Re: NAMD on a virtual grid

From: Robert Brunner (
Date: Mon Jan 26 2009 - 13:50:13 CST

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

Try to login as user root from the command line and see if you can
produce those messages.


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?

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