[petsc-users] PetscViewer with 64bit

[Mike Michell]

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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