[CIG-MC] PBS batch configurations

Eh Tan tan2 at geodynamics.org
Tue Oct 27 14:55:55 PDT 2009

Robert Moucha wrote:
> Hi Leif and Eh,
> I tried your suggestions, two questions:
> 1) In order for me to specifically use infiniband nodes, I must add
> "ib" to the PBS -l line in the script as follows:
> #PBS -l nodes=2:ib:ppn=8
>   Is this possible, or should I generate the script, edit it to add ib
> and submit it?

I will let Leif answer this question.

> 2) The number of processors np appears to be incorrectly set for
> mpirun, 
> Generates the following output; note that number of nodes for
> pycitcoms is the correct 16, but in the comment the mpirun " -np
> ${nodes} ", is the ${nodes} taken from the PBS line where nodes=2, or
> is taken from the pycitcoms line where --nodes=16.
> -------------------------------------------------

The ${nodes} will be expanded by the value in "--nodes=value". In this
case, 16 will be used.

Eh Tan
Staff Scientist
Computational Infrastructure for Geodynamics
California Institute of Technology, 158-79
Pasadena, CA 91125
(626) 395-1693

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