[gmx-developers] gmxdump segmentation fault

[Erik Lindahl]

Hi,

It's only limited by your memory.

However, it might be a bug since this is a fairly large matrix. If you rebuild with debug info enabled (-g flag) and run it in a debugger you should see what line the problem occurs on.

Cheers,

Erik

Erik Lindahl <erik.lindahl at scilifelab.se>
Professor of Biophysics
Science for Life Laboratory
Stockholm University & KTH
Office (SciLifeLab): +46 8 524 81567
Cell (Sweden): +46 73 4618050
Cell (US): +1 267 3078746


> On 29 okt 2013, at 15:59, "Sarlo, Jeffrey S" <JSarlo at Central.UH.EDU> wrote:
> 
> I have a user that is using gromacs 4.5.6 and they get a segmentation fault when using gmxdump.  I just built the latest version of gromacs 4.6.3 for them in case something had been fixed, but still get the segmentation fault.  Following is the output from the command.  Is there a limit to the size of the system the user can build?
> 
> $ gmxdump_mpi -mtx /tmp/nm.mtx
>                         :-)  G  R  O  M  A  C  S  (-:
> 
>                       GRowing Old MAkes el Chrono Sweat
> 
>                            :-)  VERSION 4.6.3  (-:
> 
>        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
>           Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
>     Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
>        Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
>           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                Michael Shirts, Alfons Sijbers, Peter Tieleman,
> 
>               Berk Hess, David van der Spoel, and Erik Lindahl.
> 
>       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>         Copyright (c) 2001-2012,2013, The GROMACS development team at
>        Uppsala University & The Royal Institute of Technology, Sweden.
>            check out http://www.gromacs.org for more information.
> 
>         This program is free software; you can redistribute it and/or
>       modify it under the terms of the GNU Lesser General Public License
>        as published by the Free Software Foundation; either version 2.1
>             of the License, or (at your option) any later version.
> 
>                             :-)  gmxdump_mpi  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>  -s      topol.tpr  Input, Opt.  Run input file: tpr tpb tpa
>  -f       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
>  -e       ener.edr  Input, Opt.  Energy file
> -cp      state.cpt  Input, Opt.  Checkpoint file
>  -p      topol.top  Input, Opt.  Topology file
> -mtx    /tmp/nm.mtx  Input, Opt!  Hessian matrix
> -om     grompp.mdp  Output, Opt. grompp input file with MD parameters
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -[no]nr      bool   yes     Show index numbers in output (leaving them out
>                            makes comparison easier, but creates a useless
>                            topology)
> -[no]sys     bool   no      List the atoms and bonded interactions for the
>                            whole system instead of for each molecule type
> 
> Reading double precision matrix generated by Gromacs VERSION 4.5.6
> Sparse matrix storage format, nrow=211077, ncols=211077
> Segmentation fault
> 
> Thanks.
> Jeff
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