From 3c97d30cd6b4f11270fc1e057f236f420542cfea Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 13 Apr 2016 10:32:05 +0200 Subject: [PATCH] Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. --- .../jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh index 3e59bbd0770..624f77c4535 100644 --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh @@ -15,6 +15,8 @@ elif [ -n "$SLURM_NTASKS" ] || [ -n "$SLURM_CPUS_PER_TASK" ]; then GALAXY_SLOTS=`expr "${SLURM_NTASKS:-1}" \* "${SLURM_CPUS_PER_TASK:-1}"` elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" +elif [ -n "$NCPUS" ]; then + GALAXY_SLOTS="$NCPUS" elif [ -n "$PBS_NCPUS" ]; then GALAXY_SLOTS="$PBS_NCPUS" elif [ -f "$PBS_NODEFILE" ]; then