AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Feb 27 2008 - 15:00:32 CST

--- Robert Duke <rduke_at_email.unc.edu> wrote:

> 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,

I was initially discouraged by the complexity of lam. Maybe i have to
reconsider it. Do you have at hand references to guidelines for installing and
using lam and mpich2 (if they are free)? (DOCK is focused on the latter)

> 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.

I am at 8 CPUs shared mem and have to increase. I have done, and I do that with
second hand components, except the mainboard. Prices here are high. In some
cases the difference is astonishing: a four-way US Robotics router priced
$39.95 in US is priced here 150 Euro. It is a limit case, usually not that bad.

Thanks
francesco pietra

> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Francesco Pietra" <chiendarret_at_yahoo.com>
> To: "Amber" <amber_at_scripps.edu>
> 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
> >Amber
> > 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
> >
> >
> >
> >
>
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