Re: Running namd on Rice Teracluster

From: Chris Samuel (csamuel_at_vpac.org)
Date: Tue Apr 13 2004 - 20:43:18 CDT

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On Mon, 12 Apr 2004 10:15 am, Amarda Shehu wrote:

> Does namd run in parallel by trying to do rsh to the
> nodes of the specified nodelist? As this is basically trying to log in to
> the nodes of the cluster, it fails because rsh to the nodes is not
> allowed. Is this the only way to run namd in parallel?

You'll need to build it as an MPI version rather than a net version.

Then instead of trying to using charmrun you can just do:

        mpiexec /path/to/namd2 alanin

Which is how our users are now using it.

Note that the MPI version of charmrun will just call mpirun, which of cause
tries to use rsh or ssh, which isn't what you want from the sound of it.

cheers!
Chris
- --
 Christopher Samuel - (03)9925 4751 - VPAC Systems & Network Admin
 Victorian Partnership for Advanced Computing http://www.vpac.org/
 Bldg 91, 110 Victoria Street, Carlton South, VIC 3053, Australia

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