AMBER Archive (2008)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Feb 27 2008 - 15:20:56 CST

For lam, go to www.lam-mpi.org/using/docs/. For mpich, go to
www-unix.mcs.anl.gov/mpi/mpich1. I find mpich easier to use than mpich2 for
a small setup and just as fast (there are arguments about run startup times
being better with mpich2 - basically because there are daemons constantly
running, it takes less time to get a job going, but if you have a small
setup, having to start/stop the bloody daemons is at least to me a bit of a
nuisance without any real benefit (not true of a large setup I am sure).
There is a bit of additional functionality in mpich2 also, but we don't need
any of it - mostly fluff from my perspective. Anyway, looking at these two
sources will provide all the doc in the world and the s/w. I do know that
the community is moving to openmpi; I just have not jumped on the bandwagon
because this other stuff has been working fine and is free too. There is a
fair bit of commentary on how to set up this stuff by Ross, me, others, at
amber.scripps.edu. It can be a bit of a pain, but we have supported it a
long time, and it is well supported in 8 and 9.
Regards - Bob Duke

----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_yahoo.com>
To: <amber_at_scripps.edu>
Sent: Wednesday, February 27, 2008 4:00 PM
Subject: Re: AMBER: Amber: shared memory vs cluster

>
> --- 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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>
>
>
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