SURF-hpcv · casparvl · Jul 2, 2025 · Jul 8, 2025 · Jul 8, 2025 · Jul 9, 2025
diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
@@ -8,7 +8,6 @@ on:
 permissions:
   contents: read # to fetch code (actions/checkout)
 env:
-  EESSI_VERSION: '2023.06'
   EESSI_ACCELERATOR_TARGETS: |
     x86_64/amd/zen2:
       - nvidia/cc80
@@ -20,33 +19,90 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # Arm CPU targets
+          # Arm CPU targets (EESSI 2023.06)
           - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2023.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/generic
           - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2023.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_n1
           - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2023.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_v1
           - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2023.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/nvidia/grace
-          # x86_64 CPU targets
+          # Arm CPU targets (EESSI 2025.06)
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/a64fx
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/generic
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_n1
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/neoverse_v1
+          - runs_on: ubuntu-24.04-arm
+            EESSI_VERSION: 2025.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: aarch64/nvidia/grace
+          # x86_64 CPU targets (EESSI 2023.06)
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen2
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen3
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen4
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/haswell
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/sapphirerapids
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/skylake_avx512
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/icelake
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/cascadelake
+          - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2023.06
+            EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/generic
+          # x86_64 CPU targets (EESSI 2025.06)
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen2
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen3
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/amd/zen4
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/haswell
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/sapphirerapids
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/skylake_avx512
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/icelake
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/intel/cascadelake
           - runs_on: ubuntu-24.04
+            EESSI_VERSION: 2025.06
             EESSI_SOFTWARE_SUBDIR_OVERRIDE: x86_64/generic
     runs-on: ${{ matrix.runs_on }}
     steps:
@@ -77,17 +133,17 @@ jobs:
         - name: Check for missing installlations
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
-              source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.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%%/*}
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${EESSI_VERSION}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               env | grep ^EESSI | sort
 
               # first check the CPU-only builds for this CPU target
               echo "first run check_missing_installations.sh for CPU-only builds"
-              for easystack_file in $(EESSI_VERSION=${EESSI_VERSION} .github/workflows/scripts/only_latest_easystacks.sh); do
+              for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} .github/workflows/scripts/only_latest_easystacks.sh); do
                   eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
                   echo "check missing installations for ${easystack_file} with EasyBuild ${eb_version}..."
                   module purge
@@ -107,7 +163,7 @@ 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 $(EESSI_VERSION=${EESSI_VERSION} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
+                      for easystack_file in $(EESSI_VERSION=${{matrix.EESSI_VERSION}} ACCEL_EASYSTACKS=1 .github/workflows/scripts/only_latest_easystacks.sh); do
                           eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*.yml/\1/g')
                           echo "check missing installations for ${easystack_file} with EasyBuild ${eb_version}..."
                           module purge
@@ -128,14 +184,14 @@ jobs:
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
-              source /cvmfs/software.eessi.io/versions/${EESSI_VERSION}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.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/${EESSI_VERSION}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.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)

diff --git a/.github/workflows/test_compare_stacks.yml b/.github/workflows/test_compare_stacks.yml
@@ -21,7 +21,9 @@ jobs:
       matrix:
         EESSI_VERSION:
         - 2023.06
+        - 2025.06
         COMPARISON_ARCH:
+        - aarch64/a64fx
         - aarch64/neoverse_n1
         - aarch64/neoverse_v1
         - aarch64/nvidia/grace
@@ -33,6 +35,9 @@ jobs:
         - x86_64/intel/sapphirerapids
         - x86_64/intel/icelake
         - x86_64/intel/cascadelake
+        exclude:
+        - EESSI_VERSION: 2023.06
+          COMPARISON_ARCH: aarch64/a64fx
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

diff --git a/bot/build.sh b/bot/build.sh
@@ -8,7 +8,7 @@ git clone https://github.com/EESSI/software-layer-scripts
 # symlink everything, except for:
 # - common files like LICENSE and README.md
 # - 'bot' subdirectory, there we need to be a bit more careful (see below)
-for file in $(ls software-layer-scripts | egrep -v 'LICENSE|README.md|^bot'); do
+for file in $(ls software-layer-scripts | egrep -v 'easystacks|LICENSE|README.md|^bot'); do
     ln -s software-layer-scripts/${file}
 done
 

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml
@@ -297,3 +297,4 @@ easyconfigs:
   - BLAST+-2.14.1-gompi-2023a.eb
   - Valgrind-3.21.0-gompi-2023a.eb
   - OrthoFinder-2.5.5-foss-2023a.eb
+  - BWA-0.7.18-GCCcore-12.3.0.eb
diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023b.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023b.yml
@@ -107,3 +107,13 @@ easyconfigs:
 #      options:
 #        from-pr: 20792
   - Valgrind-3.23.0-gompi-2023b.eb
+  # recipes taken from https://github.com/EESSI/software-layer/pull/996
+  - lit-18.1.7-GCCcore-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20902
+        from-commit: 79f4cf21490f7f5b187af889be5426c1332a497d
+  - astropy-7.0.0-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/22469
+        from-commit: fc22841fef99cbb2a221c18029b15e692e78c27c
+
diff --git a/...ks/software.eessi.io/2023.06/accel/nvidia/zen4_h100/eessi-2023.06-eb-4.9.4-2023a-CUDA.yml b/...ks/software.eessi.io/2023.06/accel/nvidia/zen4_h100/eessi-2023.06-eb-4.9.4-2023a-CUDA.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - CUDA-12.1.1.eb:
       options:
         accept-eula-for: CUDA
+  - pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb:
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023a.yml
@@ -0,0 +1,12 @@
+easyconfigs:
+  - libheif-1.17.6-GCCcore-12.3.0.eb
+  - GraphicsMagick-1.3.45-GCCcore-12.3.0.eb:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyconfigs/pull/22930
+        # We add also GraphicsMagick explicitly to make sure the version with the fix for libtiff is used
+        from-commit: ca5dddb65171a50207fd8a85559edb4b4844d69b
+  - Octave-10.1.0-foss-2023a.eb:
+      options:
+        # See https://github.com/easybuilders/easybuild-easyconfigs/pull/22932
+        from-commit: 3211d34eb16ff31b8de3dfef55ecaaf1ec205c6f
+  - MrBayes-3.2.7-gompi-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.1.1-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - openCARP-17.0-foss-2023b.eb
+  - libheif-1.19.5-GCCcore-13.2.0.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-2024a.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-2024a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - GCC-13.3.0.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-2025a.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.1.1-2025a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - GCC-14.2.0.eb