[torqueusers] Epilogue script

Diego M. Vadell dvadell at linuxclusters.com.ar
Wed Aug 23 21:04:22 MDT 2006


Maybe an alternative: the epilogue script in 
http://bellatrix.pcl.ox.ac.uk/~ben/pbs/ :

" When running parallel jobs on Linux clusters with MPICH and PBS, "slave" 
MPICH processes are often left behind on one or nodes at job abortion. PBS 
makes no attempt to clean up processes on any node except the master node, 
and so these processes can linger for some time. The approach used at the 
WGR/PDL lab is to kill these processes by means of a second MPI-enabled 
program, which is run on the same set of nodes that the main job was run on, 
by the PBS epilogue facility. This program kills all of the user's processes 
that have the relevant PBS job ID in their environment, so should leave other 
jobs on the same machine untouched. To set up this system, this C program 
should be compiled with mpicc and installed as /usr/local/bin/mpicleanup on 
every MPI node. This epilogue script should then be used by PBS on every node 
(usually it needs to be installed as /usr/spool/PBS/mom_priv/epilogue) to 
call the MPICH cleanup program properly at job termination."

I haven't tried it yet.

Hope it helps,
 -- Diego.

On Tuesday 22 August 2006 11:42, Cliff Kirby wrote:
> I currently use an epilogue script to kill all the PIDs of the user but
> that is not the best solution.  Tracking down the child processes of an
> mpirun parallel job is not an easy task because each cluster system
> participating in the parallel job creates unique PID's for the job.
> I hope your question is answered because I am want the same thing you do.
>
> - Cliff
>
> -----Original Message-----
> From: torqueusers-bounces at supercluster.org
> [mailto:torqueusers-bounces at supercluster.org] On Behalf Of Eugene van den
> Hurk
> Sent: Tuesday, August 22, 2006 4:37 AM
> To: torqueusers at supercluster.org
> Subject: [torqueusers] Epilogue script
>
>
> Hello,
>
> I am looking at implementing torque on our cluster.
> I have been looking at using an epilogue script to clean up after
> jobs, particularly if the job is aborted or deleted.
> This seems to be particularly needed in the case when running jobs
> using mpich and mpirun.
> I have looked at using mpiexec instead of mpirun. I installed mpiexec
> and it seems to work fine.
> Can anyone think of any reason why using mpiexec instead of mpirun is
> a bad idea?
> If I use mpiexec instead of mpirun would I be right in thinking that
> it still a good idea to use epilogue
> scripts for other types of jobs.
> Each node is dual processor so I do not want to kill processes based
> on username, as a user may have more than one job on a node.
> So it looks like I would have to use a script that would be able to
> kill orphaned processes based on job id.
> Would anyone have any suggestions as to how I could do this or sample
> scripts that I could try?
> Any help would be greatly appreciated.
>
> Thanks,
> Regards,
> Eugene.
>
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