[petsc-users] PetscViewer with 64bit
Dave May
dave.mayhem23 at gmail.com
Tue Feb 14 23:03:42 CST 2023
On Tue 14. Feb 2023 at 17:17, Jed Brown <jed at 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.
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.mike1021 at 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.mike1021 at 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.mike1021 at 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/>
> >>
>
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