Chamrun/NAMD processes and PBS cluster

From: Nicolas Sapay (
Date: Mon Dec 05 2005 - 07:55:15 CST

Hello everybody,
I have some questions about the processes launched when a simulation is
run using a PBS-like server. I run a simulation using the following
command line in a Shell script <> :
$NAMD/charmrun ++verbose +p$nproc ++nodelist $TMP/nodelist $NAMD/namd2
$TMP/myfile.conf > $TMP/myfile.log
with :
        - $NAMD : the path to the NAMD installation directory
        - $nproc : the number of processor
        - $TMP : a temporary directory belonging to the NAMD job where output
files are written

When I launch a NAMD job (i.e. when I submit the shell script to the PBS
server <qsub>), 3 processes appear on each node (assuming
that nodes are monoproc):
        - a suspended shell process
        - a suspended charmrun process
        - a running namd2 process

The problem is that the PBS server doesn't seem to see the namd2
process, but the chamrun one. The PBS server is consequently "deluded"
and see only the suspended charmrun process (I guess it is waiting for
So my questions are :
Is namd2 a child process of charmrun or are they independent?
Is there a way to not delude the PBSserver?

Thanks for your answers

Nicolas Sapay

_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
  7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
  69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
  France                     Web:

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