[gmx-developers] [PATCH] patch to fix segfault in gmx_anaeig.c
Alexey Shvetsov
alexxyum at gmail.com
Fri Aug 20 18:01:59 CEST 2010
Hi,
Am I right that close_trj shuld be replaced by close_trx in tools?
Since close_trj is deprecated. Or I miss something
2010/8/20 Berk Hess <hess at cbr.su.se>:
> 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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--
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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