[gmx-developers] [PATCH] patch to fix segfault in gmx_anaeig.c
Berk Hess
hess at cbr.su.se
Fri Aug 20 09:48:59 CEST 2010
Hi,
I fixed it.
Thanks for reporting this.
PS the close_trj(out) should not be removed, but should close status
instead.
Berk
On 08/20/2010 12:08 AM, Alexey Shvetsov wrote:
> 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
>
>
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