Singularity -> Apptainer

broadinstitute · Jan 17, 2025 · ebaaa32 · ebaaa32
1 parent 4c70163
commit ebaaa32
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Showing 2 changed files with 8 additions and 10 deletions.
diff --git a/src/ci/bin/test_slurm.inc.sh b/src/ci/bin/test_slurm.inc.sh
@@ -33,17 +33,18 @@ cromwell::build::slurm::setup_slurm_environment() {
     sudo mkdir -p /var/spool/slurmd
     sudo chown slurm:slurm /var/spool/slurmd
 
-    # Set up an AppArmor profile for singularity to allow non-root users to use it.
+    # Set up an AppArmor profile for Apptainer to allow non-root users to use it.
     # This became required in Ubuntu 24.04
-    sudo tee /etc/apparmor.d/singularity << 'EOF'
+    sudo tee /etc/apparmor.d/apptainer << 'EOF'
 abi <abi/4.0>,
 include <tunables/global>
 
-profile singularity /usr/bin/singularity{,-suid} flags=(unconfined) {
+profile apptainer /usr/bin/apptainer{,-suid} flags=(unconfined) {
   userns,
 }
 EOF
 
+    # Reload to get new profile created above
     sudo systemctl reload apparmor
 
     # A mash of configure-until-it-runs. Feel free to PR suggestions/fixes.

diff --git a/src/ci/resources/slurm_application.conf b/src/ci/resources/slurm_application.conf
@@ -14,27 +14,24 @@ backend {
         # https://slurm.schedmd.com/sbatch.html
         submit-docker = """
             set -euo pipefail
-            CACHE_DIR=$HOME/.singularity/cache
+            CACHE_DIR=$HOME/.apptainer/cache
             mkdir -p $CACHE_DIR
-            LOCK_FILE=$CACHE_DIR/singularity_pull_flock
+            LOCK_FILE=$CACHE_DIR/apptainer_pull_flock
             DOCKER_NAME=$(sed -e 's/[^A-Za-z0-9._-]/_/g' <<< ${docker})
             IMAGE=$CACHE_DIR/$DOCKER_NAME.sif
             (
               flock --verbose --exclusive --timeout 900 9 || exit 1
               if [ ! -e "$IMAGE" ]; then
-                singularity build $IMAGE docker://${docker}
+                apptainer build $IMAGE docker://${docker}
               fi
             ) 9>$LOCK_FILE
 
-            echo "I am..."
-            whoami
-
             sbatch \
               -J ${job_name} \
               -D ${cwd} \
               -o ${cwd}/execution/stdout \
               -e ${cwd}/execution/stderr \
-              --wrap "singularity exec --containall --bind ${cwd}:${docker_cwd} $IMAGE ${job_shell} ${docker_script}"
+              --wrap "apptainer exec --containall --bind ${cwd}:${docker_cwd} $IMAGE ${job_shell} ${docker_script}"
         """
 
         # https://slurm.schedmd.com/scancel.html