ADL: PBS script for virtual screening

M. Shahid mohammad.shahid at gmail.com
Sun Jan 20 04:26:00 PST 2008


Hi,

You dont need to call MPIRUN here, just make another shell script to
which you'll pass the arguments of your dpf's while that executes AD4,
and then call this shell script from your PBS.
With best regards,

--
Shahid.
On Jan 18, 2008 5:40 PM, Wilfred Li <wilfred at sdsc.edu> wrote:

> 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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