[CIG-MC] CitcomS launcher modify batch script

[Jonathan Perry-Houts]

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Thanks Eh,

I ran in circles with this issue for a while and decided in the end to
just use the pure C code rather than the python front end. Thanks for
your help.

Cheers,
Jonathan

On 03/04/2013 05:44 PM, tan2 wrote:
> Hi Jonathan,
> 
> The output of your dry scheduler run looks normal to me. However,
> your cluster might have special requirement on the job script. You
> will need to compare your dry scheduler run with your colleague's
> job script.
> 
> Eh
> 
> On Tue, Mar 5, 2013 at 4:21 AM, Jonathan Perry-Houts 
> <jperryhouts at gmail.com>wrote:
> 
> Oh, of course! I can't believe I didn't think of that. Thanks Eh.
> 
> As a followup question, now I'm getting the following error when I
> try to run the cookbook1 file: !!!! # of requested CPU is incorrect
> (expected: 12 got: 1)
> 
> My ~/.pyre/CitcomS/CitcomS.cfg file looks like: [CitcomS] scheduler
> = pbs [CitcomS.job] queue = generic [CitcomS.launcher] command =
> mpirun --mca btl_tcp_if_include torbr -np ${nodes} [CitcomS.pbs] 
> ppn = 4
> 
> and on dry launcher runs I get a reasonable looking output: mpirun
> --mca btl_tcp_if_include torbr -np 12 
> /home13/username/packages/CitcomS-3.2.0/bin/mpipycitcoms
> --pyre-start ...paths... pythia mpi:mpistart
> CitcomS.SimpleApp:SimpleApp cookbook1.cfg --nodes=12
> --macros.nodes=12 --macros.job.name= --macros.job.id=227074.hn1
> 
> Likewise, the dry scheduler run gives a reasonable looking output: 
> #!/bin/sh #PBS -S /bin/sh #PBS -N jobname #PBS -q generic #PBS -o
> stdout.txt #PBS -e stderr.txt #PBS -l nodes=3:ppn=4 cd
> $PBS_O_WORKDIR ... # ~~~~ submit command ~~~~ # qsub < [script]
> 
> It appears that somehow there are lots of jobs being submitted
> with one processor allocated to each rather than one job with lots
> of processors, the program spits out 12 identical pid*.cfg files.
> 
> Thanks again for your help!
> 
> Cheers, Jonathan
> 
> On 03/04/2013 01:16 AM, tan2 wrote:
>>>> Hi Jonathan,
>>>> 
>>>> You can add 'module load mpi...' in your ~/.profile (if using
>>>> bash) or ~/.login (if using tcsh).
>>>> 
>>>> 
>>>> Eh
>>>> 
>>>> On Fri, Mar 1, 2013 at 5:36 AM, Jonathan Perry-Houts 
>>>> <jperryhouts at gmail.com>wrote:
>>>> 
>>>> Hi all,
>>>> 
>>>> I was wondering if there's a simple way to modify the script
>>>> that gets run when I run the citcoms executable. The cluster
>>>> I'm using has several versions of MPI installed and I need to
>>>> run `module load mpi...` at the start of any session to set
>>>> the appropriate environment variables for the MPI version I
>>>> want.
>>>> 
>>>> The problem I'm having is that once the citcom job submits
>>>> its self to the PBS queue, it tries to use MPI without
>>>> loading the appropriate module first. Is there a way to
>>>> easily change this behavior?
>>>> 
>>>> Thanks in advance for any help!
>>>> 
>>>> Cheers, Jonathan Perry-Houts
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>>>> 
>>>> 
>>>> 
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> 
> 
> 
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