Symlink status-sacct-multi.sh

README.md

@@ -50,7 +50,7 @@ post][sichong-post] by Sichong Peng nicely explains this strategy for replacing
 
 * **New** Full support for [multi-cluster setups][multi_cluster] (using a custom
   status script requires Snakemake 7.1.1+). See the section [Multiple
-  clusters][#multiple-clusters] below
+  clusters](#multiple-clusters) below
 
 ## Limitations
 
@@ -222,6 +222,9 @@ status of the jobs. You can choose which one you'd like to use:
   from the [official profile][slurm-official]. If your HPC cluster doesn't have
   `sacct` configured, you can use this option
 
+* `status-sacct-multi.sh` - Support for multi-cluster setup (see section
+  [Multiple clusters](#multiple-clusters))
+
 To use one of these status scripts:
 
 1. Download the script to your profile directory where `config.yaml` is located

examples/multi-cluster/README.md

@@ -32,3 +32,6 @@ snakemake --profile simple/
 # Confirm the correct cluster was used
 cat output/cluster.txt
 ```
+
+**Note:** The file `simple/status-sacct-multi.sh` is a symlink to the actual
+file in `extras/`

examples/multi-cluster/simple/status-sacct-multi.sh

@@ -0,0 +1 @@
+../../../extras/status-sacct-multi.sh

extras/README.md

@@ -23,3 +23,6 @@ Scripts:
 
 * `status-scontrol.sh` - Bash script that uses `scontrol` to determine job
   status
+
+* `status-sacct-multi.sh` - Bash script that uses `sacct` to determine job
+  status in a multi-cluster setup

extras/status-sacct-multi.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+# Check status of Slurm job submitted to one of multiple clusters
+
+arg="$1"
+jobid="${arg%%;*}"
+cluster="${arg##*;}"
+
+output=`sacct --clusters="$cluster" -j "$jobid" --format State --noheader | head -n 1 | awk '{print $1}'`
+
+if [[ $output =~ ^(COMPLETED).* ]]
+then
+  echo success
+elif [[ $output =~ ^(RUNNING|PENDING|COMPLETING|CONFIGURING|SUSPENDED).* ]]
+then
+  echo running
+else
+  echo failed
+fi