[petsc-users] Writing Vector to HDF5 file - Valgrind debug

[Barry Smith]

  Very likely this is an unimportant issue within the HDF5 code that you don’t need to worry about.   We’ve found that many of the external packages we use in PETSc have places where they access uninitialized data; you might report it directly to the HDF5 team.

  Barry

On Jul 2, 2014, at 3:21 PM, Que Cat <quecat001 at gmail.com> wrote:

> Dear Petsc-User,
> 
> I used the following comment to write to a HDF5 file:
> 
> PetscViewer         H5viewer;
> PetscViewerHDF5Open(..., & H5viewer)
> PetscObjectSetName( (PetscObject) vector, Name);
> VecView(vector,H5viewer);
> PetscViewerDestroy(&H5viewer);
> 
> As I debug using valgrind, I received the following error:
> 
> ==29820== Use of uninitialised value of size 8
> ==29820==    at 0x828B87B: H5D__chunk_lookup (H5Dchunk.c:2274)
> ==29820==    by 0x82ACEA3: H5D__link_chunk_collective_io (H5Dmpio.c:856)
> ==29820==    by 0x82AC858: H5D__chunk_collective_io (H5Dmpio.c:696)
> ==29820==    by 0x82ACC8B: H5D__chunk_collective_write (H5Dmpio.c:781)
> ==29820==    by 0x82A8C47: H5D__write (H5Dio.c:672)
> ==29820==    by 0x82A72E9: H5Dwrite (H5Dio.c:265)
> ==29820==    by 0x53E6393: VecView_MPI_HDF5 (pdvec.c:786)
> ==29820==    by 0x53E6E5A: VecView_MPI (pdvec.c:851)
> ==29820==    by 0x5398A7C: VecView (vector.c:717)
> 
> I have checked that my vector used in VecView(vector,H5viewer) was initialized before calling VecView(vector,H5viewer). Check the output hdf5 file, all the data was recorded correctly. Should I worry about the error detect by valgrind? Thanks.
> 
> Que