Hi,
Thanks again for the report. gmx indeed had a bug, which has been fixed
before the 2016 release. (gmx checked the magic number, but then always
ignored whether it was valid... joy!)
Mark
On Sun, Mar 20, 2016 at 5:00 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I was able to reproduce the crash on another machine. I uploaded files
> you can use to reproduce the behavior to the bug report. Let me know
> if you need any more info.
>
> The current GitHub version of cpptraj now produces big-endian TRR
> files which work with Gromacs analysis tools.
>
> -Dan
>
> On Sun, Mar 20, 2016 at 9:29 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > I'm going to make sure I can reproduce this behavior on another
> > machine first. If so, I will then upload the files necessary for
> > reproducing the behavior.
> >
> > -Dan
> >
> > On Sun, Mar 20, 2016 at 9:26 AM, Mark Abraham <mark.j.abraham.gmail.com>
> wrote:
> >> 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
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 05 2016 - 08:30:03 PDT
