NAMD PBS Parallel Job Error

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Mon Mar 04 2013 - 03:44:15 CST

Hello All,

I have been trying to run a NAMD job using 32 processors on 4 nodes on a
supercomputing grid (CDAC PARAM YUVA II) which uses the pbs job scheduler.
However, my job gets killed generating the following error message :
"
/home/external/iitb/ranganathan/sim/namd2.9/charmrun: line 27:
/scratch/202084.yc9.en.yuva.param/202084.yc9.en.yuva.param.nodelist:
Permission denied
/home/external/iitb/ranganathan/sim/namd2.9/charmrun: line 27: exec:
/scratch/202084.yc9.en.yuva.param/202084.yc9.en.yuva.param.nodelist: cannot
execute: Permission denied"

The jobscript that I use is the pbsrun jobscript on NAMDWIKI:

The Job Script is as follows
"
#!/bin/bash
#PBS -l walltime=02:00:00
#PBS -l nodes=4:ppn=8
#PBS -A comp_parallel-PR
## Comma separated list of email address and mobile numbers

cat $PBS_NODEFILE

cd /home/external/iitb/ranganathan/sim/namd2.9

/home/external/iitb/ranganathan/sim/namd2.9/pbsrun.sh
/home/external/iitb/ranganathan/sim/namd2.9/charmrun
/home/external/iitb/ranganathan/sim/namd2.9/namd2
/home/external/iitb/ranganathan/sim/namd2.9/p53_prod.conf >
/home/external/iitb/ranganathan/sim/namd2.9/p53onYUVA.log
"

The pbsrun.sh script is as follows

"
#!/bin/csh

set nodefile = $TMPDIR/$PBS_JOBID.nodelist
echo group main >! $nodefile
set nodes = `cat $PBS_NODEFILE`
foreach node ( $nodes )
  echo host $node >> $nodefile
end

echo $nodefile

echo $#nodes nodes
set charmrun = $1
shift argv

setenv CONV_RSH ssh

$charmrun +p$#nodes ++nodelist $nodefile $*
"

Please let me know where I`m going wrong or is it something related to the
cluster settings.

Thanks and Regards

Srivastav Ranganathan
IIT Bombay
Mumbai, India

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:59 CST