AMBER Archive (2008)

Subject: Re: AMBER: Dose AMBER 10 pmemd support openmpi?

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Apr 30 2008 - 10:40:44 CDT

I think that when infiniband is shipping with an openmpi implementation,
there is more incentive to support it. Perhaps Dave can include what he has
as a starting point, or make it available on the web site. So far I have
only had access to infiniband with mvapich myself, and have not had a lot of
motivation to support yet another gigabit ethernet implementation, given
that we have lam, mpich, mpich2. I do think it is probably a simple tweak
though.
Regards - Bob
----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, April 30, 2008 11:22 AM
Subject: Re: AMBER: Dose AMBER 10 pmemd support openmpi?

> On Wed, Apr 30, 2008, Hu, Shaowen (JSC-SK)[USRA] wrote:
>>
>> I heard that AMBER 10 pmemd will support openmpi. Is this correct?
>
> I use pmemd 10 with openmpi on our inifiniband cluster, because that is
> the
> MPI version that came pre-configured from the vendor. You have to tweak
> the
> config.h file a bit. But I can post what I did, or we might get a patch
> out to update the configure script itself.
>
> Basically, there is no incompatibility, just (right now) a bit of a
> hassle.
> I've runs hundreds of nsec of simulations with openmpi without seeing any
> problems.
>
> ...regards...dac
>
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