Running NAMD on cluster

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Wed Apr 30 2008 - 04:41:53 CDT

Dear NAMD user,
      I want to run NAMD job parallely on our hp-proliant cluster. It
has 16 nodes and one master server with operating system RHEL4 and
also the home directory is automounted. To do this job, I downloaded
the NAMD_2.6_Linux-i686.tar.gz file from the UIUC site. This file is
untar in a home directory of an user account. Now I want to simulate
a water box by this NAMD program. To fire this job, the command which
I have used is written below

/home/sudipta/NAMD_2.6_Linux-i686/charmrun ++remote-shell ssh
++nodelist namd.nodelist /home/sudipta/NAMD_2.6_Linux-i686/namd2 +p3
water51.conf ++verbose

The namd.nodelist file contains,
group main
host iitkgp
host node1
host node2

The program is running fine on each node parallely. But with
increasing the number of nodes the CPU efficiency decreases. As a
result the runtime increases with increasing the number of nodes. That
means just opposite is happening with increasing the number of nodes.
Does it mean each job running on each node independently with huge
network crowding? But actually I want to run one job on multiple
processors. Could anyone suggest me what is my wrong.

Thanks and regards
Sudipta

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