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Add functionality to eessi_container.sh for specifying if a CVMFS repo should be bind or fuse mounted #50

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Merged
merged 4 commits into from
Aug 1, 2025
Merged

Add functionality to eessi_container.sh for specifying if a CVMFS repo should be bind or fuse mounted #50

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cd6a69c
allow user to specify the mount type of a cvmfs repo (fuse or bind)
bedroge Aug 1, 2025
706af7b
update usage instructions
bedroge Aug 1, 2025
7546e90
add check for bind mounts
bedroge Aug 1, 2025
2edf309
steal CI improvements from PR 51
bedroge Aug 1, 2025
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27 changes: 25 additions & 2 deletions .github/workflows/tests_scripts.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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!
# ${EB_VERSION} should be expanded, so use double quotes;
Expand Down Expand Up @@ -91,6 +92,7 @@ jobs:
- name: test install_software_layer.sh script
run: |
export SINGULARITY_CACHEDIR=$PWD
# bind current directory into container as /software-layer-scripts
export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
# force using x86_64/generic, to avoid triggering an installation from scratch
Expand All @@ -105,6 +107,7 @@ jobs:
- name: test create_directory_tarballs.sh script
run: |
export SINGULARITY_CACHEDIR=$PWD
# bind current directory into container as /software-layer-scripts
export SINGULARITY_BIND="${PWD}:/software-layer-scripts"
Expand All @@ -113,12 +116,13 @@ jobs:
# scripts need to be copied to /tmp,
# since create_directory_tarballs.sh must be accessible from within build container
./eessi_container.sh --mode run --verbose /software-layer-scripts/create_directory_tarballs.sh 2023.06
./eessi_container.sh --mode run --verbose /software-layer-scripts/create_directory_tarballs.sh "${{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"
Expand All @@ -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" ${out} | grep "software.eessi.io" || (echo "software.eessi.io did not seem to be bind mounted!" && exit 1)
72 changes: 54 additions & 18 deletions eessi_container.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -97,8 +97,8 @@ display_help() {
echo " container; can be given multiple times [default: not set]"
echo " -r | --repository CFG - configuration file or identifier defining the"
echo " repository to use; can be given multiple times;"
echo " CFG may include a suffix ',access={ro,rw}' to"
echo " overwrite the global access mode for this repository"
echo " CFG may include suffixes ',access={ro,rw},mode={bind,fuse}' to"
echo " overwrite the global access and/or mount mode for this repository"
echo " [default: software.eessi.io via CVMFS config available"
echo " via default container, see --container]"
echo " -u | --resume DIR/TGZ - resume a previous run from a directory or tarball,"
Expand Down Expand Up @@ -756,14 +756,40 @@ for cvmfs_repo in "${REPOSITORIES[@]}"
do
unset cfg_repo_id
[[ ${VERBOSE} -eq 1 ]] && echo "add fusemount options for CVMFS repo '${cvmfs_repo}'"
# split into name and access mode if ',access=' in $cvmfs_repo
if [[ ${cvmfs_repo} == *",access="* ]] ; then
cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
cvmfs_repo_access=${cvmfs_repo/*,access=/} # remove repo name part
else
cvmfs_repo_name="${cvmfs_repo}"
cvmfs_repo_access="${ACCESS}" # use globally defined access mode
# split into name, access mode, and mount mode
readarray -td, cvmfs_repo_args <<<"$cvmfs_repo"
cvmfs_repo_name=${cvmfs_repo_args[0]}
cvmfs_repo_access="${ACCESS}" # initialize to the default access mode
for arg in ${cvmfs_repo_args[@]:1}; do
if [[ $arg == "access="* ]]; then
cvmfs_repo_access=${arg/access=}
fi
if [[ $arg == "mount="* ]]; then
cvmfs_repo_mount=${arg/mount=}
# check if the specified mount mode is a valid one
if [[ ${cvmfs_repo_mount} != "bind" ]] && [[ ${cvmfs_repo_mount} != "fuse" ]]; then
echo -e "ERROR: mount mode '${cvmfs_repo_mount}' for CVMFS repository\n '${cvmfs_repo_name}' is not known"
exit ${REPOSITORY_ERROR_EXITCODE}
fi
fi
done
# if a mount mode was not specified, we use a bind mount if the repository is available on the host,
# and otherwise we use a fuse mount
if [[ -z ${cvmfs_repo_mount} ]]; then
cvmfs_repo_mount="fuse"
if [[ -x $(command -v cvmfs_config) ]] && cvmfs_config probe ${cvmfs_repo_name} >& /dev/null; then
cvmfs_repo_mount="bind"
fi
fi
[[ ${VERBOSE} -eq 1 ]] && echo "Using a ${cvmfs_repo_mount} mount for /cvmfs/${cvmfs_repo_name}"
# if a bind mount was requested, check if the repository is really available on the host
if [[ ${cvmfs_repo_mount} == "bind" ]]; then
if [[ ! -x $(command -v cvmfs_config) ]] || ! cvmfs_config probe ${cvmfs_repo_name} >& /dev/null; then
echo -e "ERROR: bind mount requested for CVMFS repository\n '${cvmfs_repo_name}', but it cannot be probed on the host"
exit ${REPOSITORY_ERROR_EXITCODE}
fi
fi

# obtain cvmfs_repo_name from EESSI_REPOS_CFG_FILE if cvmfs_repo is in cfg_cvmfs_repos
if [[ ${cfg_cvmfs_repos[${cvmfs_repo_name}]} ]]; then
[[ ${VERBOSE} -eq 1 ]] && echo "repo '${cvmfs_repo_name}' is not an EESSI CVMFS repository..."
Expand Down Expand Up @@ -795,9 +821,12 @@ 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_repo_mount} == "fuse" ]]; then
export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
elif [[ ${cvmfs_repo_mount} == "bind" ]]; then
BIND_PATHS="/cvmfs/${cvmfs_repo_name}:/cvmfs_ro/${cvmfs_repo_name},${BIND_PATHS}"
fi

# now, put the overlay-upper read-only on top of the repo and make it available under the usual prefix /cvmfs
if [[ "${OVERLAY_TOOL}" == "fuse-overlayfs" ]]; then
Expand Down Expand Up @@ -827,10 +856,14 @@ do
# basic "ro" access that doesn't require any fuseoverlay-fs
echo "Mounting '${cvmfs_repo_name}' 'read-only' without fuse-overlayfs."

export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
if [[ ${cvmfs_repo_mount} == "fuse" ]]; then
export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
export EESSI_FUSE_MOUNTS
elif [[ ${cvmfs_repo_mount} == "bind" ]]; then
BIND_PATHS="/cvmfs/${cvmfs_repo_name},${BIND_PATHS}"
fi

EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
export EESSI_FUSE_MOUNTS
fi
elif [[ ${cvmfs_repo_access} == "rw" ]] ; then
# use repo-specific overlay directories
Expand All @@ -840,9 +873,12 @@ 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}")
if [[ ${cvmfs_repo_mount} == "fuse" ]]; then
export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
elif [[ ${cvmfs_repo_mount} == "bind" ]]; then
BIND_PATHS="/cvmfs/${cvmfs_repo_name}:/cvmfs_ro/${cvmfs_repo_name},${BIND_PATHS}"
fi

if [[ "${OVERLAY_TOOL}" == "fuse-overlayfs" ]]; then
EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
Expand Down