Scott -- is the Fermi fix (and SM 1.3 trap) complete now? Ready for a
bugfix?
Thanks!
Jason
On Mon, Mar 4, 2013 at 7:42 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
> Fermi can be fixed.
>
> Pre-Fermi is hosed...
>
> GLYCAM-06EP creates large numbers of adjacent atoms with huge numbers of
> exclusions (up to 33 per atom) - more than I've ever seen before.
> Fortunately, I was forced to migrate exclusion data for Kepler into L1 so
> it handles it correctly OOTB.
>
> Fermi is currently hosed, but it can be switched to do the same but I
> suspect a perf hit will ensue.
>
> Today's solution is to run on Kepler. And given how cheap and powerful
> GTX680s are, I can't see this causing a lot of frowning.
>
>
>
>
> On Mon, Mar 4, 2013 at 3:31 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
>
> > Probably best to wait and patch when the fix is complete, just for the
> > sake of simplicity. I'm probably the only person in the whole world using
> > GLYCAM-06EP right now anyway. ;-)
> >
> > On Mar 4, 2013, at 1:32 PM, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > > 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
> > > _______________________________________________
> > > AMBER-Developers mailing list
> > > AMBER-Developers.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> > >
> > >
> >
> >
> >
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> >
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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 Wed Mar 06 2013 - 08:30:02 PST
