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

From: Ross Walker <>
Date: Thu, 28 Feb 2013 09:41:01 -0800

Excellent work Jason. :-)

Can you verify that you tested existing (no EP) runs as well like the JAC
NVE benchmark and FACTOR IX NVE benchmark. I know that a lot of the fixed
array sizes in PMEMD Bob had tuned to get maximum cache reuse so making
them arbitrarily bigger could hurt performance - unless they are only made
bigger in the EP cases such that only EP performance is affected.

A quick check on a modern CPU machine would verify if this is a concern or
not - the last time it was probably 'tweaked' was the pentium 4 days.

All the best

On 2/28/13 9:06 AM, "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
>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
>for sander and pmemd, so I had to set the FFT ewald parameters in the
>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

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Received on Thu Feb 28 2013 - 10:00:02 PST
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