[petsc-dev] problem with hdf5 plots

[Mark Adams]

I have tried a million things but I have a strange error that I am not
fixing and wanted to see if anyone has anh ideas.

I am printing an 8 field cell centered 3D field (960 variables total). I
initialize the field and print it. It looks perfect. I then do a TSSolve
and it looks fine except all the data is 0.0.

But If I do a VecView to standard just before the HDF5 print of the vector,
it has good looking data. And I added a print statement in pdvec.c before
the call to HDF5 like:

int i;
PetscPrintf(PETSC_COMM_WORLD,"%s call PetscStackCallHDF5 xin->map->n=%6D:
",__FUNCT__,xin->map->n);
for (i=0;i<xin->map->n && i<3;i++){
 PetscPrintf(PETSC_COMM_WORLD,"%10.2e ",x[i]);
}
PetscPrintf(PETSC_COMM_WORLD,"\n");
  PetscStackCallHDF5(H5Dwrite,(dset_id, memscalartype, memspace, filespace,
plist_id, x));

And this (appended) is what I get on one processor with valgrind. I see
perfectly good data plus the time step data in the second call. There is a
valgrind message in the first (good) call.

I wonder if:  ${PETSC_DIR}/bin/petsc_gen_xdmf.py ex3.h5; is getting
confused with the time data. Anyone know of a way to look at the .h5 (raw)
data?

Mark

VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=   525:   5.01e+02
0.00e+00  -3.85e-16
==94708== Use of uninitialised value of size 8
==94708==    at 0x1019405BB: H5D__chunk_lookup (in ./ex3.arch-macosx-gnu-g)
==94708==    by 0x10195757A: H5D__chunk_collective_io (in
./ex3.arch-macosx-gnu-g)
==94708==    by 0x101959BAF: H5D__chunk_collective_write (in
./ex3.arch-macosx-gnu-g)
==94708==    by 0x101954E4A: H5Dwrite (in ./ex3.arch-macosx-gnu-g)
==94708==    by 0x100304C6B: VecView_MPI_HDF5 (pdvec.c:762)
==94708==    by 0x1002DEE52: VecView_Seq (bvec2.c:654)
==94708==    by 0x100317B55: VecView (vector.c:616)
==94708==    by 0x100DACCE6: DMPlexWriteCoordinates_HDF5_Static
(plexhdf5.c:422)
==94708==    by 0x100DAA23A: DMPlexView_HDF5 (plexhdf5.c:519)
==94708==    by 0x100C60109: DMView_Plex (plex.c:829)
==94708==    by 0x1009DC80E: DMView (dm.c:851)
==94708==    by 0x100B505D1: DMView_HDF5_p8est (pforest.c:1417)
==94708==    by 0x100B3F8E8: DMView_p8est (pforest.c:1440)
==94708==    by 0x1009DC80E: DMView (dm.c:851)
==94708==    by 0x10006CCBD: PetscObjectView (destroy.c:106)
==94708==    by 0x100093282: PetscObjectViewFromOptions (options.c:2810)
==94708==    by 0x1000277BF: DMViewFromOptions (in ./ex3.arch-macosx-gnu-g)
==94708==    by 0x10001F7E1: viewDMVec (in ./ex3.arch-macosx-gnu-g)
==94708==    by 0x10001799F: main (in ./ex3.arch-macosx-gnu-g)
==94708==
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=  1664:   1.00e+00
2.97e-03  -1.90e-03
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=   960:   1.00e+00
2.97e-03  -1.90e-03
0 TS dt 1.79271 time 0.
1 TS dt 1.79271 time 1.79271
2 TS dt 1.79271 time 3.58542
TS Object: 1 MPI processes
  type: ssp
  maximum steps=2
  maximum time=1e+12
  total number of nonlinear solver iterations=0
  total number of nonlinear solve failures=0
  total number of linear solver iterations=0
  total number of rejected steps=0
  using relative error tolerance of 0.0001,   using absolute error
tolerance of 0.0001
    Scheme: rks2
CONVERGED_ITS at time 3.58542 after 2 steps
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=   525:   5.01e+02
0.00e+00  -3.85e-16
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=     1:   3.59e+00
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=     1:   3.59e+00
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=  1664:   1.02e+00
4.52e-04  -3.37e-03
VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n=   960:   1.02e+00
4.52e-04  -3.37e-03
[0] done - cleanup
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