[gmx-users] xtc_write() signals segmentation fault

[Mark Abraham]

Ok, but the trr format has no atom information, so either you need natoms
from elsewhere or to read in a matching structure file as other analysis
tools need to do.

Mark

On Fri, 29 Jul 2016 00:32 Murilo Kramar <mkramar at u.rochester.edu> wrote:

> 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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