Re: [AMBER-Developers] Suggestions for dealing with mpich2-1.2.1p1

From: Robert Duke <>
Date: Fri, 16 Apr 2010 12:38:39 -0400

I would try Alexey Onofriev's monster GB benchmark if you really want to see
what happens. This thing has lots of atoms so the arrays are big. I expect
Ross has it lying around; if not I can forward you a copy but will have to
dig out the mdin from another machine (it is a big prmtop/inpcrd - at least
2 MB zipped).
Regards - Bob
----- Original Message -----
From: "Mark Williamson" <>
To: "AMBER Developers Mailing List" <>
Sent: Friday, April 16, 2010 12:30 PM
Subject: Re: [AMBER-Developers] Suggestions for dealing with mpich2-1.2.1p1

> Robert Duke wrote:
>> Hi Mark,
>> I had the same basic idea, but hesitate because it may have an impact as
>> the processor count goes up somewhere north of 64 - hard to say; I would
>> test it at like 256 on a high atom count system and see what happens
>> there. The reason for the concern, off the top of my head - the extra
>> copy in the master stalls the master a bit at all places this gets
>> called, and that has the impact of stalling everybody else. I do realize
>> this is a heck of a mess. I am not wildly passionate about GB
>> performance (nobody has ever made it a real priority; if the amber
>> community really wanted it superfast and I had funding to do it, I could
>> make it a heck of a lot faster), so aside from a bit of
>> pride-of-ownership and cringing over anything that slows pmemd down, I
>> could probably let it go.
> Ok, this is a good point. I'll get onto our Triton cluster later on today
> and repeat that benchmark at higher process counts as indicated. Is the
> size of the benchmark good for this testing or should I try something
> else?
> regards,
> Mark
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Received on Fri Apr 16 2010 - 10:00:05 PDT
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