[torqueusers] multiple commands in one qsub script

Chandler Wilkerson chwilk at rice.edu
Thu Jun 27 13:34:24 MDT 2013


It's not ideal usage--a job array would be better on a normal cluster. 
In our 32 core/node Power7 (P755) cluster, we don't allow jobs of less 
than 8 cores on our nodes, which are 4-way multi-threaded. Torque 
reports each node as having ppn 128. We tell the serial users who would 
otherwise run single core processes on a ppn=32 slice of the cluster to 
employ this trick with 8 background processes.

I'm sure there's a better way, but this way works for us.

--
Chandler

On 06/27/2013 12:52 PM, Matt Britt wrote:
> Yes, and if you only asked for one processor, doing that just used four
> processors.   If your system allocates by processor and not by whole
> node, this would impact both yourself and other users.  If you did ask
> for 4 processors, it then ties up resources unnecessarily, unless all 4
> jobs end at the same time.
>
> Thanks,
>     - Matt
>
> --------------------------------------------
> Matthew Britt
> CAEN HPC Group - College of Engineering
> msbritt at umich.edu <mailto:msbritt at umich.edu>
>
>
> On Thu, Jun 27, 2013 at 1:50 PM, Jack Wilkinson
> <jwilkinson at stoneeagle.com <mailto:jwilkinson at stoneeagle.com>> wrote:
>
>     In the example you've given, doesn't that put all four jobs on the
>     same box tho?  Not spread across four different nodes?  I'm just
>     curious.
>
>     Thanks!
>     jack
>
>     -----Original Message-----
>     From: torqueusers-bounces at supercluster.org
>     <mailto:torqueusers-bounces at supercluster.org>
>     [mailto:torqueusers-bounces at supercluster.org
>     <mailto:torqueusers-bounces at supercluster.org>] On Behalf Of Chandler
>     Wilkerson
>     Sent: Thursday, June 27, 2013 12:12 PM
>     To: torqueusers at supercluster.org <mailto:torqueusers at supercluster.org>
>     Subject: Re: [torqueusers] multiple commands in one qsub script
>
>     If you would like commands in a qsub script to run in parallel, you
>     can employ a useful trick we've been recommending to some of our users.
>
>     Basically, you allocate multiple cores for your job (on a single
>     node), then run a process per core backgrounded (with the & symbol)
>     then put a wait statement at the end of your script.
>
>     e.g.
>     #PBS -l nodes=1:ppn=4
>     prog1 &
>     prog2 &
>     prog3 &
>     prog4 &
>
>     wait
>
>     This will run the four programs in parallel and wait for all of them
>     to finish before exiting the job.
>
>     On 6/27/13 8:23 AM, Mahmood Naderan wrote:
>      > Hi
>      > Assume I put more than one command in a typical qsub script. Are
>     these
>      > commands executed sequentially or in parallel? For example, the
>     script
>      > looks like
>      >
>      > #PBS -N temporal
>      > #PBS -V
>      > #PBS -q tigerq
>      > #PBS -l nodes=1
>      > cd $PBS_O_WORKDIR
>      > ls
>      > env
>      >
>      > I want to know if 'ls' and 'env' executes in parallel or sequential.
>      > Thanks.
>      > Regards,
>      > Mahmood*
>      > *
>      >
>      >
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