Re: [AMBER-Developers] pbsa crashes

From: MengJuei Hsieh <>
Date: Thu, 15 Oct 2009 15:14:46 -0700


I just committed our current progress on pbsa by cleaning up some
subroutines with incompatible licensing and adding additional non-linear
solvers. Let's see if you still get the same errors on this new one.

I am using gfortran (gcc version 4.5.0 20091001) on mac os x 10.6 for my
primary testing machine. But I am not sure if the gfortran version is a
deterministic factor.

Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
> From: Andreas Svrcek-Seiler <>
> Reply-To: AMBER Developers Mailing List <>
> Date: Thu, 15 Oct 2009 22:51:38 +0200 (CEST)
> To: AMBER Developers Mailing List <>
> Subject: [AMBER-Developers] pbsa crashes
> Dear colleagues,
> the current version of pbsa crashes during various pbsa test-cases,
> when I compile pbsa with gfortran (I tried 4.3.2 and 4.4.2).
> Curiously, every 10th time or so I run e.g.
> $AMBERHOME/test/pbsa_trx/Run.trxox.min, it runs through.
> However, valgrinding the run
> (as in valgrind ../../exe/pbsa -O -i mdin -c trxox.2.4ns.x ),
> I get loads of errors starting with
> Conditional jump or move depends on uninitialised value(s)
>     at 0x402B42: pbsa_ (_pbsa.f:514)
> Uninitialised value was created by a stack allocation
>    at 0x402518: pbsa_ (_pbsa.f:165)
> ...which doesn't tell me much (of course I looked up those lines).
> When I compile pbsa with ifort, the same test always runs through but
> valgrind still complains, but curiously at other locations:
> Conditional jump or move depends on uninitialised value(s)
> solvent_accessibilitysa_driver_mp_exclud_ (_sa_driver.f:1252)
> ...
> Uninitialised value was created by a stack allocation
> solvent_accessibilitysa_driver_mp_sa_arc_ (_sa_driver.f:970)
> Conclusion: I don't understand this and was unable to find the "real"
> cause. Maybe someone else should hav a look. Usually ignoring valgrind
> warnings comes back at you.
> best
> Andreas
> P.S.: According to an Intel(R)-guy, valgrind gives false warnings
> when icc/ifort use higly optimized string functions (strlen() etc.
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Received on Thu Oct 15 2009 - 15:30:03 PDT
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