Can you share a reproducer? I think I recall the format requiring certain things to be Int32.
Mike Michell <mi.mike1...@gmail.com> writes: > Thanks for the note. > I understood that PETSc calculates the offsets for me through "boffset" > variable in plexvtu.c file. Please correct me if it is wrong. > > If plexvtu.c has a bug, it could be around "write file header" part in > which the boffset is also computed. Is this correct? I am not using complex > number. > There are several mixed parts among "Int32, UInt8, PetscInt_FMT, > PetscInt64_FMT" in writing the header. > > Which combination of those flags is correct for 64bit indices? I am gonna > modify plexvtu.c file with "#if defined(PETSC_USE_64BIT_INDICES)" > statement, but I do not know what is the correct form of the header flag > for 64bit indices. > > It is also confusing to me: > boffset += gpiece[r].ncells * sizeof(PetscInt) + sizeof(int); > How is sizeof(PetscInt) different from sizeof(int)? > > Thanks, > Mike > > >> On Tue, Feb 14, 2023 at 11:45 AM Mike Michell <mi.mike1...@gmail.com> >> wrote: >> >>> I was trying to modify the header flags from "Int32" to "Int64", but the >>> problem was not resolved. Could I get any additional comments? >>> >> >> The calculated offsets are not correct I think. >> >> Matt >> >> >>> Thanks, >>> Mike >>> >>> >>>> Thanks for the comments. >>>> To be precise on the question, the entire part of the header of the .vtu >>>> file is attached: >>>> >>>> <?xml version="1.0"?> >>>> <VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian"> >>>> <UnstructuredGrid> >>>> <Piece NumberOfPoints="4872" NumberOfCells="4000"> >>>> <Points> >>>> <DataArray type="Float64" Name="Position" NumberOfComponents="3" >>>> format="appended" offset="0" /> >>>> </Points> >>>> <Cells> >>>> <DataArray type="Int32" Name="connectivity" >>>> NumberOfComponents="1" format="appended" offset="116932" /> >>>> <DataArray type="Int32" Name="offsets" >>>> NumberOfComponents="1" format="appended" offset="372936" /> >>>> <DataArray type="UInt8" Name="types" >>>> NumberOfComponents="1" format="appended" offset="404940" /> >>>> </Cells> >>>> <CellData> >>>> <DataArray type="Int32" Name="Rank" NumberOfComponents="1" >>>> format="appended" offset="408944" /> >>>> </CellData> >>>> <PointData> >>>> <DataArray type="Float64" Name="Vec_0x37c89c0_4Field_0.0" >>>> NumberOfComponents="1" format="appended" offset="424948" /> >>>> </PointData> >>>> </Piece> >>>> <Piece NumberOfPoints="4872" NumberOfCells="4000"> >>>> <Points> >>>> <DataArray type="Float64" Name="Position" NumberOfComponents="3" >>>> format="appended" offset="463928" /> >>>> </Points> >>>> <Cells> >>>> <DataArray type="Int32" Name="connectivity" >>>> NumberOfComponents="1" format="appended" offset="580860" /> >>>> <DataArray type="Int32" Name="offsets" >>>> NumberOfComponents="1" format="appended" offset="836864" /> >>>> <DataArray type="UInt8" Name="types" >>>> NumberOfComponents="1" format="appended" offset="868868" /> >>>> </Cells> >>>> <CellData> >>>> <DataArray type="Int32" Name="Rank" NumberOfComponents="1" >>>> format="appended" offset="872872" /> >>>> </CellData> >>>> <PointData> >>>> <DataArray type="Float64" Name="Vec_0x37c89c0_4Field_0.0" >>>> NumberOfComponents="1" format="appended" offset="888876" /> >>>> </PointData> >>>> </Piece> >>>> </UnstructuredGrid> >>>> <AppendedData encoding="raw"> >>>> >>>> >>>> Thanks, >>>> Mike >>>> >>>> >>>>> On Sun, Feb 12, 2023 at 6:15 PM Mike Michell <mi.mike1...@gmail.com> >>>>> wrote: >>>>> >>>>>> Dear PETSc team, >>>>>> >>>>>> I am a user of PETSc with Fortran. My code uses DMPlex to handle dm >>>>>> object. To print out output variable and mesh connectivity, I use >>>>>> VecView() >>>>>> by defining PetscSection on that dm and borrow a vector. The type of the >>>>>> viewer is set to PETSCVIEWERVTK. >>>>>> >>>>>> With 32bit indices, the above work flow has no issue. However, if >>>>>> PETSc is configured with 64bit indices, my output .vtu file has an error >>>>>> if >>>>>> I open the file with visualization tools, such as Paraview or Tecplot, >>>>>> saying that: >>>>>> "Cannot read cell connectivity from Cells in piece 0 because the >>>>>> "offsets" array is not monotonically increasing or starts with a value >>>>>> other than 0." >>>>>> >>>>>> If I open the .vtu file from terminal, I can see such a line: >>>>>> ... >>>>>> <DataArray type="Int32" Name="connectivity" NumberOfComponents="1" >>>>>> format="appended" offset="580860" /> >>>>>> ... >>>>>> >>>>>> I expected "DataArray type="Int64", since the PETSc has 64bit indices. >>>>>> Could I get recommendations that I need to check to resolve the issue? >>>>>> >>>>> >>>>> This is probably a bug. We will look at it. >>>>> >>>>> Jed, I saw that Int32 is hardcoded in plexvtu.c, but sizeof(PetscInt) >>>>> is used to calculate the offset, which looks inconsistent. Can you take a >>>>> look? >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> >>>>>> Thanks, >>>>>> Mike >>>>>> >>>>> >>>>> >>>>> -- >>>>> What most experimenters take for granted before they begin their >>>>> experiments is infinitely more interesting than any results to which their >>>>> experiments lead. >>>>> -- Norbert Wiener >>>>> >>>>> https://www.cse.buffalo.edu/~knepley/ >>>>> <http://www.cse.buffalo.edu/~knepley/> >>>>> >>>> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> <http://www.cse.buffalo.edu/~knepley/> >>
