AMBER Archive (2005)

Subject: Re: AMBER: amber with mpich-G2

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sun Mar 06 2005 - 22:07:21 CST

Putra -
Okay, it may be possible, but I think it would also be ill-advised. If I
understand correctly, mpich-g2 is "grid-enabled", meaning supporting the use
of different architecture machines, and perhaps also widely distributed. I
know that for pmemd there could be problems in mixing architectures, in that
there are a few calculations done on all nodes where identical results from
the computation are expected. Thus, you may be able to mix p3's and p4's,
but if you threw a completely different chip into the mix, there might be
problems. Secondly, mpich-g2 may need to do data translation between
different architectures, which would not be particularly efficient, and
mpich over gb ethernet is already stretched to handle the inter-node
communications load. Finally, I think a grid could be rather widely
distributed, with some rather low bandwidth segments in the net. Also not
so good for a tightly coupled application like sander or pmemd. If you ran
this stuff in such a way that you selected machines of the same architecture
connected by a high speed interconnect, it should basically work, though.
Regards - Bob Duke

----- Original Message -----
From: "putra abdullah" <putra77_at_rocketmail.com>
To: <amber_at_scripps.edu>
Sent: Sunday, March 06, 2005 9:55 PM
Subject: AMBER: amber with mpich-G2

> Hello,
>
> Just want to ask if amber can be use with mpich-G2 or not.
>
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