[gmx-developers] gmxdump segmentation fault

[Mark Abraham]

On Tue, Oct 29, 2013 at 4:16 PM, Erik Lindahl <erik.lindahl at scilifelab.se>wrote:

> 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)


...which is most simply done with cmake .. -DCMAKE_BUILD_TYPE=Debug

Mark

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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