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" <mjw.sdsc.edu>
To: "AMBER Developers Mailing List" <amber-developers.ambermd.org>
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
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Apr 16 2010 - 10:00:05 PDT
