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
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>>
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--
-------------------------
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)
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Received on Sun Mar 20 2016 - 08:30:07 PDT
