[gmx-developers] [PATCH] patch to fix segfault in gmx_anaeig.c
Alexey Shvetsov
alexxyum at gmail.com
Fri Aug 20 00:08:42 CEST 2010
Hi all!
Patch that fixes segfault in gmx_anaeig.c attached to mail. It can be
applyed with git am =)
Datails about segfault
(gdb) run -v eigenvec.trr -f ../tip49a.md.trr -s ../tip49a.md.tpr -eig
eigenval.xvg -proj -2d -extr -nframes 10
Starting program: /usr/bin/g_anaeig -v eigenvec.trr -f
../tip49a.md.trr -s ../tip49a.md.tpr -eig eigenval.xvg -proj -2d -extr
-nframes 10
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/lib64/ld-2.12.1.so.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libgmxana_d.so.6.0.0.debug
[Thread debugging using libthread_db enabled]
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libgsl.so.0.15.0.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libgslcblas.so.0.0.0.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libgmx_d.so.6.0.0.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libmd_d.so.6.0.0.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib64/libfftw3.so.3.2.4.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/usr/lib/gcc/x86_64-pc-linux-gnu/4.4.4/libgfortran.so.3.0.0.debug
warning: no loadable sections found in added symbol-file
/usr/lib64/debug/lib64/libz.so.1.2.5.debug
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 4.5-beta3-20100818-974c2df-dirty (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
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 General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /usr/bin/g_anaeig (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-v eigenvec.trr Input Full precision trajectory: trr trj cpt
-v2 eigenvec2.trr Input, Opt. Full precision trajectory: trr trj cpt
-f ../tip49a.md.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt
-s ../tip49a.md.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96
pdb
-n index.ndx Input, Opt. Index file
-eig eigenval.xvg Input, Opt! xvgr/xmgr file
-eig2 eigenval2.xvg Input, Opt. xvgr/xmgr file
-comp eigcomp.xvg Output, Opt. xvgr/xmgr file
-rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file
-proj proj.xvg Output, Opt! xvgr/xmgr file
-2d 2dproj.xvg Output, Opt! xvgr/xmgr file
-3d 3dproj.pdb Output, Opt. Structure file: gro g96 pdb etc.
-filt filtered.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-extr extreme.pdb Output, Opt! Trajectory: xtc trr trj gro g96 pdb cpt
-over overlap.xvg Output, Opt. xvgr/xmgr file
-inpr inprod.xpm Output, Opt. X PixMap compatible matrix file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-first int 1 First eigenvector for analysis (-1 is select)
-last int 8 Last eigenvector for analysis (-1 is till the
last)
-skip int 1 Only analyse every nr-th frame
-max real 0 Maximum for projection of the eigenvector on the
average structure, max=0 gives the extremes
-nframes int 10 Number of frames for the extremes output
-[no]split bool no Split eigenvector projections where time is zero
-[no]entropy bool no Compute entropy according to the Quasiharmonic
formula or Schlitter's method.
-temp real 298.15 Temperature for entropy calculations
-nevskip int 6 Number of eigenvalues to skip when computing the
entropy due to the quasi harmonic approximation.
When you do a rotational and/or translational fit
prior to the covariance analysis, you get 3 or 6
eigenvalues that are very close to zero, and
which should not be taken into account when
computing the entropy.
trn version: GMX_trn_file (double precision)
Read non mass weighted reference structure with 456 atoms from eigenvec.trr
Read non mass weighted average/minimum structure with 456 atoms from
eigenvec.trr
Read 1000 eigenvectors (for 456 atoms)
Read 1368 eigenvalues from eigenval.xvg
Program received signal SIGSEGV, Segmentation fault.
gmx_anaeig (argc=1, argv=<value optimized out>) at
../../../gromacs-9999/src/tools/gmx_anaeig.c:1002
1002 gpbc = gmx_rmpbc_init(&top.idef,ePBC,atoms->nr,topbox);
(gdb) up
#1 0x0000000000400649 in main (argc=-13832, argv=0x0) at
../../../gromacs-9999/src/tools/g_anaeig.c:49
49 gmx_anaeig(argc,argv);
(gdb) q
--
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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