[CIG-MC] PBS batch configurations
leif at geodynamics.org
Tue Oct 27 18:40:24 PDT 2009
In that case, I would insert "ib" directly into line 99 of your
~/.pyre/CitcomS/schedulers/pbs.odb file -- i.e., change
"nodes=%d:ppn=%d" % ...
"nodes=%d:ib:ppn=%d" % ...
Then, remove "resource-list" from your .cfg file.
I'll try to figure out a name for the above string, so it can be
customized from .cfg files in future versions of the code.
Robert Moucha wrote:
> Thanks so much for your help on this Leif. I believe we are almost
> there. I did what you said and the dry run now gives:
> #PBS -l ib,nodes=2:ppn=8,walltime=1:00:00
> I do not know the syntax that is expected, but from what I gather the
> ib should be followed by : not a ,
> or something a long the line (as given by our cluster user wiki):
> #PBS -l nodes=2:ib:ppn=8,walltime=1:00:00
> On Tue, Oct 27, 2009 at 7:04 PM, Leif Strand <leif at geodynamics.org> wrote:
>> Robert Moucha wrote:
>>> 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?
>> Our code doesn't allow for this; fortunately, it is easy to patch.
>> Place the attached file in a new subdirectory named "schedulers" alongside
>> your CitcomS.cfg file:
>> mkdir ~/.pyre/CitcomS/schedulers
>> mv pbs.odb ~/.pyre/CitcomS/schedulers/
>> You will now be able to use a new "resource-list" option:
>> ppn = 8 ; processors per node
>> resource-list = ib
>> Note that nodes/ppn/walltime will be added by the Python code.
Sent from my Newton
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