[gmx-users] xtc_write() signals segmentation fault

[Murilo Kramar]

Hello,

The segmentation occurs because I was trying to access
t_trxframe::atoms::nr, but for some reason t_trxframe::atoms is returning
NULL


On Thu, Jul 28, 2016 at 4:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Generally one gets good value from running
>
> gdb --args template -f whatever
>
> And then you can inspect the state of the program. But we're off topic for
> this GROMACS list, so please have a look for gdb tutorials! :-)
>
> Mark
>
> On Fri, 29 Jul 2016 00:04 Murilo Kramar <mkramar at u.rochester.edu> wrote:
>
> > 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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