Use the system cvmfs repositories for eessi_container.sh if they are available

.github/workflows/tests_scripts.yml

@@ -45,13 +45,14 @@ jobs:
 
     - name: test load_easybuild_module.sh script
       run: |
+        export SINGULARITY_CACHEDIR=$PWD
         # bind current directory into container as /software-layer-scripts
         export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
 
         # can't test with EasyBuild versions older than v4.5.2 when using EESSI 2023.06,
         # since Python in compat layer is Python 3.11.x;
         # testing with a single EasyBuild version takes a while in GitHub Actions, so stick to a single sensible version
-        for EB_VERSION in '4.6.0'; do
+        for EB_VERSION in '5.1.0'; do
           # Create script that uses load_easybuild_module.sh which we can run in compat layer environment
           # note: Be careful with single vs double quotes below!
           #       ${EB_VERSION} should be expanded, so use double quotes;
@@ -91,6 +92,7 @@ jobs:
 
     - name: test install_software_layer.sh script
       run: |
+          export SINGULARITY_CACHEDIR=$PWD
           # bind current directory into container as /software-layer-scripts
           export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
           # force using x86_64/generic, to avoid triggering an installation from scratch
@@ -105,6 +107,7 @@ jobs:
 
     - name: test create_directory_tarballs.sh script
       run: |
+          export SINGULARITY_CACHEDIR=$PWD
           # bind current directory into container as /software-layer-scripts
           export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
 
@@ -113,12 +116,13 @@ jobs:
 
           # scripts need to be copied to /tmp,
           # since create_directory_tarballs.sh must be accessible from within build container
-          ./eessi_container.sh --mode run --verbose /software-layer-scripts/create_directory_tarballs.sh 2023.06
+          ./eessi_container.sh --mode run --verbose /software-layer-scripts/create_directory_tarballs.sh "${{matrix.EESSI_VERSION}}"
           # check if tarballs have been produced
           ls -l *.tar.gz
 
     - name: test create_lmodsitepackage.py script
       run: |
+          export SINGULARITY_CACHEDIR=$PWD
           # bind current directory into container as /software-layer-scripts
           export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
 
@@ -140,3 +144,22 @@ jobs:
           for pattern in "^Site Pkg location.*/software-layer-scripts/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*/software-layer-scripts/.lmod/SitePackage.lua"; do
             grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)
           done
+
+    - name: Mount EESSI CernVM-FS repository
+      uses: eessi/github-action-eessi@v3
+      with:
+        eessi_stack_version: ${{matrix.EESSI_VERSION}}
+        use_eessi_module: true
+
+    - name: Verify that mounted repositories are passed through directly
+      run: |
+          export SINGULARITY_CACHEDIR=$PWD
+          # run wrapper script + capture & check output
+          export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
+          # make sure that correct EESSI version is used (required because default is a placeholder version)
+          export EESSI_VERSION_OVERRIDE="${{matrix.EESSI_VERSION}}"
+
+          out="${PWD}/eb-${EB_VERSION}.out"
+          ./eessi_container.sh --access rw --mode run --verbose /software-layer-scripts/run_in_compat_layer_env.sh ls 2>&1 | tee ${out}
+          echo $(grep "SINGULARITY_BIND" ${out})
+          grep "SINGULARITY_BIND" ${out} | grep "software.eessi.io" || (echo "software.eessi.io did not seem to be bind mounted!" && exit 1)

eessi_container.sh

@@ -747,7 +747,14 @@ declare -a EESSI_FUSE_MOUNTS=()
 # mount cvmfs-config repo (to get access to EESSI repositories such as software.eessi.io) unless env var
 # EESSI_DO_NOT_MOUNT_CVMFS_CONFIG_CERN_CH is defined
 if [ -z ${EESSI_DO_NOT_MOUNT_CVMFS_CONFIG_CERN_CH+x} ]; then
-    EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
+    if cvmfs_config stat cvmfs-config.cern.ch ; then
+      # if the system has the repo available just pass it through
+      BIND_PATHS="${BIND_PATHS},/cvmfs/cvmfs-config.cern.ch:/cvmfs/cvmfs-config.cern.ch"
+    else
+      # otherwise use apptainer capabilities to make it available within the container
+      EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
+      export EESSI_FUSE_MOUNTS
+    fi
 fi
 
 
@@ -795,9 +802,14 @@ do
             echo "  session. Will use it as left-most directory in 'lowerdir' argument for fuse-overlayfs."
 
             # make the target CernVM-FS repository available under /cvmfs_ro
-            export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
-
-            EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+            if cvmfs_config stat ${cvmfs_repo_name} ; then
+              # if the system has the repo available just pass it through
+              BIND_PATHS="${BIND_PATHS},/cvmfs/${cvmfs_repo_name}:/cvmfs_ro/${cvmfs_repo_name}"
+            else
+              # otherwise use apptainer capabilities to make it available within the container
+              export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
+              EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+            fi
 
             # now, put the overlay-upper read-only on top of the repo and make it available under the usual prefix /cvmfs
             if [[ "${OVERLAY_TOOL}" == "fuse-overlayfs" ]]; then
@@ -827,10 +839,15 @@ do
             # basic "ro" access that doesn't require any fuseoverlay-fs
             echo "Mounting '${cvmfs_repo_name}' 'read-only' without fuse-overlayfs."
 
-            export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
-
-            EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
-            export EESSI_FUSE_MOUNTS
+            if cvmfs_config stat ${cvmfs_repo_name} ; then
+              # if the system has the repo available just pass it through
+              BIND_PATHS="${BIND_PATHS},/cvmfs/${cvmfs_repo_name}:/cvmfs/${cvmfs_repo_name}"
+            else
+              # otherwise use apptainer capabilities to make it available within the container
+              export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
+              EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+              export EESSI_FUSE_MOUNTS
+            fi
         fi
     elif [[ ${cvmfs_repo_access} == "rw" ]] ; then
         # use repo-specific overlay directories
@@ -839,10 +856,15 @@ do
 
         [[ ${VERBOSE} -eq 1 ]] && echo -e "TMP directory contents:\n$(ls -l ${EESSI_TMPDIR})"
 
-        # set environment variables for fuse mounts in Singularity container
-        export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
-
-        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        # make the target CernVM-FS repository available under /cvmfs_ro
+        if cvmfs_config stat ${cvmfs_repo_name} ; then
+          # if the system has the repo available just pass it through
+          BIND_PATHS="${BIND_PATHS},/cvmfs/${cvmfs_repo_name}:/cvmfs_ro/${cvmfs_repo_name}"
+        else
+          # otherwise use apptainer capabilities to make it available within the container
+          export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
+          EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        fi
 
         if [[ "${OVERLAY_TOOL}" == "fuse-overlayfs" ]]; then
             EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"