foss-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
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# NOTE, below commit is the merge commit for PR 21765
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from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23
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- WSClean-3.5-foss-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
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# NOTE, below commit is the merge commit for PR 21765
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from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23
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- EveryBeam-0.6.1-foss-2023b.eb:
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options:
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/21765
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# NOTE, below commit is the merge commit for PR 21765
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from-commit: c7e4bfe1a57cf9781ce346ba8ae9081644408c23

‎easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-001-system.yml‎

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- Java-11.0.27.eb
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- Java-17.0.15.eb
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- Java-21.0.7.eb
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- Trimmomatic-0.39-Java-11.eb
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- FastQC-0.12.1-Java-11.eb

‎easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023a.yml‎

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options:
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# See https://github.com/easybuilders/easybuild-easyconfigs/pull/22932
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from-commit: 3211d34eb16ff31b8de3dfef55ecaaf1ec205c6f
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- MrBayes-3.2.7-gompi-2023a.eb

‎easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023b.yml‎

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easyconfigs:
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- openCARP-17.0-foss-2023b.eb
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- libheif-1.19.5-GCCcore-13.2.0.eb
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- Subread-2.1.1-GCC-13.2.0.eb

‎easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-001-system.yml‎

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easyconfigs:
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# note: M4 is only listed here because it's a build dependency for GCCcore,
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# but it was still filtered out as dependency when GCCcore/13.3.0 and GCCcore/14.2.0 got built;
4+
# now Autotools/Automake/libtool/M4 are retained as (build) dependency because the newer versions
5+
# in EESSI 2025.06 compat layer can cause problems with some installations (like OpenMPI);
6+
# see also https://github.com/EESSI/software-layer-scripts/pull/74
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- M4-1.4.19.eb

‎easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-2024a.yml‎

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easyconfigs:
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- GCC-13.3.0.eb
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- gfbf-2024a.eb
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- FFTW-3.3.10-GCC-13.3.0

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