[petsc-users] false-positive leak report in log_view?

[Mohammad Mirzadeh]

OK so I just ran the example under valgrind, and if I use two VecViews, it
complains about following leak:

==66838== 24,802 (544 direct, 24,258 indirect) bytes in 1 blocks are
definitely lost in loss record 924 of 926
==66838==    at 0x100009EBB: malloc (in
/usr/local/Cellar/valgrind/3.11.0/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
==66838==    by 0x10005E638: PetscMallocAlign (in
/usr/local/Cellar/petsc/3.7.2/real/lib/libpetsc.3.7.2.dylib)
==66838==    by 0x100405F00: DMCreate_DA (in
/usr/local/Cellar/petsc/3.7.2/real/lib/libpetsc.3.7.2.dylib)
==66838==    by 0x1003CFFA4: DMSetType (in
/usr/local/Cellar/petsc/3.7.2/real/lib/libpetsc.3.7.2.dylib)
==66838==    by 0x100405B7F: DMDACreate (in
/usr/local/Cellar/petsc/3.7.2/real/lib/libpetsc.3.7.2.dylib)
==66838==    by 0x1003F825F: DMDACreate2d (in
/usr/local/Cellar/petsc/3.7.2/real/lib/libpetsc.3.7.2.dylib)
==66838==    by 0x100001D89: main (main_test.cpp:7)

By I am destroying the dm ... also I dont get this when using a single
VecView. As a bonus info, PETSC_VIEWER_STDOUT_WORLD is just fine, so this
looks like it is definitely vtk related.

On Wed, Aug 3, 2016 at 2:05 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
wrote:

> On Wed, Aug 3, 2016 at 10:59 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Tue, Aug 2, 2016 at 12:40 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
>> wrote:
>>
>>> I often use the memory usage information in log_view as a way to check
>>> on memory leaks and so far it has worked perfect. However, I had long
>>> noticed a false-positive report in memory leak for Viewers, i.e.
>>> destruction count is always one less than creation.
>>>
>>
>> Yes, I believe that is the Viewer being used to print this information.
>>
>
> That makes sense.
>
>>
>>
>>> Today, I noticed what seems to be a second one. If you use VecView to
>>> write the same DA to vtk, i.e. call VecView(A, vtk); twice, it also report
>>> a memory leak for vectors, vecscatters, dm, etc. I am calling this a
>>> false-positive since the code is valgrind-clean.
>>>
>>> Is this known/expected?
>>>
>>
>> The VTK viewers have to hold everything they output until they are
>> destroyed since the format does not allow immediate writing.
>> I think the VTK viewer is not destroyed at the time of this output. Can
>> you make a small example that does this?
>>
>
> Here's a small example that illustrates the issues
>
> #include <petsc.h>
>
>
> int main(int argc, char *argv[]) {
>
>   PetscInitialize(&argc, &argv, NULL, NULL);
>
>
>   DM dm;
>
>   DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX,
>
>                -10, -10, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL,
>
>                &dm);
>
> //  DMDASetUniformCoordinates(dm, -1, 1, -1, 1, 0, 0);
>
>
>   Vec sol;
>
>   DMCreateGlobalVector(dm, &sol);
>
>   VecSet(sol, 0);
>
>
>   PetscViewer vtk;
>
>   PetscViewerVTKOpen(PETSC_COMM_WORLD, "test.vts", FILE_MODE_WRITE, &vtk);
>
>   VecView(sol, vtk);
>
> //  VecView(sol, vtk);
>
>   PetscViewerDestroy(&vtk);
>
>
>   DMDestroy(&dm);
>
>   VecDestroy(&sol);
>
>
>   PetscFinalize();
>
>   return 0;
>
> }
>
>
> If you uncomment the second VecView you get reports for leaks in
> VecScatter and dm. If you also uncomment the DMDASetUniformCoordinates, and
> use both VecViews, you also get a leak report for Vecs ... its quite
> bizarre ...
>
>
>> I have switched to HDF5 and XDMF due to the limitations of VTK format.
>>
>>
> I had used XDMF + raw binary in the past and was satisfied with the
> result. Do you write a single XDMF as a "post-processing" step when the
> simulation is finished? If I remember correctly preview could not open xmf
> files as time-series.
>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Here's the relevant bit from log_view:
>>>
>>> --- Event Stage 0: Main Stage
>>>
>>>               Vector     8              7       250992     0.
>>>       Vector Scatter     2              0            0     0.
>>>     Distributed Mesh     2              0            0     0.
>>> Star Forest Bipartite Graph     4              0            0     0.
>>>      Discrete System     2              0            0     0.
>>>            Index Set     4              4        83136     0.
>>>    IS L to G Mapping     2              0            0     0.
>>>               Viewer     2              1          784     0.
>>>
>>> ========================================================================================================================
>>>
>>>
>>
>>
>> --
>> 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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