Merge pull request #152 from bedroge/container_run_call_exec

let EESSI container script's `run` mode call `apptainer exec` instead of `apptainer run`

Author: casparvl

.github/workflows/test_eessi_container_script.yml

@@ -18,6 +18,7 @@ jobs:
         - listrepos_default
         - listrepos_custom
         - no_cvmfs_mounts
+        - exec
         - run
         - shell
         - container
@@ -74,19 +75,30 @@ jobs:
               # test use of --repository None
               elif [[ ${{matrix.SCRIPT_TEST}} == 'no_cvmfs_mounts' ]]; then
                 outfile=out_nocvmfs.txt
-                ./eessi_container.sh --verbose --repository None --mode run mount | tee ${outfile}
+                ./eessi_container.sh --verbose --repository None --mode exec mount | tee ${outfile}
                 # make sure that there are no CVMFS mounts in the container, i.e. mount does not have any lines line:
                 # cvmfs2 on /cvmfs/...
                 ! grep "^cvmfs" ${outfile}
 
-              # test use of --mode run
+              # test use of --mode exec
+              elif [[ ${{matrix.SCRIPT_TEST}} == 'exec' ]]; then
+                outfile=out_exec.txt
+                echo "${test_cmd}" > test_script.sh
+                chmod u+x test_script.sh
+                export SINGULARITY_BIND="$PWD:/test"
+                ./eessi_container.sh --verbose --mode exec /test/test_script.sh | tee ${outfile}
+                grep "${out_pattern}" ${outfile}
+
+              # test use of --mode run, which should now print a warning
               elif [[ ${{matrix.SCRIPT_TEST}} == 'run' ]]; then
                 outfile=out_run.txt
                 echo "${test_cmd}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
                 ./eessi_container.sh --verbose --mode run /test/test_script.sh | tee ${outfile}
                 grep "${out_pattern}" ${outfile}
+                warn_message="Note: the behaviour of the run mode has changed."
+                grep "${warn_message}" ${outfile}
 
               # test use of --mode shell
               elif [[ ${{matrix.SCRIPT_TEST}} == 'shell' ]]; then
@@ -109,7 +121,7 @@ jobs:
                 echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
-                ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile}
+                ./eessi_container.sh --verbose --access rw --mode exec /test/test_script.sh > ${outfile}
 
                 tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g")
                 # note: must use '--access rw' again here, since touched file is in overlay upper dir
@@ -152,7 +164,7 @@ jobs:
                 export SINGULARITY_BIND="$PWD:/test"
                 echo 'ls -ld /cvmfs*/software.eessi.io/*' > test_script.sh
                 chmod u+x test_script.sh
-                ./eessi_container.sh --verbose --container ${container} --access rw --overlay-tool unionfs --mode run /test/test_script.sh 2>&1 | tee ${outfile}
+                ./eessi_container.sh --verbose --container ${container} --access rw --overlay-tool unionfs --mode exec /test/test_script.sh 2>&1 | tee ${outfile}
                 for pattern in "/cvmfs/software.eessi.io/versions" "/cvmfs_ro/software.eessi.io/versions"; do
                   grep "${pattern}" ${outfile} || (echo "Pattern '${pattern}' not found in ${outfile}"; exit 1)
                 done

.github/workflows/tests_scripts.yml

@@ -85,7 +85,7 @@ jobs:
 
           # run wrapper script + capture & check output
           out="${PWD}/eb-${EB_VERSION}.out"
-          ./eessi_container.sh --access rw --mode run --verbose /software-layer-scripts/run_in_compat_layer_env.sh /software-layer-scripts/eb-${EB_VERSION}.sh 2>&1 | tee ${out}
+          ./eessi_container.sh --access rw --mode exec --verbose /software-layer-scripts/run_in_compat_layer_env.sh /software-layer-scripts/eb-${EB_VERSION}.sh 2>&1 | tee ${out}
           pattern="^This is EasyBuild ${EB_VERSION} "
           grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)
         done
@@ -103,7 +103,7 @@ jobs:
           # make sure that correct EESSI version is used (required because default is a placeholder version)
           export EESSI_VERSION_OVERRIDE="${{matrix.EESSI_VERSION}}"
 
-          ./eessi_container.sh --mode run --verbose /software-layer-scripts/install_software_layer.sh
+          ./eessi_container.sh --mode exec --verbose /software-layer-scripts/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script
       run: |
@@ -116,7 +116,7 @@ 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 "${{matrix.EESSI_VERSION}}"
+          ./eessi_container.sh --mode exec --verbose /software-layer-scripts/create_directory_tarballs.sh "${{matrix.EESSI_VERSION}}"
           # check if tarballs have been produced
           ls -l *.tar.gz
 
@@ -140,7 +140,7 @@ jobs:
           export EESSI_VERSION_OVERRIDE="${{matrix.EESSI_VERSION}}"
 
           out="${PWD}/test_create_lmodsitepackage.out"
-          ./eessi_container.sh --mode run --verbose /software-layer-scripts/run_in_compat_layer_env.sh /software-layer-scripts/test_lmod_sitepackage.sh 2>&1 | tee ${out}
+          ./eessi_container.sh --mode exec --verbose /software-layer-scripts/run_in_compat_layer_env.sh /software-layer-scripts/test_lmod_sitepackage.sh 2>&1 | tee ${out}
           for pattern in "^Site Pkg location.*/software-layer-scripts/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*/software-layer-scripts/.lmod/SitePackage.lua"; do
             grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)
           done
@@ -160,6 +160,6 @@ jobs:
           export EESSI_VERSION_OVERRIDE="${{matrix.EESSI_VERSION}}"
 
           out="${PWD}/eb-${EB_VERSION}.out"
-          ./eessi_container.sh --repository software.eessi.io,access=rw,mount=bind --mode run --verbose /software-layer-scripts/run_in_compat_layer_env.sh ls 2>&1 | tee ${out}
+          ./eessi_container.sh --repository software.eessi.io,access=rw,mount=bind --mode exec --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

@@ -86,7 +86,7 @@ display_help() {
   echo "                            [default: /..storage../opt-eessi]"
   echo "  -l | --list-repos       - list available repository identifiers [default: false]"
   echo "  -m | --mode MODE        - with MODE==shell (launch interactive shell) or"
-  echo "                            MODE==run (run a script or command) [default: shell]"
+  echo "                            MODE==exec/run (run a script or command) [default: shell]"
   echo "  -n | --nvidia MODE      - configure the container to work with NVIDIA GPUs,"
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
@@ -119,7 +119,7 @@ display_help() {
   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
-  echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
+  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"
   echo " '--' to let eessi_container.sh stop parsing arguments."
 }
@@ -377,10 +377,18 @@ fi
 # HOST_STORAGE_ERROR_EXITCODE
 
 # (arg -m|--mode) check if MODE is known
-if [[ "${MODE}" != "shell" && "${MODE}" != "run" ]]; then
+if [[ "${MODE}" != "shell" && "${MODE}" != "exec" && "${MODE}" != "run" ]]; then
     fatal_error "unknown execution mode '${MODE}'" "${MODE_UNKNOWN_EXITCODE}"
 fi
 
+# the run mode should actually call "apptainer exec", so simply override run to exec
+if [[ "${MODE}" == "run" ]]; then
+    echo_yellow "Note: the behaviour of the run mode has changed."
+    echo_yellow "Previously, it mistakenly ran 'apptainer/singularity run', but it now runs 'apptainer/singularity exec' instead."
+    echo_yellow "You can silence this message by using --mode exec instead of --mode run."
+    MODE="exec"
+fi
+
 # Also validate the NVIDIA GPU mode (if present)
 if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
     if [[ "${NVIDIA_MODE}" != "run" && "${NVIDIA_MODE}" != "install" && "${NVIDIA_MODE}" != "all" ]]; then
@@ -443,8 +451,8 @@ done
 # TODO (arg -y|--https-proxy) check if https proxy is accessible
 # HTTPS_PROXY_ERROR_EXITCODE
 
-# check if a script is provided if mode is 'run'
-if [[ "${MODE}" == "run" ]]; then
+# check if a script is provided if mode is 'exec'
+if [[ "${MODE}" == "exec" ]]; then
   if [[ $# -eq 0 ]]; then
     fatal_error "no command specified to run?!" "${RUN_SCRIPT_MISSING_EXITCODE}"
   fi