I will wait until there is a Fermi fix before making the patch (unless we
should just release this now and release a Fermi patch when it's available?)
On Mon, Mar 4, 2013 at 1:26 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
> I've run several MDs with this now using pmemd.cuda. Seems to work, as
> long as you're on a Kepler card anyway, as we discussed. Compiled with GNU.
> Thanks Jason! :-)
>
> On Feb 28, 2013, at 12:06 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > This email is primarily targeted toward the GLYCAM folks, so sorry to the
> > rest of you for the noise.
> >
> > Jodi posted a recent reminder of this bug on bugzilla, which made me
> > realize how similar it was in some respects to a bug that I recently
> > (within the last 2 weeks) found in my own code. Sure enough, it was
> caused
> > by an array overflow due to an allocation of too little space -- it was a
> > pretty quick find when I knew what to look for and had the sander code to
> > compare with. The overflowed array was a 1-4 non-bonded pair array,
> which
> > is why all the EP-water models were unaffected.
> >
> > This was more of an informational message to the interested parties not
> > following the Amber git emails and/or the relevant bugzilla thread.
> >
> > I only tested this with the Intel compilers, so if someone in the GLYCAM
> > community can vet this with their systems and make sure it's the 'right'
> > fix (for GNU, too, preferably), then I can turn this into a bugfix. As a
> > side-note, the test system provided in bugzilla had different default
> nfft1
> > for sander and pmemd, so I had to set the FFT ewald parameters in the
> input
> > file to compare, but sander and pmemd gave identical answers.
> >
> > All the best,
> > Jason
> >
> > P.S. pmemd.cuda also appears to work for the test case, so enjoy the
> > sander->pmemd.cuda performance boost ;).
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> >
>
>
>
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 04 2013 - 11:00:02 PST
