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

[Dave May]

On 4 August 2016 at 10:10, Patrick Sanan <patrick.sanan at gmail.com> wrote:

> I have a patch that I got from Dave that he got from Jed which seems
> to be related to this. I'll make a PR.
>

Jed wrote this variant of the VTK viewer so please mark him as a reviewer
for my bug fix.


>
>
> On Wed, Aug 3, 2016 at 8:18 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
> wrote:
> > 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.
>

Mohammad,

I can confirm that this VTK functionality bleeds memory if you write more
than 1 vector to disk.

Cheers
  Dave



> >
> > 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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