Re: mpi problems on opteron

From: Kyle Gustafson (
Date: Thu Aug 04 2005 - 07:54:20 CDT

Thanks Dow, I will post any successful protocol,


---- Original message ----
>Date: Wed, 03 Aug 2005 23:39:35 -0400
>From: Dow Hurst <>
>Subject: Re: namd-l: mpi problems on opteron
>To: Kyle Gustafson <>
>Cc: Leandro Martínez <>, namd-
>Fixing up ssh for public key authentication requires what
Gengbin said
>but just make sure the passphrase is empty. Or, if you
want to have a
>passphrase then have ssh-agent startup on login with
>environment variables as described here:
>there are other pages on this but this procedure works for
me. You run
>ssh-add to add your keys to the agent who will manage them
as you
>connect to remote machines.
>I think most clusters are setup with empty passphrases!
>Here is the procedure I used to link the Ammasso MPI to
charm for
>compilation of NAMD 2.6b1, which was given to me by Eric
>"I find it far simpler just to make the Ammasso mpich the
first (or even
>only) mpi in your path. This ensures that its libraries
and binaries
>will be the ones used.
>(I'd just follow Eric's advice and have only the MPI you
want used in
>your path)
>export PATH=$PATH:/opt/mpicham.gcc/mpich-1.2.5/bin (My
>location for the Ammasso MPI installation)
>./build charm++ mpi-linux-amd64 -O -nobs
>Which gave me a completely functional charm.
>Then I downloaded NAMD.
>Revised Make.charm to point to my charm.
>and made the NAMD build dir
>./config Linux-amd64-MPI
>cd Linux-amd64-MPI
>mpirun -np 4 ./namd src/alanin
>And it works."
>Now, Eric's procedure didn't include fftw and he mentioned
that to me.
>I'll deal with that later. If you can check the source
your using, mine
>didn't have the arch/All-Unix.plugins file. Maybe it
isn't needed
>now, I'm not sure. I was bouncing between the Wiki for
AMD64 and the
>Release Notes for 2.6b1 so I may have some steps screwed up
when I tried
>to compile before I got Eric's procedure. Post your
procedure if you
>get everything working the way you'd like. Thanks,
>Leandro Martínez wrote:
>>Hi Kyle,
>>We have a cluster similar to yours, but running fedora.
Probably the
>>problem is that you need to set ssh to be used without
>>between the nodes. We are actually using rsh in our nodes
>>because it was easier to configure. You need to put in your
>>home directory a file named .rhosts containing
>> username
>> username
>> username
>> username
>> username

Kyle B. Gustafson
Department of Physics
University of Maryland
College Park, MD USA

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