Re: [AMBER-Developers] pbsa crashes

From: Ray Luo <>
Date: Fri, 16 Oct 2009 09:33:42 -0700


Thanks a lot for tracing it down! We'll also take a look of the
fortran/c interface to sff.

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

Andreas Svrcek-Seiler wrote:
> Hi,
>> Testing with
>> gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)
>> has all the pbsa tests passing.
> ...I still (after a cvs update) get this weird behavior:
> Sometimes e.g. pbsa_trx runs through and then echoes PASSED, most
> times it crashes. I even tested other machines to exclude faulty
> hardware from the possible sources of error.
> Valgrind also still reports numerous instances of corrupted memory,
> no matter which compiler (also tried icc/ifort in ia32 mode) I use.
> usually one gets such on/off errors with competing threads and
> faulty openmp programming, but there's no openmp and only one thread,
> so I'm stumped.
> The last time I observed such puzzling behavior this was caused
> by the use of an uninitialzed variable (which was multiplied by zero,
> so it never caused numerical trouble). But this was in C (inside NAB),
> where it's much easier for me to follow the code.
> ...very interesting.
> best
> Andreas
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Received on Fri Oct 16 2009 - 10:00:03 PDT
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