[petsc-users] PetscViewer with 64bit

Dave May dave.mayhem23 at gmail.com
Tue Feb 14 23:24:02 CST 2023 

On Tue 14. Feb 2023 at 21:03, Dave May <dave.mayhem23 at gmail.com> wrote:

>
>
> 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.
>

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.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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