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Updated run toil script #6

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Updated run toil script #6

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cd4972e
Removes temp files, saves singularity images
michael-kotliar Dec 13, 2023
4a7bacc
Set default CWL_SINGULARITY_CACHE to SINGULARITY_TMP_DIR
michael-kotliar Dec 13, 2023
30295df
Change the order of params
michael-kotliar Dec 13, 2023
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35 changes: 25 additions & 10 deletions run_toil_REAL.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,16 @@ RUN_ID=$6
TOIL_ENV_FILE=$7
SINGULARITY_TMP_DIR=$8
NJS_CLIENT_PORT=${9:-"3069"}
MEMORY=${10:-"68719476736"}
CPU=${11:-"8"}
CWL_SINGULARITY_CACHE=${10:-"${SINGULARITY_TMP_DIR}"}
MEMORY=${11:-"68719476736"}
CPU=${12:-"8"}


# remove file formats from cwl
sed -i '/"format": /d' $WORKFLOW

JOBSTORE="${TMPDIR}/jobstore"
LOGS="${TMPDIR}/logs/${DAG_ID}_${RUN_ID}"
JOBSTORE="${TMPDIR}/${DAG_ID}_${RUN_ID}/jobstore"
LOGS="${TMPDIR}/${DAG_ID}_${RUN_ID}/logs"


cleanup()
Expand All @@ -34,18 +35,20 @@ cleanup()
trap cleanup SIGINT SIGTERM SIGKILL ERR

/cm/shared/apps/lsf10/10.1/linux3.10-glibc2.17-x86_64/bin/bsub -J "${DAG_ID}_${RUN_ID}" \
-M 16000 \
-M 64000 \
-W 48:00 \
-n 4 \
-R "rusage[mem=16000] span[hosts=1]" \
-R "rusage[mem=64000] span[hosts=1]" \
-o "${OUTDIR}/stdout.txt" \
-e "${OUTDIR}/stderr.txt" << EOL
module purge
module load nodejs anaconda3 singularity/3.7.0
source $TOIL_ENV_FILE
mkdir -p ${OUTDIR} ${TMPDIR} ${JOBSTORE} ${LOGS}
export TMPDIR="${TMPDIR}"
mkdir -p ${OUTDIR} ${LOGS}
rm -rf ${JOBSTORE}
export TMPDIR="${TMPDIR}/${DAG_ID}_${RUN_ID}"
export SINGULARITY_TMPDIR=$SINGULARITY_TMP_DIR
export CWL_SINGULARITY_CACHE=$CWL_SINGULARITY_CACHE
export TOIL_LSF_ARGS="-W 48:00"
toil-cwl-runner \
--logDebug \
Expand All @@ -57,7 +60,7 @@ toil-cwl-runner \
--disableCaching \
--defaultMemory ${MEMORY} \
--defaultCores ${CPU} \
--jobStore "${JOBSTORE}/${DAG_ID}_${RUN_ID}" \
--jobStore "${JOBSTORE}" \
--writeLogs ${LOGS} \
--outdir ${OUTDIR} ${WORKFLOW} ${JOB} > ${OUTDIR}/results.json
EOL
Expand All @@ -75,4 +78,16 @@ RESULTS=`cat ${OUTDIR}/results.json`
PAYLOAD="{\"payload\":{\"dag_id\": \"${DAG_ID}\", \"run_id\": \"${RUN_ID}\", \"results\": $RESULTS}}"
echo "Sending workflow execution results from ${OUTDIR}/results.json"
echo $PAYLOAD
curl -X POST http://localhost:${NJS_CLIENT_PORT}/airflow/results -H "Content-Type: application/json" -d "${PAYLOAD}"
curl -X POST http://localhost:${NJS_CLIENT_PORT}/airflow/results -H "Content-Type: application/json" -d "${PAYLOAD}"

echo "Cleaning temporary directory ${TMPDIR}/${DAG_ID}_${RUN_ID}"
/cm/shared/apps/lsf10/10.1/linux3.10-glibc2.17-x86_64/bin/bsub -J "${DAG_ID}_${RUN_ID}_cleanup" \
-M 16000 \
-W 8:00 \
-n 2 \
-R "rusage[mem=16000] span[hosts=1]" \
-o "${OUTDIR}/cleanup_stdout.txt" \
-e "${OUTDIR}/cleanup_stderr.txt" << EOL
rm -rf "${TMPDIR}/${DAG_ID}_${RUN_ID}"
EOL
/cm/shared/apps/lsf10/10.1/linux3.10-glibc2.17-x86_64/bin/bwait -w "ended(${DAG_ID}_${RUN_ID}_cleanup)"