ADL: PBS script for virtual screening

Wilfred Li wilfred at sdsc.edu
Fri Jan 18 08:40:43 PST 2008


The Scripps virtual screening tutorial contains a PBS sample script for
use on their bluefish cluster, which is also available at the NBCR
Summer Institute archive,
https://nbcr.net/pub/wiki/uploads/7/7d/VSTutorial2_Handouts2per.pdf. The
last two pages.

It's best to discuss with your cluster administrator as well since they
are normally able to provide a version that works with the local
cluster.

Regards,

Wilfred


-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu]
On Behalf Of Amor A. San Juan
Sent: Friday, January 18, 2008 1:32 AM
To: autodock at scripps.edu
Subject: ADL: PBS script for virtual screening

Hi everyone,

I need help in writing a PBS script to submit to linux cluster. I am
stuck
and need your assistance so greatly, as I dont have enough programming
skills.

I already generated all the rest of input files for executable autodock,
such as *dpf, gridmaps etc. Now I need simple PBS script to submit to
cluster.

Below is the default PBS script, which I dont have precise idea on how
to
put some arguments prior submitting to cluster.

#!/bin/sh
#PBS -l arch=x86_64
#PBS -q MP
#PBS -l nodes=4:ppn=4:smp
#PBS -l ncpus=4
#PBS -l walltime=00:05:00
#PBS -l mem=100mb
#PBS -V
#PBS -m bea
#PBS -o Output_File
#PBS -e Error_File
cd $PBS_O_WORKDIR
mpirun -np 4 -machinefile $PBS_NODEFILE ./a.out
~

Would someone please explain in detail or send a file of  the  PBS
script
submitted to cluster?

Thanks
Amor



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