Yes
On Mar 6, 2013 8:01 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
> 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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> > > >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > 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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> > > 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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Received on Wed Mar 06 2013 - 11:30:03 PST
