Hi,
Just as Prof. Case suggested, the information is not enough to debug your
problem. So you problem could be on AMBER side or on PBS side. You can try
the following. First, make sure your Amber installation is valid. As Prof.
Case said, run some short simulations without using the PBS system. Then,
if the installation is OK, contact your system administrator, give him your
script, let him tell you how to use your cluster. That's all I can help.
Cheers
Terry
On Thu, Nov 1, 2012 at 2:13 PM, hari krishna <haricoolguy111.gmail.com>wrote:
> Dear Terry,
>
> Now i changed the path in the script file.
>
> Openmpi is at /home/p_kumar/openmpi/bin/mpirun
>
> using this I have recompiled amber12 in parallel. with export
> DO_PARALLEL='mpirun -np 8' and using make test command amber12 installation
> was successfully tested with no errors. But still after submitting the jobs
> and while started running no output file was created.
>
> any suggestions please
>
> S.harikrishna
>
>
> From: Terry <terrencesun.gmail.com<
> terrencesun.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20Problem%20in%20running%20parallel
> >>
>
> Date: Wed, 31 Oct 2012 13:33:15 +0800
>
> On Wed, Oct 31, 2012 at 12:56 PM, hari krishna <haricoolguy111.gmail.com
> >wrote:
>
>
> *> Dear all, *
> *> *
> *> I have successfully installed serial and parallel version of AMBER12 in
> the *
> *> server (in my user user only) using gnu compiled openmpi. Also the test
> was *
> *> successfully completed. I used ./configure_openmpi in AmberTools/src for
> *
> *> openmpi. *
> *> *
> *> while using PBS script to run the program in parallel, in the queue, the
> *
> *> program is running and processors are allocated and the program is shown
> *
> *> like running in the server. But no output files are created in the given
> *
> *> folder even after long time. Please look at the following PBS script.
> Any *
> *> suggestions. *
> *> *
> *> *#!/bin/bash *
> *> *
> *> #PBS -l nodes=8:ppn=8 *
> *> #PBS -l pmem=700mb *
> *> #PBS -l walltime=600:00:00 *
> *> *
> *> export AMBERHOME=/home/p_kumar/amber12 *
> *> export LD_LIBRARY_PATH=/home/p_kumar/amber12/lib:$LD_LIBRARY_PATH *
> *> export DO_PARALLEL="$AMBERHOME/bin/mpirun -np 64" *
> *> *
>
> mpirun is not in $AMBERHOME.
>
> Terry
>
>
> *> *
> *> cd /home/p_kumar/thioflavin/dynamics/parallel *
> *> *
> *> $DO_PARALLEL $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod.out -p *
> *> complexsol.prmtop -c equil.rst -r prod.rst -x prod.mdcrd -ref equil.rst*
> *
> *> *
> *> *
> *> Sincerely *
> *> S.Harikrishna *
> *> _______________________________________________ *
> *> AMBER mailing list *
> *> AMBER.ambermd.org *
> *> http://lists.ambermd.org/mailman/listinfo/amber *
> *> *
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> Received on Tue Oct 30 2012 - 23:00:05 PDT
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Received on Thu Nov 01 2012 - 00:00:02 PDT
