fix: set singularity cachedir & tmpdir in submission script

for eddie, need to set cachedir to /exports/eddie/scratch/$USER/.singularity and set sing tmpdir to \$TMPDIR
CCBR · Jan 21, 2025 · 440cee9 · 440cee9
1 parent 1740bc2
commit 440cee9
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Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/charlie b/charlie
@@ -437,7 +437,8 @@ function run() {
     fi
     preruncleanup
 
-    $EXPORT_SING_CACHE_DIR_CMD
+    export SINGULARITY_CACHEDIR=$SING_CACHE_DIR
+    export SINGULARITY_TMPDIR=$TMPDIR
 
     snakemake -s $SNAKEFILE\
     --directory $WORKDIR \
@@ -466,15 +467,15 @@ function run() {
 
     preruncleanup
     cat ${WORKDIR}/config/${PLATFORM}/submit_script.sh |\
-      envsubst '$CLUSTER_PROFILE $CONFIGFILE $EXPORT_SING_CACHE_DIR_CMD $MODULE_LOAD $PARTITION $SINGULARITY_BINDS $SNAKEFILE $trigger $WORKDIR' \
+      envsubst '$CLUSTER_PROFILE $CONFIGFILE $SING_CACHE_DIR $MODULE_LOAD $PARTITION $SINGULARITY_BINDS $SNAKEFILE $trigger $WORKDIR' \
       > ${WORKDIR}/submit_script.sh
     sbatch ${WORKDIR}/submit_script.sh
 
   elif [ "$1" == "qsub" ]; then
 
     preruncleanup
     cat ${WORKDIR}/config/${PLATFORM}/submit_script.sh |\
-      envsubst '$CLUSTER_PROFILE $CONFIGFILE $EXPORT_SING_CACHE_DIR_CMD $MODULE_LOAD $PARTITION $SINGULARITY_BINDS $SNAKEFILE $trigger $WORKDIR' \
+      envsubst '$CLUSTER_PROFILE $CONFIGFILE $SING_CACHE_DIR $MODULE_LOAD $PARTITION $SINGULARITY_BINDS $SNAKEFILE $trigger $WORKDIR' \
       > ${WORKDIR}/run_script.sh
     pushd $WORKDIR && bash run_script.sh && popd
 
@@ -593,12 +594,14 @@ function main(){
   if [[ -z "$SING_CACHE_DIR" ]]; then
     if [[ -d "/data/$USER" ]]; then
       SING_CACHE_DIR="/data/$USER/.singularity"
+    elif [[ "$PLATFORM" == "eddie" ]]; then
+      SING_CACHE_DIR="/exports/eddie/scratch/$USER/.singularity"
     else
       SING_CACHE_DIR="${WORKDIR}/.singularity"
     fi
+    export SING_CACHE_DIR
     echo "singularity cache dir (--singcache) is not set, using ${SING_CACHE_DIR}"
   fi
-  export EXPORT_SING_CACHE_DIR_CMD="export SINGULARITY_CACHEDIR=\"${SING_CACHE_DIR}\""
 
   # required files
   export CONFIGFILE="${WORKDIR}/config.yaml"

diff --git a/config/biowulf/submit_script.sh b/config/biowulf/submit_script.sh
@@ -8,7 +8,7 @@
 
 cd $SLURM_SUBMIT_DIR
 $MODULE_LOAD
-$EXPORT_SING_CACHE_DIR_CMD
+export SINGULARITY_CACHEDIR=$SING_CACHE_DIR
 
 snakemake -s $SNAKEFILE \
     --directory $WORKDIR \

diff --git a/config/eddie/submit_script.sh b/config/eddie/submit_script.sh
@@ -4,7 +4,8 @@
 
 . /etc/profile.d/modules.sh
 $MODULE_LOAD
-$EXPORT_SING_CACHE_DIR_CMD
+export SINGULARITY_CACHEDIR=$SING_CACHE_DIR
+export SINGULARITY_TMPDIR=$TMPDIR
 
 snakemake -s $SNAKEFILE \
     --directory $WORKDIR \

diff --git a/config/fnlcr/submit_script.sh b/config/fnlcr/submit_script.sh
@@ -8,7 +8,7 @@
 
 cd $SLURM_SUBMIT_DIR
 $MODULE_LOAD
-$EXPORT_SING_CACHE_DIR_CMD
+export SINGULARITY_CACHEDIR=$SING_CACHE_DIR
 
 snakemake -s $SNAKEFILE \
     --directory $WORKDIR \