Can you send the PBS script as attachment, instead of copying and
pasting to the email? Thanks.
Guanglei
Jiten wrote:
> Hello,
>
> This is what I get in the PBS output file
>
> node001
> node002
> node004
> node007
> /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -machinefile: command not found
> /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -O: command not found
>
> Where do I need to modify again ?
>
> Sincerely,
>
> JIten
>
> ----- Original Message ----- From: "Guanglei Cui" <cuigl.csb.sunysb.edu>
> To: <amber.scripps.edu>
> Sent: Friday, September 24, 2004 1:20 AM
> Subject: Re: AMBER: Amber job submission using PBS
>
>
>> You didn't specify topology file ... are you using the default name?
>> You might want to check out the PBS output to be sure.
>>
>> Jiten wrote:
>>
>>> Thanks,
>>>
>>> I also tried to construct using the sample script from
>>> http://amber.scripps.edu/cluster_info/pbs_script.html as follows. But
>>> it is still not working. COuld anybody help me out ?
>>>
>>> #!/bin/bash
>>> #PBS -l nodes=2, ppn=2
>>> #PBS -l walltime=50:00:00
>>> #PBS -j oe
>>> #PBS -q normal
>>> #PBS -N amber-jiten
>>> #PBS -l pmem=2048MB
>>> #PBS -l vmem=2048MB
>>> cat $PBS_NODEFILE
>>>
>>> cd /home2/e953kks/amber8/test/4096wat
>>>
>>> set mpich_run =
>>> "/opt/mpich/1.2.5..10/gm-2.0.12-2.4.20-28.7smp-i686/smp/gnu/ssh/bin//mpirun"
>>> set sander = "/home2/e953kks/amber8/exe/sander"
>>>
>>> $mpich_run -machinefile $PBS_NODEFILE -np `wc -l < $PBS_NODEFILE`
>>> $sander \
>>> -O -i gbin -c eq1.x -o mdout.test
>>>
>>>
>>> Sincerely,
>>>
>>> Jiten
>>>
>>> ----- Original Message ----- From: "Guanglei Cui" <cuigl.csb.sunysb.edu>
>>> To: <amber.scripps.edu>
>>> Sent: Friday, September 24, 2004 12:52 AM
>>> Subject: Re: AMBER: Amber job submission using PBS
>>>
>>>
>>>> Hi,
>>>>
>>>> You can check out this page. The example is down almost at the bottom.
>>>> http://gears.aset.psu.edu/hpc/systems/lionxm/userguide/
>>>>
>>>> Guanglei
>>>>
>>>> Jiten wrote:
>>>>
>>>>> Dear Amber users,
>>>>> I am wondering if someone could provide me a template for the
>>>>> script for the amber job submission using Portable Batch System
>>>>> (PBS).
>>>>> Thanks in advance,
>>>>> Sincerely,
>>>>> N. Jiten Singh
>>>>> C/O Prof. Kwang S. Kim
>>>>> Department of Chemistry
>>>>> Pohang University of Science and Technology
>>>>> San 31, Hyojadong, Namgu
>>>>> Pohang 790-784, Korea
>>>>> Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
>>>>> Fax : 82-54-279-8137 (or +82-54-279-3399)
>>>>> Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
>>>>> Home Page : http://www.geocities.com/njs_19
>>>>
>>>>
>>>> -----------------------------------------------------------------------
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber.scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>>
>>>>
>>>
>>> -----------------------------------------------------------------------
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>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>
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Received on Thu Sep 23 2004 - 18:53:00 PDT
