Re: NAMD on a virtual grid

From: Benjamin Bouvier (
Date: Mon Jan 26 2009 - 14:38:56 CST

On Mon, 26 Jan 2009 20:50:13 +0100, Robert Brunner <>
> Those "authenticity" messages are coming from SSH via Charm++. You need
> to get rid of them by setting up SSH so they don't occur. Depending on
> your system setup, you can probably do this by just manually running ssh
> from the host node to every other node and answering the questions, or
> by editing $HOME/.ssh/known_hosts or $HOME/.ssh/known_hosts2 and adding
> the proper host name keys to those files.
> Try to login as user root from the command line and see if you can
> produce those messages.

Thanks for the suggestion Robert. But logging from the command line (using
ssh root_at_xx.xx.xx.xx) works great, and does not trigger password prompts
or security questions...
Hence my fear that Charm++ might not actually be using ssh, but rsh (cf
the output messages)...

> Robert
> On Jan 26, 2009, at 9:38 AM, Benjamin Bouvier wrote:
>> 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 using:
>> ssh
>> 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
>> established.
>> 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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