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Merged
bedroge merged 20 commits into from
Apr 16, 2026
Merged

Use sandbox mode which is more robust in singularity cleanup phase #193

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a69b4e6
Use sandbox mode which is more robust in singularity cleanup phase
julianmorillo Mar 26, 2026
47406ac
Now with correct bash syntax
julianmorillo Mar 26, 2026
149dfaf
Now with the singularity build command in place
julianmorillo Mar 26, 2026
46d3725
Merge branch 'main' into build-sandbox
julianmorillo Mar 31, 2026
d06e00f
Make the use of sandbox optional through an environment variable
julianmorillo Mar 31, 2026
8cd8dc7
Merge branch 'main' into build-sandbox
julianmorillo Apr 7, 2026
bfb6e27
Merge branch 'main' into build-sandbox
julianmorillo Apr 9, 2026
2f11ce2
Add --force to avoid error if sandbox build target already exists
julianmorillo Apr 9, 2026
69cc7fa
Merge branch 'build-sandbox' of github.com:julianmorillo/software-lay…
julianmorillo Apr 9, 2026
78cba78
Add the "--force" also to the echo to be consistent
julianmorillo Apr 9, 2026
c075097
Merge branch 'main' into build-sandbox
julianmorillo Apr 13, 2026
62a178f
Add hook for Dyninst (it needs libiberty from binutils provided by
julianmorillo Apr 15, 2026
b91483d
Add specific paths
julianmorillo Apr 15, 2026
eb48ca4
Add log message
julianmorillo Apr 15, 2026
08e9362
Merge branch 'EESSI:main' into build-sandbox
julianmorillo Apr 16, 2026
2a0f763
Remove Dyninst pre-configure hook
julianmorillo Apr 16, 2026
fe3541e
Add sandbox mode option to eessi_container.sh
julianmorillo Apr 16, 2026
3f87df9
Update eessi_container.sh
julianmorillo Apr 16, 2026
3d79958
Allow "-S" as a shortcut for "--sandbox"
julianmorillo Apr 16, 2026
aed015b
Fix indentation
bedroge Apr 16, 2026
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26 changes: 23 additions & 3 deletions eessi_container.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,9 @@ display_help() {
echo " [default: not set]; uses env var \$http_proxy if set"
echo " -y | --https-proxy URL - provides URL for the env variable https_proxy"
echo " [default: not set]; uses env var \$https_proxy if set"
echo " --sandbox - use sandbox mode (i.e. convert .sif image to sandbox and then run"
echo " it instead"
echo " [default: not set]"
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echo
echo " If value for --mode is 'exec' or 'run', the SCRIPT/COMMAND provided is executed. If"
echo " arguments to the script/command start with '-' or '--', use the flag terminator"
Expand Down Expand Up @@ -293,6 +296,10 @@ while [[ $# -gt 0 ]]; do
export https_proxy=${HTTPS_PROXY}
shift 2
;;
--sandbox)
SANDBOX=1
shift 1
;;
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--)
shift
POSITIONAL_ARGS+=("$@") # save positional args
Expand Down Expand Up @@ -1039,10 +1046,23 @@ for arg in "${PASS_THROUGH[@]}"; do
ADDITIONAL_CONTAINER_OPTIONS+=(${arg})
done

echo "Launching container with command (next line):"
echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"
singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} "$@"
# EESSI_SINGULARITY_SANDBOX is an environment variable (typically set in site_config.sh, if needed)
if [[ -n "$EESSI_SINGULARITY_SANDBOX" || $SANDBOX -eq 1 ]]; then
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# using a sandbox image mode is more robust at the cleanup phase at the end
CONTAINER_SANDBOX="${CONTAINER%.sif}.sandbox"
echo "Building a sandbox image with command (next line):"
echo "singularity build --sandbox --force ${CONTAINER_SANDBOX} ${CONTAINER}"
singularity build --sandbox --force ${CONTAINER_SANDBOX} ${CONTAINER}
echo "Launching sandbox container with command (next line):"
echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER_SANDBOX} $@"
singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER_SANDBOX} "$@"
exit_code=$?
else
echo "Launching container with command (next line):"
echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"
singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} "$@"
exit_code=$?
fi

# 6. save tmp if requested (arg -s|--save)
if [[ ! -z ${SAVE} ]]; then
Expand Down
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