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readd /dev/shm and rm SLURM_ARRAY_TASK_MIN check #130

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Feb 26, 2024
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readd /dev/shm and rm SLURM_ARRAY_TASK_MIN check #130

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13 changes: 2 additions & 11 deletions sequence_processing_pipeline/templates/nuqc_job.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,13 @@

echo "---------------"
echo "Run details:"
echo "$SLURM_JOB_NAME $SLURM_JOB_ID $SLURMD_NODENAME"
echo "$SLURM_JOB_NAME $SLURM_JOB_ID $SLURMD_NODENAME $SLURM_ARRAY_TASK_ID"
echo "---------------"

if [[ -z "${SLURM_ARRAY_TASK_ID}" ]]; then
echo "Not operating within an array"
exit 1
fi

if [[ "${SLURM_ARRAY_TASK_MIN}" -ne 1 ]]; then
echo "Min array ID is not 1"
exit 1
fi
if [[ -z ${MMI} ]]; then
echo "MMI is not set"
exit 1
Expand Down Expand Up @@ -56,11 +51,7 @@ fi
# DO NOT do this casually. Only do a clean up like this if
# you know for sure TMPDIR is what you want.

# we might got back to this TMPDIR once the slurm scheduler controls it
# TMPDIR=/dev/shm
# right now, let's use ${OUTPUT}, note that each worker will create a new tmp
# folder two lines below
TMPDIR=${OUTPUT}
TMPDIR=/dev/shm
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export TMPDIR=${TMPDIR}
export TMPDIR=$(mktemp -d)
echo $TMPDIR
Expand Down
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