<div dir="ltr">Toby, this problem is comming from Forest. It appears Forest takes a Vecs viewer during a solve (I don't see where else it could be). This is why the code worked before the solve, it was calling different methods than after the solve. Here is the problematic stack trace. In tracing what was written to the HDF5 file it looks like the only difference between the original (good) and the Forest method (bad) was that a vector of size one, with the time, was written. Actually it is written twice. (And I do see time stuff in Visit.)<div><br></div><div>Do you think you could take a look at this and see if you come up with a solution (like disable the time stuff) and I could test it or you can in branch mark/feature-picell:</div><div><br></div><div>src/dm/impls/picell/examples/tutorials > make ex3</div><div><div>src/dm/impls/picell/examples/tutorials > make runex3</div></div><div><br></div><div>and you should get a ex3.xmf file that Visit will show has all zero data.</div><div><br></div><div>Thanks,<br><div><br></div><div><div>#0 VecView (vec=0x1041b4a60, viewer=0x1041e6660) at /Users/markadams/Codes/petsc/src/vec/vec/interface/vector.c:583</div><div>#1 0x000000010006ca6e in PetscObjectView (obj=0x1041b4a60, viewer=0x1041e6660) at /Users/markadams/Codes/petsc/src/sys/objects/destroy.c:106</div><div>#2 0x0000000100093033 in PetscObjectViewFromOptions (obj=0x1041b4a60, bobj=warning: (Internal error: pc 0x0 in read in psymtab, but not in symtab.)</div><div><br></div><div>0x0, optionname=0x101d243a6 "-vec_view") at /Users/markadams/Codes/petsc/src/sys/objects/options.c:2810</div><div>#3 0x00000001003119b0 in VecViewFromOptions (A=0x1041b4a60, B=warning: (Internal error: pc 0x0 in read in psymtab, but not in symtab.)</div><div><br></div><div>0x0, name=0x101d243a6 "-vec_view") at /Users/markadams/Codes/petsc/include/petscvec.h:129</div><div>#4 0x00000001003117ef in VecAssemblyEnd (vec=0x1041b4a60) at /Users/markadams/Codes/petsc/src/vec/vec/interface/vector.c:193</div><div>#5 0x0000000100da814a in DMSequenceView_HDF5 (dm=0x1040e1260, seqname=0x101d6ed54 "time", seqnum=2, value=3.5868277344680086, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/plex/plexhdf5.c:32</div><div>#6 0x0000000100da683b in VecView_Plex_Local_HDF5 (v=0x1041f2a60, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/plex/plexhdf5.c:96</div><div>#7 0x0000000100c4d522 in VecView_Plex_Local (v=0x1041f2a60, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/plex/plex.c:88</div><div>#8 0x0000000100da8a06 in VecView_Plex_HDF5 (v=0x104b3c860, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/plex/plexhdf5.c:169</div><div>#9 0x0000000100c50dd2 in VecView_Plex (v=0x104b3c860, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/plex/plex.c:203</div><div>#10 0x0000000100b509d4 in VecView_p8est (vec=0x104b3c860, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/dm/impls/forest/p4est/pforest.c:4332</div><div>#11 0x0000000100317a13 in VecView (vec=0x104b3c860, viewer=0x104137a60) at /Users/markadams/Codes/petsc/src/vec/vec/interface/vector.c:619</div><div>#12 0x00000001000216a1 in viewDMVec ()</div><div>#13 0x000000010001a074 in main ()</div></div><div><br></div></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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