[gmx-developers] [PATCH] patch to fix segfault in gmx_anaeig.c

Alexey Shvetsov alexxyum at gmail.com
Fri Aug 20 10:17:06 CEST 2010


Hi,

Ahh ok =)

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
>>
>>
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>



-- 
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



More information about the gromacs.org_gmx-developers mailing list