AMBER Archive (2004)

Subject: Re: AMBER: Amber job submission using PBS

From: Jiten (jiten_at_postech.ac.kr)
Date: Thu Sep 23 2004 - 11:57:35 CDT

Hello,

Even after including -p prmtop, it is still not working.

I do not know how to check the PBS output file. Could you tell me?

Sincerely,

JIten

----- Original Message -----
From: "Guanglei Cui" <cuigl_at_csb.sunysb.edu>
To: <amber_at_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_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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