[torqueusers] PBS in Cluster

Garrick Staples garrick at usc.edu
Mon Feb 1 11:13:05 MST 2010

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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