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 <[email protected]> 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 > >
