<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Oct 29, 2013 at 4:16 PM, Erik Lindahl <span dir="ltr"><<a href="mailto:erik.lindahl@scilifelab.se" target="_blank">erik.lindahl@scilifelab.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
It's only limited by your memory.<br>
<br>
However, it might be a bug since this is a fairly large matrix. If you rebuild with debug info enabled (-g flag) </blockquote><div><br></div><div>...which is most simply done with cmake .. -DCMAKE_BUILD_TYPE=Debug</div><div>
</div><div>Mark</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">and run it in a debugger you should see what line the problem occurs on.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
Erik Lindahl <<a href="mailto:erik.lindahl@scilifelab.se">erik.lindahl@scilifelab.se</a>><br>
Professor of Biophysics<br>
Science for Life Laboratory<br>
Stockholm University & KTH<br>
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<div class="HOEnZb"><div class="h5"><br>
<br>
> On 29 okt 2013, at 15:59, "Sarlo, Jeffrey S" <<a href="mailto:JSarlo@Central.UH.EDU">JSarlo@Central.UH.EDU</a>> wrote:<br>
><br>
> 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?<br>
><br>
> $ gmxdump_mpi -mtx /tmp/nm.mtx<br>
> :-) G R O M A C S (-:<br>
><br>
> GRowing Old MAkes el Chrono Sweat<br>
><br>
> :-) VERSION 4.6.3 (-:<br>
><br>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,<br>
> Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,<br>
> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,<br>
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,<br>
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,<br>
> Michael Shirts, Alfons Sijbers, Peter Tieleman,<br>
><br>
> Berk Hess, David van der Spoel, and Erik Lindahl.<br>
><br>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
> Copyright (c) 2001-2012,2013, The GROMACS development team at<br>
> Uppsala University & The Royal Institute of Technology, Sweden.<br>
> check out <a href="http://www.gromacs.org" target="_blank">http://www.gromacs.org</a> for more information.<br>
><br>
> This program is free software; you can redistribute it and/or<br>
> modify it under the terms of the GNU Lesser General Public License<br>
> as published by the Free Software Foundation; either version 2.1<br>
> of the License, or (at your option) any later version.<br>
><br>
> :-) gmxdump_mpi (-:<br>
><br>
> Option Filename Type Description<br>
> ------------------------------------------------------------<br>
> -s topol.tpr Input, Opt. Run input file: tpr tpb tpa<br>
> -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<br>
> -e ener.edr Input, Opt. Energy file<br>
> -cp state.cpt Input, Opt. Checkpoint file<br>
> -p topol.top Input, Opt. Topology file<br>
> -mtx /tmp/nm.mtx Input, Opt! Hessian matrix<br>
> -om grompp.mdp Output, Opt. grompp input file with MD parameters<br>
><br>
> Option Type Value Description<br>
> ------------------------------------------------------<br>
> -[no]h bool no Print help info and quit<br>
> -[no]version bool no Print version info and quit<br>
> -nice int 0 Set the nicelevel<br>
> -[no]nr bool yes Show index numbers in output (leaving them out<br>
> makes comparison easier, but creates a useless<br>
> topology)<br>
> -[no]sys bool no List the atoms and bonded interactions for the<br>
> whole system instead of for each molecule type<br>
><br>
> Reading double precision matrix generated by Gromacs VERSION 4.5.6<br>
> Sparse matrix storage format, nrow=211077, ncols=211077<br>
> Segmentation fault<br>
><br>
> Thanks.<br>
> Jeff<br>
> --<br>
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</div></div></blockquote></div><br></div></div>