[gmx-users] Re: Segmantation fault at g_traj
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 13 17:22:50 CEST 2010
Susanne Fritz wrote:
> Dear All,
> I think I have the same problem as Jorge Alberto Jover Galtier recently.
> Since I haven't found any solution within the archive, I try asking again.
> If I try to get the atom coordinates from a trajectory file with g_traj,
> g_traj exits with segmentation fault and the generated .xvg file is
> This always happens. It dosn't matter if the trajectory is big or small
> or if I extract coordinates for one or thousands of atoms or timesteps.
> It is even independent from the input file (.trr, .xtc, .gro). It
> happens on different machines and independently from the actual memory
> in use. And it is not a problem with the trajectory (checked with
> gmxcheck, vmd and trjconv).
> It only seems to be a problem with the newer version of g_traj. I
> recently switched from gmx 4.0.7 to 4.5.1. If I use a .gro, .mdp and
> .xtc file from a gmx 4.5.1 simulation and generate an "old" run input
> file with gmx 4.0.7, I can get the coordinates with g_traj (4.0.7)
> without problems.
> The segmentation fault always occurs when g_traj "has finished". For
> example: for the same trajectory, when I extract 100 or 200 timesteps
> there are always the last two timesteps missing in the .xvg-file. Giving
> the command >g_traj -f -s -ox repeatedly leads to .xvg-files stopping at
> approximately but not exactly the same position.
> Since the new gromacs version runs much more efficient on our system and
> g_traj is very important for my simulations, I would be very very
> grateful for any help!
Relevant fixes have been made in the git (development) version of the code. You
can check it out by following these instructions:
Or you can wait until version 4.5.2 is released, but I have no idea when that
will be (maybe soon?).
> best regards,
> additional information:
> gmx 4.5.1 was compiled with gcc 4.5 and fftw3 (according to the
> suggested installation procedure) on coreI7 and Athlon64 machines,
> running with suse 11.3 (64 bit).
> Jorge Alberto Jover Galtier wrote:
> > Dear friends:
> > Running several simulations, we have found a problem with the 'g_traj'
> > utility. It doesn't finish properly the files it generates, and gives a
> > segmentation fault. This is what we have done:
> > We are working with double precision. With the file .mdp that is at the
> > end of the mail, we have used 'grompp_d' to generate the .tpr file:
> > grompp_d -maxwarn 1000 -f temp_prueba_mail-list_001_mdpmdp -c
> > ../data/in/pep_ini.gro -r ../data/in/pep_ini.gro -p ../data/in/pep.top
> > -o temp_prueba_mail-list_001_tpr.tpr
> > After that, we ran the simulation with 'mdrun_d':
> > mdrun_d -s temp_prueba_mail-list_001_tpr.tpr -o
> > temp_prueba_mail-list_001_trr.trr -c
> > ../data/out/gro_unconstr_1.00_000001.gro -g
> > ../data/out/log_unconstr_1.00_000001.log -e
> > temp_prueba_mail-list_001_edr.edr
> > Then we tried to get the coordinates of the atoms with 'g_traj_d':
> > g_traj_d -f temp_prueba_mail-list_001_trr.trr -s
> > temp_prueba_mail-list_001_tpr.tpr -ox temp_prueba_mail-list_001_ox.xvg
> > At the terminal, we tell the program to get the coordinates from the
> > group 0 (system), although the error appears also for other groups.
> > Here is where the problem appears. When the program is about to finish,
> > it makes segmentation fault and ends abruptly. The .xvg file has only
> > some of the last lines missing, but those are the lines we are
> > interested in. We have tried different ways: we have used different
> > number of steps, we have get velocities and forces instead of
> > coordinates... and always the same problem appears.
> > We would be very thankful if someone could tell us what is going wrong.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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