[GE users] File copy from local /scratch on job termination

reuti reuti at staff.uni-marburg.de
Mon Dec 15 14:20:25 GMT 2008


Hi,

Am 15.12.2008 um 15:09 schrieb Bart Willems:

> I recently urged our cluster users to use local scratch space on the
> cluster nodes instead of the NFS mounted RAID during their  
> calculations.
> In the example submission file below all required files for the job  
> are
> copied over to the node's local hard disk ($TMPDIR is /scratch) and  
> copied
> back when the job completes. However, the files only get copied  
> back when
> the job exits normally. If SGE terminates the job because it  
> exceeds the
> requested CPU time or if a user manually terminates a job with  
> qdel, the
> files are not copied back from the node's local hard disk to the  
> RAID. Is
> there any way around this?

yes.

> Thanks,
> Bart
>

You have to submit the job with -notify


> #!/bin/bash
>
> #$ -S /bin/bash
> #$ -j y
> #$ -N helloworld_test
> #$ -l h_cpu=00:02:00
> #$ -cwd

# Two single quotes
trap '' usr1 usr2


> # Copy job files to local scratch space
> JOBFILE=jobfiles.job-id-$JOB_ID.tgz
> tar cfz $JOBFILE helloworld
> cp $JOBFILE $TMPDIR
> rm -rf $JOBFILE
> cd $TMPDIR
> tar xfz $JOBFILE
> rm -rf $JOBFILE

Maybe you can avoid the local file:

tar cj helloworld | tar xj -C $TMPDIR
cd $TMPDIR

> # Computational command to run
> ./helloworld

replace with:

(trap - usr1 usr2; exec ./helloworld)


> # Copy all files back.
> OUTFILE=outfiles.job-id-$JOB_ID.tgz
> tar cfz $OUTFILE *
> cp $OUTFILE $SGE_CWD_PATH
> cd $SGE_CWD_PATH
> tar xfz $OUTFILE
> rm -rf $OUTFILE

tar -cj $OUTFILE * | tar xj -C $SGE_CWD_PATH


HTH - Reuti


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