Hi,
That initial report (from do_x3dna) isn't from a GROMACS tool. However,
Daniel has said it can be reproduced with gmx. To reproduce a segfault and
see how to stop it, I need one of these "little-endian TRR" input files
that might segfault. Hopefully someone who has cpptraj installed and knows
how to make one can do so, and e.g. upload at
http://redmine.gromacs.org/issues/1926 :-)
Mark
On Sun, Mar 20, 2016 at 4:03 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Mar 19, 2016 at 12:32 PM, Mark Abraham <mark.j.abraham.gmail.com>
> wrote:
>
> > Hi,
> >
> > On Sat, Mar 19, 2016 at 7:33 PM Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Fri, Mar 18, 2016 at 9:04 PM, Mark Abraham <
> mark.j.abraham.gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The GROMACS TRR format is based on XDR, which is defined to be a
> > > big-endian
> > > > format in a 20-year-old IETF standard. I think there is no good
> reason
> > to
> > > > write a tool to be able to write non-confoming XDR, and so no reason
> > for
> > > > any tools to be able to read such files. I also think we have better
> > > things
> > > > to do than rippling "please support little-endian TRR" requests to
> all
> > > the
> > > > different software packages that might handle such files! :-)
> > > >
> > >
> > > Perhaps, but the current behavior of choking by segfault is decidedly
> > > suboptimal.
> >
> >
> > I'm skeptical that this is the behaviour.
>
>
>
> http://redmine.gromacs.org/issues/1926
> -- the behavior there (and the reason it took so long to debug) is a
> GROMACS segfault in basic analysis.
>
> Here's the initial report: http://archive.ambermd.org/201603/0335.html
>
> And the repro by the cpptraj developer:
> http://archive.ambermd.org/201603/0336.html
>
> So yea, it was a segfault.
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 20 2016 - 08:30:06 PDT
