AMBER Archive (2004)

Subject: Re: AMBER: Amber job submission using PBS

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Thu Sep 23 2004 - 11:20:30 CDT

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_at_csb.sunysb.edu>
> To: <amber_at_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
>>
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>>
>
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