[petsc-users] local/global DMPlex Vec output
Matteo Semplice
matteo.semplice at uninsubria.it
Thu Oct 24 17:04:52 CDT 2024
Hi. The HDF5 solution looks good to me, but I now get this error
$ ../src/saveDemo
Creating mesh with (10,10) faces
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Need to call DMCreateDS() before calling DMGetDS()
[0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbj6ii1DUw$ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.21.5, unknown
[0]PETSC ERROR: ../src/saveDemo on a named dentdherens by matteo Fri
Oct 25 00:00:44 2024
[0]PETSC ERROR: Configure options --COPTFLAGS="-O3 -march=native
-mtune=native -mavx2" --CXXOPTFLAGS="-O3 -march=native -mtune=native
-mavx2" --FOPTFLAGS="-O3 -march=native -mtune=native -mavx2" --PETSC_ARCH=op
t --with-strict-petscerrorcode --download-hdf5
--prefix=/home/matteo/software/petsc/3.21-opt/ --with-debugging=0
--with-gmsh --with-metis --with-parmetis --with-triangle
PETSC_DIR=/home/matteo/software/petsc --
force
[0]PETSC ERROR: #1 DMGetDS() at
/home/matteo/software/petsc/src/dm/interface/dm.c:5525
[0]PETSC ERROR: #2 DMPlexInsertBoundaryValues_Plex() at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1136
[0]PETSC ERROR: #3 DMPlexInsertBoundaryValues() at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1274
[0]PETSC ERROR: #4 VecView_Plex_HDF5_Internal() at
/home/matteo/software/petsc/src/dm/impls/plex/plexhdf5.c:477
[0]PETSC ERROR: #5 VecView_Plex() at
/home/matteo/software/petsc/src/dm/impls/plex/plex.c:656
[0]PETSC ERROR: #6 VecView() at
/home/matteo/software/petsc/src/vec/vec/interface/vector.c:806
[0]PETSC ERROR: #7 main() at saveDemo.cpp:123
[0]PETSC ERROR: No PETSc Option Table entries
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
with errorcode 73.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
I attach the modified sample code that produced the above error.
Thanks
Matteo
Il 24/10/24 22:20, Matthew Knepley ha scritto:
> I just looked at the code. The VTK code is very old, and does not
> check for cell overlap.
>
> We have been recommending that people use either HDF5 or CGNS, both of
> which work in this case
> I believe. I can fix VTK if that is what you want, but it might take
> me a little while as it is very busy at
> work right now. However, if you output HDF5, then you can run
>
> ./lib/petsc/bin/petsc_gen_xdmf.py mesh.h5
>
> and it will generate an XDMF file so you can load it into ParaView. Or
> you can output CGNS which I think
> ParaView understands.
>
> Thanks,
>
> Matt
>
> On Thu, Oct 24, 2024 at 4:02 PM Semplice Matteo
> <matteo.semplice at uninsubria.it> wrote:
>
> Hi,
> I tried again today and have (re?)discovered this example
> https://urldefense.us/v3/__https://petsc.org/release/src/dm/impls/plex/tutorials/ex14.c.html__;!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbiLx3Cm6A$ ,
> but I cannot understand if in my case I should call
> PetscSFCreateSectionSF
> <https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFCreateSectionSF/__;!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbhTy11XoA$ > and,
> if so, how should I then activate the returned SF.
> Matteo
> ------------------------------------------------------------------------
> *Da:* Semplice Matteo
> *Inviato:* martedì 22 ottobre 2024 00:24
> *A:* Matthew Knepley <knepley at gmail.com>
> *Cc:* PETSc <petsc-users at mcs.anl.gov>
> *Oggetto:* Re: [petsc-users] local/global DMPlex Vec output
>
> Dear Matt,
>
> I guess you're right: thresholding by rank==0 and rank==1 in
> paraview reveals that it is indeed the overlap cells that are
> appear twice in the output.
>
> The attached file is not exactly minimal but hopefully short
> enough. If I run it in serial, all is ok, but with
>
> mpirun -np 2 ./saveDemo
>
> it creates a 10x10 grid, but I get "output.vtu" with a total of
> 120 cells. However the pointSF of the DMPlex seems correct.
>
> Thanks
>
> Matteo
>
> Il 21/10/24 19:15, Matthew Knepley ha scritto:
>> On Mon, Oct 21, 2024 at 12:22 PM Matteo Semplice via petsc-users
>> <petsc-users at mcs.anl.gov> wrote:
>>
>> Dear petsc-users,
>>
>> I am having issues with output of parallel data attached
>> to a DMPlex (or maybe more fundamental ones about DMPlex...).
>>
>> So I currently
>>
>> 1. create a DMPlex (DMPlexCreateGmshFromFile or
>> DMPlexCreateBoxMesh)
>> 2. partition it
>> 3. and create a section for my data layout with
>> DMPlexCreateSection(ctx.dmMesh, NULL, numComp, numDof,
>> numBC, NULL, NULL, NULL, NULL, &sUavg)
>> 4. DMSetLocalSection(ctx.dmMesh, sUavg)
>> 5. create solLoc and solGlob vectors with
>> DMCreateGlobalVector and DMCreateLocalVector
>> 6. solve ....
>> 7. VecView(ctx.solGlob, vtkViewer) on a .vtu file
>>
>> but when I load data in ParaView I get more cells than
>> expected and it is as if the cells in the halo are put twice
>> in output. (I could create a MWE if the above is not clear)
>>
>> I think we need an MWE here, because from the explanation above,
>> it should work.
>>
>> However, I can try to guess the problem. When you partition the
>> mesh, I am guessing that you have cells in the overlap. These cells
>> must be in the point SF in order for the global section to give
>> them a unique owner. Perhaps something has gone wrong here.
>>
>> Thanks,
>>
>> Matt
>>
>> I guess that the culprit is point (4), but if I replace it
>> with DMSetGlobalSection then I cannot create the local vector
>> at point (5).
>>
>> How should I handle this properly? In my code I need to
>> create both local and global vectors, to perform at least
>> GlobalToLocal and to save the global data.
>>
>> (On a side note, I tried also HDF5 but then it complains
>> about the DM not having a DS...; really, any working solution
>> that allows data to be explored with Paraview is fine)
>>
>> Thanks for any advice!
>>
>> Matteo Semplice
>>
>>
>>
>> --
>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbixfvYF1A$
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbiaSaocIA$ >
>
> --
> ---
> Professore Associato in Analisi Numerica
> Dipartimento di Scienza e Alta Tecnologia
> Università degli Studi dell'Insubria
> Via Valleggio, 11 - Como
>
>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbixfvYF1A$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!aQGZ72ku3riSEIsR_uRzVpbrS8s0nCNB91RQiigaVSevPhI-eLawlvrtybboEPpmaKHwaeqhEaTP5EpUDnBn2BsaaYMpSbiaSaocIA$ >
--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como
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