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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Received on Mon Mar 04 2013 - 16:00:03 PST
