NAMD on a virtual grid

From: Benjamin Bouvier (
Date: Mon Jan 26 2009 - 09:38:30 CST

Hi all,

I'm trying to run NAMD on a grid of virtual machines. Once
reserved/deployed, these machines can be accessed from a frontend computer
where the xx's are the virtual machine's local IP adress. Due to the smart
forwading of an ssh-agent, this does not require typing any password. The
login, however, changes from a standard user name on the frontend, to root
on the virtual machines (hence the 'root@' in the ssh command).

This is what I did:

-I set the CONV_RSH env. variable to 'ssh'.
-My nodefile looks like this (for 2 virtual machines in this case):
  host ++shell ssh ++login root
  host ++shell ssh ++login root
-Finally, I try to launch NAMD using:
  charmrun namd2 +p2 ++remote-shell ssh ++verbose ++nodelist my_nodelist
bench.namd > bench.log

What I get is:

Charmrun> charmrun started...
Charmrun> using my_nodelist as nodesfile
Charmrun> rsh ( started
Charmrun> rsh ( started
Charmrun> node programs all started
The authenticity of host ' (' can't be
RSA key fingerprint is 07:2b:f8:c4:8b:53:79:98:4c:41:38:12:f3:b3:ce:d9.
Are you sure you want to continue connecting (yes/no)? Charmrun> Error 1
returned from rsh (

What could go wrong? I see rsh instead of ssh everywhere in the output,
should I be worried?

Also, would I be better off using MPI instead of Charm++ in this case?



Benjamin Bouvier
Structural Bioinformatics
IBCP Lyon - UMR 5086 CNRS
7, passage du Vercors
Tel: +33(0)4-37-65-29-44

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