[torqueusers] PBS in Cluster

Tim timlee126 at yahoo.com
Mon Feb 1 15:12:24 MST 2010


Thanks, Axel!

Are you saying that if submit several background jobs, for better control of assignment of resources via PBS commands, better not to put them into a single PBS file and submit the file just once, but to put each job in different PBS files and submit the PBS files one by one?

If yes, I think I do not need to put the jobs in background, since the reason I want to background them is because I have these several jobs in a single file and I want to run them in parallel instead of one start after another finishes.


--- On Mon, 2/1/10, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:

> From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
> Subject: Re: [torqueusers] PBS in Cluster
> To: "Tim" <timlee126 at yahoo.com>
> Cc: torqueusers at supercluster.org
> Date: Monday, February 1, 2010, 9:29 AM
> On Sat, Jan 30, 2010 at 7:58 PM, Tim
> <timlee126 at yahoo.com>
> wrote:
> > Hi,
> 
> tim,
> 
> > I am learning and have some questions about using PBS
> to submit jobs in a cluster.
> >
> > (1) If not using qsub to submit a job, will the job be
> running only on the single node where it is submitted?
> >
> > Even if the job is parallelized by MPI and run by
> mpirun, is it still running on the single node, not the
> others?
> >
> > So is qsub used for submit job to running on other
> nodes in the cluster?
> 
> qsub will ask to reserve nodes but it knows nothing about
> MPI.
> similarly mpirun can be set up so that it will as the batch
> system
> about which nodes are reserved for it, but this is not
> needlessly so.
> you can use mpirun interactively and without batch/qsub by
> providing
> a host list. some MPI libraries do need this always. hence
> $PBS_NODEFILE.
> 
> >
> > (2) In a pbs script that is submitted by qsub, are all
> the commands executed one after the other?
> 
> it is a regular shell script.
> 
> > If I want to run several executables at the same time,
> is it to make these calls background by adding "&" at
> the end?
> 
> if you background them, they will execute in parallel. if
> you need
> them in sequence,
> you can try using job dependencies (-W afterok:####).
> 
> > (3) In the pbs script, if the several calls to run the
> executables are running the same time by running background,
> are the number of nodes and processors per nodes specified
> to be the total needed by all those calls?
> 
> the script submitted to qsub will run as a regular shell
> script on the
> first(!) host assigned to the job.
> no job distribution or limitation is done. exectly this is
> why one
> would submit each execution in
> separate jobs. if you use OpenMPI, you can consider using
> an appfile
> to scatter multiple jobs
> across the allocated nodes, but keep in mind, that when
> those jobs
> take different amounts of
> time, you'll have idle nodes that cannot be used by other
> jobs.
> 
> > If yes, and the number of nodes and processors per
> nodes specified are not completely available but enough to
> run some of the calls, will some of these calls be run first
> or delayed until the requested total resources are
> completely available?
> 
> again, this kind of load balancing is exactly what batch
> systems in
> itself are for.
> just submit all requests in individual qsub statements and
> all this will happen.
> 
> cheers,
>     axel.
> 
> > Thanks and regards!
> >
> >
> >
> > _______________________________________________
> > torqueusers mailing list
> > torqueusers at supercluster.org
> > http://www.supercluster.org/mailman/listinfo/torqueusers
> >
> 
> 
> 
> -- 
> Dr. Axel Kohlmeyer    akohlmey at gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 


      


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