[AMBER-Developers] pmemd GLYCAM EP segfault fixed

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 28 Feb 2013 12:06:58 -0500

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,

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
AMBER-Developers mailing list
Received on Thu Feb 28 2013 - 09:30:03 PST
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