add slurm status check

ktmeaton · Oct 2, 2020 · f5da223 · f5da223
1 parent aa7e551
commit f5da223
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diff --git a/profiles/graham/config.yaml b/profiles/graham/config.yaml
@@ -19,3 +19,4 @@ log-handler-script: workflow/scripts/slack_log.py
 
 # slurm execution
 cluster: "sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o /home/keaton/projects/def-briang/keaton/plague-phylogeography/workflow/logs_slurm/{rule}_{wildcards} -e /home/keaton/projects/def-briang/keaton/plague-phylogeography/workflow/logs_slurm/{rule}_{wildcards}"
+cluster-status: workflow/scripts/slurm_status.py
diff --git a/workflow/scripts/slurm_status.py b/workflow/scripts/slurm_status.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+import subprocess
+import sys
+
+jobid = sys.argv[1]
+
+output = str(subprocess.check_output("sacct -j %s --format State --noheader | head -1 | awk '{print $1}'" % jobid, shell=True).strip())
+
+running_status=["PENDING", "CONFIGURING", "COMPLETING", "RUNNING", "SUSPENDED"]
+if "COMPLETED" in output:
+  print("success")
+elif any(r in output for r in running_status):
+  print("running")
+else:
+  print("failed")