[gmx-users] segmentation fault

David van der Spoel spoel at xray.bmc.uu.se
Thu May 31 08:57:25 CEST 2007

Marius Retegan wrote:
> Hello
> I have a problem with Gromacs v3.3.1 installed in my $HOME on a SGI 
> Altix 350 with 10 Itanium 2 64 bits processors runing SuSE Linux. I've 
> tried to run a QMMM optimization (with CPMD for the QM part) but even 
> before CPMD is called the memory start to go crazy (I saw the memory 
> usage arriving at 4GB) and in the end I get "Segmentation fault".
> For the compilation of Gromacs I've used different setups: gcc version 
> 3.3.3 with fftw2 (instaled in my $HOME directory), gcc version 3.3.3 
> with fftw2 already compiled on the machine, icc (Intel Compiler) with 
> fftw2 and icc with mkl. Nothing worked.
> Than I thought that my input is messed up and I recompiled Gromacs on my 
> Linux box, a Intel Core 2 Duo with Fedora Core 6 with the gcc version 
> 4.1.1 20070105 and fftw2. The same *tpr file runs excelent on my 
> machine. So I guess that excludes the possibility that my input is bad.
> Could this be a compiler related error?
> I would appreciate very much any kind of help that you can give me.

it could be. but before you do complicated things like QMMD please 
verify that gromacs runs with normal systems and that CPMD runs 
normally. For gromacs you may want to upgrade the fftw library to 3.1.x

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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