Adding sbatch params for jobs supporting OpenMPI

OpenOmics · Nov 14, 2023 · ec69f8b · ec69f8b
1 parent 6f9bf2d
commit ec69f8b
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/config/cluster.json b/config/cluster.json
@@ -4,7 +4,10 @@
         "mem": "48g",
         "partition": "norm",
         "threads": "4",
-        "time": "1-18:00:00"
+        "time": "1-18:00:00",
+        "ntasks": "",
+        "ntasks_per_core": "",
+        "exclusive": ""
     },
     "trim": {
         "mem": "64g",
@@ -89,5 +92,13 @@
     "MACS2_narrow": {
         "threads": "4",
         "mem": "50g"
+    },
+    "MEME": {
+        "threads": "56",
+        "mem": "32g",
+        "time": "1-00:00:00",
+        "ntasks": "--ntasks=28",
+        "ntasks_per_core": "--ntasks-per-core=1",
+        "exclusive": "--exclusive"
     }
 }
diff --git a/src/run.sh b/src/run.sh
@@ -192,7 +192,7 @@ function submit(){
           # --keep-remote --restart-times 3 -j 500 --use-singularity 
           # --singularity-args -B {}.format({bindpaths}) --local-cores 24
           SLURM_DIR="$3/logfiles/slurmfiles"
-          CLUSTER_OPTS="sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
+          CLUSTER_OPTS="sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out {cluster.ntasks} {cluster.ntasks_per_core} {cluster.exclusive}"
           # Check if NOT running on Biowulf
           # Assumes other clusters do NOT 
           # have GRES for local node disk,
@@ -207,7 +207,7 @@ function submit(){
           # SLURM is not configured to use 
           # GRES, remove prefix single quote
           if [[ ${6#\'} != /lscratch* ]]; then
-            CLUSTER_OPTS="sbatch --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
+            CLUSTER_OPTS="sbatch --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out {cluster.ntasks} {cluster.ntasks_per_core} {cluster.exclusive}"
           fi
           # Create sbacth script to build index
     cat << EOF > kickoff.sh