[CIG-MC] Running citcoms using pbs scheduler

[Dan Bower]

Hi all,

I'd like to load modules in the citcoms submission script, something
like (see ***):

#!/bin/sh
#PBS -S /bin/sh
#PBS -N ghk16b
#PBS -q default
#PBS -o stdout.txt
#PBS -e stderr.txt
#PBS -l nodes=96:ppn=1,walltime=2160:00:00

module load intel/intel-11 ***
module load mpich/intel-11 ***

cd $PBS_O_WORKDIR
/home/danb/cig/CitcomS_assim/bin/pycitcoms --pyre-start
/home/danb/cig/CitcomS_assim/python/merlin-1.7.egg:/home/danb/cig/CitcomS_assim/python/Cheetah-2.0rc8-py2.5-linux-x86_64.egg:/panfs/panasas-1/home/danb/cig/CitcomS_assim:/home/danb/cig/CitcomS_assim/python/pythia-0.8.1.11-py2.6.egg:/panfs/panasas-1/home/danb/cig/CitcomS_assim/bin:/home/danb/cig/CitcomS_assim/python:/net/beno/home1/danb/gplates_citcoms_utils:/usr/python26/lib/python26.zip:/usr/python26/lib/python2.6/lib-dynload:/usr/python26/lib/python2.6/site-packages:/usr/python26/lib/python2.6:/usr/python26/lib/python2.6/plat-linux2:/usr/python26/lib/python2.6/lib-tk:/usr/python26/lib/python2.6/lib-old
pythia pyre.schedulers:jobstart
--scheduler-class=pyre.schedulers.SchedulerPBS:SchedulerPBS
CitcomS.SimpleApp:SimpleApp --scheduler.dry ghk16b.cfg --nodes=96
--macros.nodes=96 --macros.job.name=ghk16b


Is there a way I can include these commands?  I've forwarded a
previous discussion which provides a way to include another #PBS
option, but is there a way to include something without the #PBS
prefix?

Thanks in advance,

Dan




---------- Forwarded message ----------
From: Eh Tan <tan2 at mail.utexas.edu>
Date: Sat, Mar 13, 2010 at 12:31 PM
Subject: Re: [CIG-MC] running citcoms using pbs scheduler
To: CLINT CONRAD <clintc at hawaii.edu>, cig-mc at geodynamics.org


Hi Clint,

You can add the following lines to your input cfg file:

   [CitcomS.scheduler]
   qsub-options = "-A STAFF0000"


This is a generic option. You can add arbitrary PBS options via:
    qsub-options = opt1,opt2,...


Cheers,
Eh Tan
-------
Postdoc
Institute of Geophysics
University of Texas, Austin
J.J. Pickle Research Campus, Bldg 196 (ROC)
10100 Burnet Rd. (R2200),
Austin, TX 78758-4445
(512) 475-9568


CLINT CONRAD wrote:
> Hi,
>
> I am setting up some CitcomS runs on a new shared system.  We are
> required to submit jobs using the pbs system in a slightly different
> way than I have done before. Specifically, we have to submit an
> account number using
> #PBS -A accountnumber
> It seems that -A is not included in the job or scheduler options that
> you can set in the Citcom.cfg file.
> (the available options are: name, queue, walltime, stdin, stdout, and
> stderr). Is there an easy way to run citcom using pbs scheduler
> that allows me to input the account? I've pasted a sample pbs script
> below for running on this system.
>
> Thanks in advance for any help!
> Clint
>
> #!/bin/bash
> # 10 minute wall time
> #PBS -l walltime=00:10:00
> # selecting 2 nodes = 2 * 4 = 8 processors for use, mpiprocs needs to
> equal ncpus and doesn't exceed 4
> #PBS -l select=2:mpiprocs=4:ncpus=4
> # scatter required
> #PBS -l place=scatter
> # account required
> #PBS -A STAFF0000
>
> cd $PBS_O_WORKDIR
> echo "RUNNING ON: `/usr/bin/uniq $PBS_NODEFILE`"
> # note you must use mpirun_jaws to submit MPI jobs on our cluster
> mpirun_jaws ./my_openmpi_executable
>
>
>
>
>
> ---------------------------------------------
> Clint Conrad              Assistant Professor
> Dept. Geology & Geophysics,  SOEST,  804 POST
> Univ. Hawaii at Manoa        ph: 808-956-6649
> 1680 East-West Road         fax: 808-956-5154
> Honolulu, HI 96822          clintc at hawaii.edu <mailto:clintc at hawaii.edu>
> http://www.soest.hawaii.edu/GG/FACULTY/conrad
> ---------------------------------------------
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> CIG-MC mailing list
> CIG-MC at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-mc
>


--
Eh Tan
-------
Postdoc
Institute of Geophysics
University of Texas, Austin
J.J. Pickle Research Campus, Bldg 196 (ROC)
10100 Burnet Rd. (R2200),
Austin, TX 78758-4445
(512) 475-9568


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