[petsc-users] PetscViewer with 64bit

Jed Brown jed at jedbrown.org
Tue Feb 14 23:27:03 CST 2023 

Dave May <dave.mayhem23 at gmail.com> writes:

> 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"

You mean in the header of the .vtu? Do you happen to have an example or pointers to docs describing this feature? Can we always do this? It isn't mentioned in these: 

https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf   (PDF was created in 2003)
https://kitware.github.io/vtk-examples/site/VTKFileFormats/#xml-file-formats

> 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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