[petsc-dev] problem with hdf5 plots

[Mark Adams]

FYI, by commenting out these lines in VecView_Plex_Local_HDF5, I can now
see my data;

  /* ierr = DMGetOutputSequenceNumber(dm, &seqnum, &seqval);CHKERRQ(ierr);
*/
  /* ierr = PetscViewerHDF5SetTimestep(viewer, seqnum);CHKERRQ(ierr); */
  /* ierr = DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar) seqval,
viewer);CHKERRQ(ierr); */

I'm not sure what the problem is here. Something in the DMSequenceView_HDF5
and/or petsc_gen_xdmf.py. I tried this with ParaView and got an error
message so it looks like it is not a Visit problem.



On Sat, Oct 22, 2016 at 1:51 PM, Mark Adams <mfadams at lbl.gov> wrote:

> 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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