AMBER Archive (2004)

Subject: Re: AMBER: Amber job submission using PBS

From: Jiten (jiten_at_postech.ac.kr)
Date: Thu Sep 23 2004 - 11:11:41 CDT

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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu