AMBER Archive (2009)

Subject: [AMBER] mpirun error

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Mon Dec 28 2009 - 21:00:11 CST

Dear Experts,

I am running MD simulation.

The script I am using is as bellow:

#!/bin/csh
#PBS -l select=1:ncpus=64
setenv MPI_BUFS_PER_PROC 65536
setenv MPI_MAPPED_HEAP_SIZE 268435456
setenv MPI_DSM_DISTRIBUTE
setenv OMP_NUM_THREADS 1
unsetenv NCPUS
setenv MKL_LIBRARY serial
limit stacksize unlimited
setenv AMBERHOME /home/vijay/bin/amber9
cd $PBS_O_WORKDIR

mpirun -np 64 $AMBERHOME/exe/pmemd -O -i e1malto-highLyo-equi01.in -o e1malto-highLyo-equi01.out -p maltose-highLyo-v6.top -c malto-h
ighLyo-v6-mdy-09.rst -ref malto-highLyo-v6-mdy-09.rst -r e1malto-highLyo-equi02.rst < /dev/null
ambpdb -p maltose-highLyo-v6.top < e1malto-highLyo-equi02.rst > e1malto-highLyo-equi02.pdb

Previously this script was running fine. No problem at all. BUT now it doesn't run.

If I send the job using PBS Pro, it terminates. When I look into the error file, it is stated like below:

mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
mpirun must be used to launch all MPI applications
..
.
.
.
.
.
.

I can't figure out why this problem occurred. IS that due to system failure or any wrong in the script I am using.

Please guide me in this issue.
Your help will be really appreciated.

Thank you.
Vijay

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana_at_gmail.com

      

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber