AMBER Archive (2008)

Subject: Re: AMBER: Amber: shared memory vs cluster

From: Robert Duke (
Date: Wed Feb 27 2008 - 12:37:31 CST

I probably won't get around to adding openmpi myself before release, but it
is the sort of thing that can be added pretty easily after release, since it
is just a matter of some config files and perhaps a few lines in the config
script. I guess I have found both mpich and lam very suitable for use
myself, so have not been in a panic to add every mpi implementation
imaginable. As of the last release, I looked at openmpi and actually chose
to not add it at that time because they effectively had no documentation
yet; I found it hard to believe that documentation is unnecessary. To me, a
much bigger issue on cluster usability is interconnect hardware. Folks
often buy gigabit ethernet because it is cheap, but infiniband will do a
much better job. If you are only talking about 2-4 cpu's, it may not be
such a big deal.
Regards - Bob Duke

----- Original Message -----
From: "Francesco Pietra" <>
To: "Amber" <>
Sent: Wednesday, February 27, 2008 1:08 PM
Subject: AMBER: Amber: shared memory vs cluster

>I need more power from my private computing equipments, currently running
> 9, Dock6.1 and NWChem5.1 on Debian Linux amd64 multi dual opteron shared
> memory.
> In the perspective of Amber 10, where should my (modest) investment be
> better
> directed: shared memory or cluster? I mean, will Amber 10 deal efficiently
> with
> a home-arranged cluster from dual-opteron units? All that in the
> perspective
> that for both NWChem and Dock I also need much much RAM.
> In particular, will efforts by Amber developers be spent to let easily
> compile
> pmend on OpenMPI? I found OpenMPI easy to use in combination with Intel
> compilers, while I had no good config file from where to start, this is
> the
> reason.
> Thanks for helping my planning
> francesco pietra
> ____________________________________________________________________________________
> Looking for last minute shopping deals?
> Find them fast with Yahoo! Search.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to