gilgamesh: root access while I am gone

[Craig Maloney]

Hi Jason,

Important points:

1) make sure you build your mpi  code after a "module load openmpi-psm- 
gcc" command.
2) put that same command into your pbs script right before the "cd  
$PBS_O_WORKDIR" command
3) make sure to put a cput limit and the node/process number request  
on the command-line when issuing the qsub command.  it looks like pbs  
is ignoring any "-l cput" or "-l nodes=:ppn=" directives in the script  
file, but I'm not positive about that.

Here's the script I am using where "../lmp_generic" is the executable  
I built with the appropriate environment and "../input-10" is a  
parameter file I'm sending to ../lmp_generic on stdin.

----------
#!/bin/bash
cd $PBS_O_WORKDIR
module load openmpi-psm-gcc
mpirun -np `cat $PBS_NODEFILE | wc -l` ../lmp_generic < ../input-10
---------------

Typical qsub command:
qsub -l cput=12:00:00 -l nodes=2:ppn=16 ../ljMelt-20

where "../ljMelt-20" is the pbs script.

Good luck,
Craig


On Aug 5, 2010, at 11:00 AM, Jason Larkin wrote:

> Hi Craig,
>
> This is Jason, one of Alan's students.  I see that you have some  
> jobs running on the ChemE cluster.  Could you send me the queue  
> script file you used to submit these jobs?  I'm having trouble  
> getting my job to submit to the queue system.  Thanks,
>
> Jason
>
>
> Alan McGaughey wrote:
>> Spencer's email is rommel at cmu.edu.
>>
>> You can look up anyone at CMU here:
>>
>> http://directory.andrew.cmu.edu/
>>
>> -----Original Message-----
>> From: Jason Larkin [mailto:jmlarkin at andrew.cmu.edu] Sent: Thursday,  
>> August 05, 2010 10:15 AM
>> To: Alan McGaughey
>> Cc: 'Minyoung Lee'
>> Subject: Re: FW: root access while I am gone
>>
>>
>> Alan,
>>
>> How can I get in touch with Spencer?  Do you have his email?  I  
>> need him to do something only the root can,
>>
>> Jason
>>
>> Alan McGaughey wrote:
>>
>>> fyi
>>>
>>>
>>> From: johnrkitchin at gmail.com [mailto:johnrkitchin at gmail.com] On  
>>> Behalf Of
>>> John Kitchin
>>> Sent: Wednesday, August 04, 2010 5:50 PM
>>> To: Alan McGaughey; Craig Maloney
>>> Cc: Spencer Miller
>>> Subject: root access while I am gone
>>>
>>>
>>> Hi Alan, Craig,
>>>
>>> I am heading out of the country tomorrow afternoon, and will be  
>>> out of
>>>
>> email
>>
>>> contact until 8/15. I think the cluster is setup so you can do  
>>> most of
>>>
>> what
>>
>>> you need without root access. If something comes up and you think  
>>> it is
>>> essential that it be done before I am back, I have left the root  
>>> password
>>> with Spencer.  He isn't planning to use it for anything, unless  
>>> there is
>>> some emergency.
>>>
>>> John
>>>
>>> -----------------------------------
>>> John Kitchin
>>> Assistant Professor
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>
>

-----------------------------------------------
Contact info:
http://www.ce.cmu.edu/People/faculty/maloney.html



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