Slurm no longer supports --workdir

bbimber · bbimber · commit 1084c624c8c7 · 2022-03-26T06:30:39.000-07:00
diff --git a/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java b/cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java
@@ -527,9 +527,11 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                         writer.write(line + "\n");
                     }
 
-                    writer.write("#SBATCH --workdir=\"" + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\"\n");
+                    // NOTE: --workdir no longer support in sbatch
+                    //writer.write("#SBATCH --workdir=\"" + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\"\n");
 
                     String args = StringUtils.join(getConfig().getJobArgs(outDir, serializedJobFile, job, this), " ");
+                    writer.write("cd " + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\n");
                     writer.write("srun " + getConfig().getRemoteExecutable() + " " + args);
                 }
             }

Original file line number	Diff line number	Diff line change
`@@ -527,9 +527,11 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException`
`527`	`527`	`writer.write(line + "\n");`
`528`	`528`	`}`
`529`	`529`
`530`		`- writer.write("#SBATCH --workdir=\"" + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\"\n");`
	`530`	`+ // NOTE: --workdir no longer support in sbatch`
	`531`	`+ //writer.write("#SBATCH --workdir=\"" + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\"\n");`
`531`	`532`
`532`	`533`	`String args = StringUtils.join(getConfig().getJobArgs(outDir, serializedJobFile, job, this), " ");`
	`534`	`+ writer.write("cd " + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\n");`
`533`	`535`	`writer.write("srun " + getConfig().getRemoteExecutable() + " " + args);`
`534`	`536`	`}`
`535`	`537`	`}`