Added slurm job submission support

VUmcCGP · Mar 1, 2016 · e3d9efd · e3d9efd
1 parent 26fa9f1
commit e3d9efd
Showing 1 changed file with 40 additions and 0 deletions.
diff --git a/submit/slurm.sh b/submit/slurm.sh
@@ -0,0 +1,40 @@
+# SLURM translator
+submit() {
+    echo ${ARGS[@]}
+	for ARG in ${ARGS[@]}
+	do
+		ANAME=`echo $ARG | cut -d ':' -f1`
+		AVAL=`echo $ARG | cut -d ':' -f2`
+		if [ $ANAME = "cpu" ]
+		then
+			SUBARGS="$SUBARGS -c $(($AVAL<$ARG_JOB_CPU_MAX?$AVAL:$ARG_JOB_CPU_MAX))"
+		fi
+
+		if [ $ANAME = "array" ]
+		then
+			SUBARGS="$SUBARGS -a ${AVAL//,/:}"
+		fi
+	done
+
+	# Obtain hold ids, replace splitting tag by actual arguments
+	HOLDFOR=""
+	if [ ${#REQS} -ne "0" ]
+	then
+		HOLDFOR=`getHoldIds`
+		HOLDFOR=${HOLDFOR//;/,}
+		HOLDFOR="-d ${HOLDFOR/,/}"
+	fi
+
+	# Submit to SGE
+	JOBID=`sbatch \
+		$HOLDFOR \
+		-J $JOB_NAME \
+		-e $FILE_LOG_ERR \
+		-o $FILE_LOG_OUT \
+		$SUBARGS \
+		$NODE \
+		$ADDS`
+
+	# Fix the JobID
+	JOBID=`echo $JOBID | cut -d\  -f4`
+}