[CIG-MC] Running citcoms using pbs scheduler

[Eh Tan]

Hi Dan,

You can add those module command to your .login file.

If you still want to execute additional command in the job script, you 
can do it in the launcher by (untested):

[CitcomS.launcher]
command = module load intel/intel-11 && module load mpich/intel-11 && 
mpirun -np ${nodes}

Cheers,
Eh


On 1/27/11 7:31 PM, Dan Bower wrote:
> 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
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>>
>
> --
> 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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