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.
On Wed, Aug 3, 2016 at 8:18 PM, Mohammad Mirzadeh <[email protected]> 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. > > On Wed, Aug 3, 2016 at 2:05 PM, Mohammad Mirzadeh <[email protected]> > wrote: >> >> On Wed, Aug 3, 2016 at 10:59 AM, Matthew Knepley <[email protected]> >> wrote: >>> >>> On Tue, Aug 2, 2016 at 12:40 PM, Mohammad Mirzadeh <[email protected]> >>> 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 >> >> >
