running precompiled NAMD with multiple processors

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Aug 26 2008 - 01:04:57 CDT

Dear NAMD community,

I have installed a precompiled version of NAMD (Linux i-686 version) into
our 32 node Intel cluster. The head node is type 'DL 380 GS', and the
computational nodes are type 'BL 460 C'. The cluster has Intel MPI. We use
PBS for submitting jobs, and this is the submit file:

****************************
!/bin/bash
#PBS -N testNAMD
#PBS -l nodes=1:ppn=4
#PBS -e error.file
#PBS -o output.file
#PBS -r n
#PBS -V
## (export the current environment variables to the job being submitted)

echo PBS JOB id is $PBS_JOBID
echo PBS_NODEFILE is $PBS_NODEFILE
echo PBS_QUEUE is $PBS_QUEUE
cat $PBS_NODEFILE

cd /home/atanwar/NAMD/trialruns
which namd2
/home/atanwar/NAMD/charmrun +p4 /home/atanwar/NAMD/namd2 nve09.inp >
nve09.out
****************************

These are the errors I am getting:

connect to address 127.0.0.1: Connection refused
connect to address 127.0.0.1: Connection refused
trying normal rsh (/usr/bin/rsh)
connect to address 127.0.0.1: Connection refused
connect to address 127.0.0.1: Connection refused
connect to address 127.0.0.1: Connection refused
trying normal rsh (/usr/bin/rsh)
connect to address 127.0.0.1: Connection refused
trying normal rsh (/usr/bin/rsh)
connect to address 127.0.0.1: Connection refused
connect to address 127.0.0.1: Connection refused
trying normal rsh (/usr/bin/rsh)
localhost.localdomain: Connection refused
localhost.localdomain: Connection refused
localhost.localdomain: Connection refused
localhost.localdomain: Connection refused
Charmrun> Error 1 returned from rsh (localhost:0)
****************************

I was wondering if anybody has faced something like this, and would like to
share their experience in solving the issue. Please note that I have been
able to run NAMD with a single processor on the command line (hence the
precompiled version should be compatible with our cluster).

Thanks,
Neelanjana

~~~~~~~~~~~~~~~~~~~~
Dr. Neelanjana Sengupta
Physical and Materials Chemistry Division
National Chemical Laboratory
Dr. Homi Bhaba Road
Pune 411008, India
Phone: +91-20-2590 2087
~~~~~~~~~~~~~~~~~~~~

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