merging with CCBR/activeDev gerge branch 'activeDev' of https://githu…

…b.com/CCBR/Pipeliner into activeDev
CCBR · Nov 2, 2018 · 1621904 · 1621904
2 parents f2a9b3a + 7e07271
commit 1621904
Showing 1 changed file with 12 additions and 6 deletions.
diff --git a/submit_slurm.template b/submit_slurm.template
@@ -1,5 +1,5 @@
 #!/bin/bash
-#
+
 
 cd $SLURM_SUBMIT_DIR
 
@@ -28,10 +28,16 @@ mv $R/Reports/makeasnake.log $R/Reports/makeasnake.log.$modtime2
 
 touch $R/Reports/makeasnake.log
 touch $R/Reports/snakemake.log
+BUY_IN_NODE=$(ACCOUNT_SPONSOR=$(sacctmgr -rn list user | awk '{print $2}') && scontrol show partitions | grep -i $ACCOUNT_SPONSOR -B1 | grep '^PartitionName' | cut -d '=' -f2 | grep -iv 'gpu'| tr '\n' ',' | sed 's/.$//')
 
-#sbatch $Slrm_J --partition=centos7 --gres=lscratch:200 --time=24:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh
-sbatch $Slrm_J --partition=norm --gres=lscratch:200 --time=10-00:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh
-# sbatch --partition=ccr,norm --gres=lscratch:200 --time=120:00:00  $R/pipeline_ctrl.sh
-
-
+if [[ $BUY_IN_NODE =~ "ccr" ]]; then
+	BUY_IN_NODE="ccr,norm"
+	sed -i 's/\"norm\"/\"ccr,norm\"/g' $R/cluster.json
+else
+	BUY_IN_NODE="norm"
+fi
 
+sbatch $Slrm_J --partition=$BUY_IN_NODE --gres=lscratch:200 --time=120:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh
+#sbatch $Slrm_J --partition=centos7 --gres=lscratch:200 --time=24:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh
+#sbatch $Slrm_J --partition=norm --gres=lscratch:200 --time=10-00:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh
+#sbatch --partition=ccr,norm --gres=lscratch:200 --time=120:00:00  $R/pipeline_ctrl.sh