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Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables.

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This commit is contained in:
Nate Coraor
2016-01-04 10:54:29 -05:00
parent d24bc3df1e
commit 1c21ba8241
1 changed files with 10 additions and 1 deletions
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lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
+10 -1
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@@ -1,5 +1,14 @@
export GALAXY_SLOTS_CONFIGURED="1"
if [ -n "$SLURM_NTASKS" ] || [ -n "$SLURM_CPUS_PER_TASK" ]; then
if [ -n "$SLURM_CPUS_ON_NODE" ]; then
# This should be valid on SLURM except in the case that srun is used to
# submit additional job steps under an existing allocation, which we do not
# currently do.
GALAXY_SLOTS="$SLURM_CPUS_ON_NODE"
elif [ -n "$SLURM_NTASKS" ] || [ -n "$SLURM_CPUS_PER_TASK" ]; then
# $SLURM_CPUS_ON_NODE should be set correctly on SLURM (even on old
# installations), but keep the $SLURM_NTASKS logic as a backup since this
# was the previous method under SLURM.
#
# Multiply these values since SLURM_NTASKS is total tasks over all nodes.
# GALAXY_SLOTS maps to CPUS on a single node and shouldn't be used for
# multi-node requests.