Re: [AMBER-Developers] pmemd GLYCAM EP segfault fixed

From: Jodi Ann Hadden <>
Date: Mon, 4 Mar 2013 18:26:43 +0000

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 <> 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

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Received on Mon Mar 04 2013 - 10:30:02 PST
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