[petsc-users] PetscViewer with 64bit
Jed Brown
jed at jedbrown.org
Thu Feb 16 21:39:50 CST 2023
Thanks, Dave.
Mike, can you test that this branch works with your large problems? I tested that .vtu works in parallel for small problems, where works = loads correctly in Paraview and VisIt.
https://gitlab.com/petsc/petsc/-/merge_requests/6081
Dave May <dave.mayhem23 at gmail.com> writes:
> On Tue 14. Feb 2023 at 21:27, Jed Brown <jed at jedbrown.org> wrote:
>
>> 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?
>
>
> Yeah, within the open VTKFile tag.
> Like this
> < VTKFile type=“xxx”, byte_order="LittleEndian" header_type="UInt64" >
>
> Do you happen to have an example or pointers to docs describing this
>> feature?
>
>
> Example yes - will send it to you tomorrow. Docs… not really. Only stuff
> like this
>
> https://kitware.github.io/paraview-docs/latest/python/paraview.simple.XMLPStructuredGridWriter.html
>
>
> https://kitware.github.io/paraview-docs/v5.8.0/python/paraview.simple.XMLMultiBlockDataWriter.html
>
> All the writers seem to support it.
>
>
> Can we always do this?
>
>
> Yep!
>
>
> 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
>>
>
> Yes I know. I’ve tied myself in knots for years because the of the
> assumption that the offset had to be an int.
>
> Credit for the discovery goes to Carsten Uphoff. He showed me this.
>
> Cheers,
> Dave
>
>
>
>> > 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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