On Tue 14. Feb 2023 at 21:03, Dave May <dave.mayhe...@gmail.com> wrote:
> > > On Tue 14. Feb 2023 at 17:17, Jed Brown <j...@jedbrown.org> wrote: > >> Can you share a reproducer? I think I recall the format requiring certain >> things to be Int32. > > > By default, the byte offset used with the appended data format is UInt32. > I believe that’s where the sizeof(int) is coming from. This default is > annoying as it limits the total size of your appended data to be < 3 GB. > Oops, I meant to type 4 GB That said, in the opening of the paraview file you can add this attribute > > header_type="UInt64" > > then the size of the offset is now UInt64 and now large files can be > finally written. > > > Cheers, > Dave > > > > >> >> 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/> >> >> >> >
