[gmx-users] xtc_write() signals segmentation fault

[Murilo Kramar]

Hi Mark,

Probably is my library misuse  that provoked such behaviour. I compiled my
program using the -g flag. Using gdb and running the program I get the
following result after backtrace:

#0  0x00000000004069f4 in HydrateFinder::analyzeFrame (this=0x6125f0,
frnr=0,
    fr=..., pbc=0x7fffffffda70, pdata=0xb59dc0) at template.cpp:338

The core file generated is too large and can't be opened by 'gedit'. Sorry
for the basic question, but how can I further investigate that?

Best wishes,

Murilo.


On Tue, Jul 26, 2016 at 4:49 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You need to use a debugger to find out where the segfault happens, in order
> to know whether the problem is in the library or your use of it.
>
> Mark
>
> On Mon, 25 Jul 2016 21:39 Murilo Kramar <mkramar at u.rochester.edu> wrote:
>
> > Greetings everyone,
> >
> > My Gromacs version is 5.1.2 under CentOs 6.5.
> >
> > I'm currently using xtc_write() inside a template.cpp based program, but
> in
> > the very first frame it crashes and shows a segmentation fault message.
> >
> > The opening statement:
> >
> >  t_fileio* traj = open_xtc("new_traj.xtc", "w+");
> >
> > returns a number different than zero, indicating that the file was opened
> > correctly.
> >
> > After that, inside analyzeFrame I call write_xtc() to copy the actual
> > information into another file in order to check whether the function
> works
> > or not:
> >
> > write_xtc(traj,
> >               fr.atoms->nr, fr.step, fr.time,
> >               const_cast <real (*) [3]> (fr.box), fr.x, 10.0);
> >
> > The frame number 0 signals a segmentation fault. Is write_xtc recommended
> > in newer version of Gromacs?
> >
> >
> > Best Regards,
> >
> > Murilo. G. K.
> > --
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