[gmx-developers] gmxdump segmentation fault

Sarlo, Jeffrey S JSarlo at Central.UH.EDU
Tue Oct 29 15:59:31 CET 2013

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
-[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


More information about the gromacs.org_gmx-developers mailing list