<div dir="ltr">FYI, by commenting out these lines in VecView_Plex_Local_HDF5, I can now see my data;<div><br></div><div> /* ierr = DMGetOutputSequenceNumber(dm, &seqnum, &seqval);CHKERRQ(ierr); */</div><div> /* ierr = PetscViewerHDF5SetTimestep(viewer, seqnum);CHKERRQ(ierr); */</div><div> /* ierr = DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar) seqval, viewer);CHKERRQ(ierr); */</div><div><br></div><div>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.</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Oct 22, 2016 at 1:51 PM, Mark Adams <span dir="ltr"><<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.<div><br></div><div>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. </div><div><br></div><div>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:</div><div><br></div><div><div>int i;</div><div>PetscPrintf(PETSC_COMM_WORLD,"<wbr>%s call PetscStackCallHDF5 xin->map->n=%6D: ",__FUNCT__,xin->map->n);</div><div>for (i=0;i<xin->map->n && i<3;i++){</div><div> PetscPrintf(PETSC_COMM_WORLD,<wbr>"%10.2e ",x[i]);</div><div>}</div><div>PetscPrintf(PETSC_COMM_WORLD,"<wbr>\n");</div><div> PetscStackCallHDF5(H5Dwrite,(<wbr>dset_id, memscalartype, memspace, filespace, plist_id, x));</div></div><div><br></div><div>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.</div><div><br></div><div>I wonder if: ${PETSC_DIR}/bin/petsc_gen_<wbr>xdmf.py ex3.h5; is getting confused with the time data. Anyone know of a way to look at the .h5 (raw) data?</div><div><br></div><div>Mark</div><div><font face="monospace, monospace"><br></font></div><div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 525: 5.01e+02 0.00e+00 -3.85e-16 </font></div><div><font face="monospace, monospace">==94708== Use of uninitialised value of size 8</font></div><div><font face="monospace, monospace">==94708== at 0x1019405BB: H5D__chunk_lookup (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x10195757A: H5D__chunk_collective_io (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x101959BAF: H5D__chunk_collective_write (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x101954E4A: H5Dwrite (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x100304C6B: VecView_MPI_HDF5 (pdvec.c:762)</font></div><div><font face="monospace, monospace">==94708== by 0x1002DEE52: VecView_Seq (bvec2.c:654)</font></div><div><font face="monospace, monospace">==94708== by 0x100317B55: VecView (vector.c:616)</font></div><div><font face="monospace, monospace">==94708== by 0x100DACCE6: DMPlexWriteCoordinates_HDF5_<wbr>Static (plexhdf5.c:422)</font></div><div><font face="monospace, monospace">==94708== by 0x100DAA23A: DMPlexView_HDF5 (plexhdf5.c:519)</font></div><div><font face="monospace, monospace">==94708== by 0x100C60109: DMView_Plex (plex.c:829)</font></div><div><font face="monospace, monospace">==94708== by 0x1009DC80E: DMView (dm.c:851)</font></div><div><font face="monospace, monospace">==94708== by 0x100B505D1: DMView_HDF5_p8est (pforest.c:1417)</font></div><div><font face="monospace, monospace">==94708== by 0x100B3F8E8: DMView_p8est (pforest.c:1440)</font></div><div><font face="monospace, monospace">==94708== by 0x1009DC80E: DMView (dm.c:851)</font></div><div><font face="monospace, monospace">==94708== by 0x10006CCBD: PetscObjectView (destroy.c:106)</font></div><div><font face="monospace, monospace">==94708== by 0x100093282: PetscObjectViewFromOptions (options.c:2810)</font></div><div><font face="monospace, monospace">==94708== by 0x1000277BF: DMViewFromOptions (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x10001F7E1: viewDMVec (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== by 0x10001799F: main (in ./ex3.arch-macosx-gnu-g)</font></div><div><font face="monospace, monospace">==94708== </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 1664: 1.00e+00 2.97e-03 -1.90e-03 </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 960: 1.00e+00 2.97e-03 -1.90e-03 </font></div><div><font face="monospace, monospace">0 TS dt 1.79271 time 0.</font></div><div><font face="monospace, monospace">1 TS dt 1.79271 time 1.79271</font></div><div><font face="monospace, monospace">2 TS dt 1.79271 time 3.58542</font></div><div><font face="monospace, monospace">TS Object: 1 MPI processes</font></div><div><font face="monospace, monospace"> type: ssp</font></div><div><font face="monospace, monospace"> maximum steps=2</font></div><div><font face="monospace, monospace"> maximum time=1e+12</font></div><div><font face="monospace, monospace"> total number of nonlinear solver iterations=0</font></div><div><font face="monospace, monospace"> total number of nonlinear solve failures=0</font></div><div><font face="monospace, monospace"> total number of linear solver iterations=0</font></div><div><font face="monospace, monospace"> total number of rejected steps=0</font></div><div><font face="monospace, monospace"> using relative error tolerance of 0.0001, using absolute error tolerance of 0.0001</font></div><div><font face="monospace, monospace"> Scheme: rks2</font></div><div><font face="monospace, monospace">CONVERGED_ITS at time 3.58542 after 2 steps</font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 525: 5.01e+02 0.00e+00 -3.85e-16 </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 1: 3.59e+00 </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 1: 3.59e+00 </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 1664: 1.02e+00 4.52e-04 -3.37e-03 </font></div><div><font face="monospace, monospace">VecView_MPI_HDF5 call PetscStackCallHDF5 xin->map->n= 960: 1.02e+00 4.52e-04 -3.37e-03 </font></div><div><font face="monospace, monospace">[0] done - cleanup</font></div></div><div><br></div></div>
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