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
>>>
>> _______________________________________________
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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)
--
-------------------------
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 - 09:30:04 PDT
