[gmx-users] Re: Segmantation fault at g_traj

[Justin A. Lemkul]

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 
> incomplete.
> 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:

http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Stable_version

Or you can wait until version 4.5.2 is released, but I have no idea when that 
will be (maybe soon?).

-Justin

> best regards,
> Susanne
> 
> 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.
>  >

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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