AMBER Archive (2008)

Subject: RE: AMBER: pmemd

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Nov 20 2008 - 10:36:51 CST

Hi Jeremy,

 

It's very hard to work out what is going on here. Do you get any other error
messages? Any other output files at all?

 

I would start by asking for an interactive session. This is normally done
with something like:

 

qsub -i -nodes=.....

 

Then simply try mpirun -np ... on pmemd.

 

A few other things to check. Was pmemd compiled for parallel and using the
same lam mpi that you are running with here?

 

All the best

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Jeremy Harris
Sent: Thursday, November 20, 2008 8:27 AM
To: amber_at_scripps.edu
Subject: AMBER: pmemd

 

Hello,

I am simulating a protein in explicit water, and I've been using sander with
lamwrapper, but want to use pmemd, as I understand it is faster. However,
I've been having trouble running the jobs. I'm not sure where to start with
this, so any help would be appreciated.

My submission script is:

#PBS -N run11
#PBS -q s2
#PBS -l walltime=00:15:00
cd $PBS_O_WORKDIR
#
#Write usefull things to the output file
#
echo "Starting job $PBS_JOBID"
echo
echo "PBS assigned these nodes:"
cat $PBS_NODEFILE
echo
#
echo First task running on:
uname -a
echo at
date
#
export PATH=/usr/local/amber9:$PATH
/usr/local/bin/lamwrapper -- /usr/local/amber9/exe/pmemd -O -i run.in -o
run11.out -p 1CDL_wat.prmtop -c run10.rst -r run11.rst -x run11.mdcrd

The output file is:

PBS assigned these nodes:
comp00
comp00

First task running on:
Linux comp00 2.6.11.4-21.10-1SCORE-smp #1 SMP Tue Jan 10 16:02:23 GMT 2006
x86_64 x86_64 x86_64 GNU/Linux
at
Thu Nov 20 15:53:18 GMT 2008

LAM 7.1.1/MPI 2 C++/ROMIO - Indiana University

No dedicated nodes so no cleanup done.

Thanks in advance,
Jeremy Harris

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