[petsc-users] Optimized run crashes on one machine but not another

[Matthew Knepley]

On Wed, Aug 28, 2013 at 12:52 PM, Garnet Vaz <garnet.vaz at gmail.com> wrote:

> Thanks Jed. I did as you told and the code finally crashes on both
> builds. I installed the 3.4.2 release now.
>
> The problem now seems to come from DMPlexDistribute(). I have two
> versions to load the mesh. One creates a mesh using Triangle
> from PETSc and the other loads a mesh using DMPlexCreateFromCellList().
>
> Is the following piece of code for creating a mesh using Triangle right?
>

Okay, something is really very wrong here. It is calling
EnlargePartition(), but for
that path to be taken, you have to trip and earlier exception. It should
not be possible
to call it. So I think you have memory corruption somewhere.

Can you send a sample code we can run?

  Thanks,

      Matt


>   ierr = DMPlexCreateBoxMesh(comm,2,interpolate,&user->dm);CHKERRQ(ierr);
>   if (user->dm) {
>     DM        refinedMesh     = NULL;
>     DM        distributedMesh = NULL;
>     ierr =
> DMPlexSetRefinementLimit(user->dm,refinementLimit);CHKERRQ(ierr);
>     ierr = DMRefine(user->dm,PETSC_COMM_WORLD,&refinedMesh);CHKERRQ(ierr);
>     if (refinedMesh) {
>       ierr     = DMDestroy(&user->dm);CHKERRQ(ierr);
>       user->dm = refinedMesh;
>     }
>     ierr   =
> DMPlexDistribute(user->dm,"chaco",1,&distributedMesh);CHKERRQ(ierr);
>     if (distributedMesh) {
>       ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
>       user->dm  = distributedMesh;
>     }
>   }
>
> Using gdb, the code gives a SEGV during distribution. The backtrace when
> the fault
> occurs points to an invalid pointer for ISGetIndices(). Attached is a
> screenshot of the
> gdb backtrace.
> Do I need to set up some index set here?
>
> The same error occurs when trying to distribute a mesh using
> DMPlexCreateFromCellList().
>
> Thanks for the help.
>
>
> -
> Garnet
>
>
> On Wed, Aug 28, 2013 at 6:38 AM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>
>> Garnet Vaz <garnet.vaz at gmail.com> writes:
>>
>> > Hi,
>> >
>> > I just rebuilt PETSc on both my laptop and my desktop.
>> > On both machines the output of >grep GIT configure.log
>> >         Defined "VERSION_GIT" to
>> > ""d8f7425765acda418e23a679c25fd616d9da8153""
>> >         Defined "VERSION_DATE_GIT" to ""2013-08-27 10:05:35 -0500""
>>
>> Thanks for the report.  Matt just merged a bunch of DMPlex-related
>> branches (about 60 commits in total).  Can you 'git pull && make' to let
>> us know if the problem is still there?  (It may not fix the issue, but
>> at least we'll be debugging current code.)
>>
>> When dealing with debug vs. optimized issues, it's useful to configure
>> --with-debugging=0 COPTFLAGS='-O2 -g'.  This allows valgrind to include
>> line numbers, but it (usually!) does not affect whether the error
>> occurs.
>>
>> > My code runs on both machines in the debug build without causing
>> > any problems. When I try to run the optimized build, the code crashes
>> > with a SEGV fault on my laptop but not on the desktop. I have built
>> > PETSc using the same configure options.
>> >
>> > I have attached the outputs of valgrind for both my laptop/desktop for
>> > both the debug/opt builds. How can I figure out what differences are
>> > causing the errors in one case and not the other?
>>
>> It looks like an uninitialized variable.  Debug mode often ends up
>> initializing local variables where as optimized leaves junk in them.
>> Stack allocation alignment/padding is also often different.
>> Unfortunately, valgrind is less powerful for debugging stack corruption,
>> so the uninitialized warning is usually the best you get.
>>
>
>
>
> --
> Regards,
> Garnet
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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