[torqueusers] PBS in Cluster

Tim timlee126 at yahoo.com
Mon Feb 1 15:15:57 MST 2010


Thanks, Garrick!

--- On Mon, 2/1/10, Garrick Staples <garrick at usc.edu> wrote:

> From: Garrick Staples <garrick at usc.edu>
> Subject: Re: [torqueusers] PBS in Cluster
> To: torqueusers at supercluster.org
> Date: Monday, February 1, 2010, 1:13 PM
> On Sat, Jan 30, 2010 at 04:58:10PM
> -0800, Tim alleged:
> > Hi,
> > 
> > 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? 
> 
> If you didn't use qsub, then the job was never submitted.
> There is no "job".
> 
>  
> > 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 is how you create a job. It is used for all jobs of
> all types.
> 
> 
> > (2) In a pbs script that is submitted by qsub, are all
> the commands executed one after the other? 
> 
> Yup. It is just a shell script. It follows the rules of
> whatever shell you have
> in the #! line at the top.
> 
>  
> > If I want to run several executables at the same time,
> is it to make these calls background by adding "&" at
> the end?
> 
> Yup. And you probably want to 'wait' for backgrounded
> processes at the end of
> the script.
> 
>  
> > (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?
> 
> That would be the common case, yes, but it is up to you to
> actually do it.
> 
> If you want processes on other nodes, then you script needs
> to use ssh or TM to
> spawn remote processes. 'pbsdsh' and OSC's mpiexec are
> handy utilities.
> 
>  
> > 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?
> 
> The batch script just does whatever you code it do it. If
> you code 100
> background processes, then you get 100 background
> processes.
> 
> PBS does not intervene with the execution of your script.
> At runtime, the list
> of assigned nodes is in $PBS_NODESFILE. Your script should
> look at that file to
> determine what to do.
> 
> -- 
> Garrick Staples, GNU/Linux HPCC SysAdmin
> University of Southern California
> 
> Life is Good!
> 
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