NAMD PBS Parallel Job Error

From: Aditya Ranganathan (
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:
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
#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


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

/home/external/iitb/ranganathan/sim/namd2.9/p53_prod.conf >

The script is as follows


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

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

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