Re: [AMBER-Developers] Problems with pmemd.cuda.MPI

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 13 Mar 2014 11:52:38 -0600

The reason I initially used intel compilers is they are the default on
stampede (and other HPC centers as well). However, the issue exists with
GNU compilers as well, version 4.4.6, mvapich 1.9, cuda 5.0 (diffs and log
attached). The differences are similar (though not 100% exactly) to those
seen with the intel compilers.

Let me know if you need any more information.

-Dan


On Thu, Mar 13, 2014 at 10:39 AM, Scott Le Grand <varelse2005.gmail.com>wrote:

> Why do you guys bother with Intel's compilers for the CUDA edition? I
> can't even get my hands on them without paying the big bucks so there's
> zero incentive for me to debug Intel compiler issues other than saying
> don't use them. That said, if it's broken with gcc, then it's interesting.
>
>
>
>
>
> On Thu, Mar 13, 2014 at 9:24 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi All,
> >
> > First, this time I promise I am using an up-to-date GIT tree:
> >
> > commit 8f81fff98e4d3095d0c66070eb3375f6a72708c0
> > Merge: 4de7ced 72c975d
> > Author: Pawel Janowski <pjanowsk.eden.rutgers.edu>
> > Date: Thu Mar 13 09:55:44 2014 -0400
> >
> > I am running on stampede (Tesla K20m) using intel compilers 13.1.0, cuda
> > 5.0, and mvapich 1.9. For pmemd.cuda.MPI the PME tests go haywire
> (absolute
> > error as high as 1.31e+06!!). No segfaults though. Diffs and log
> attached.
> > Going back to commit d8024087a4d8c4c1e801192839df57d760bcadd2 (Wed Feb 5
> > 22:17:48 2014 -0500) fixes the problems, although I have not
> systematically
> > gone back to see at what commit the code breaks. The problems happen even
> > if I run on just 1 thread. GB seems OK, and pmemd.cuda seems OK as well.
> >
> > Has anyone else seen issues like these? I will try using GNU compilers
> next
> > to see if the issue happens with them as well.
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> >
> _______________________________________________
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>



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)



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Received on Thu Mar 13 2014 - 11:00:04 PDT
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