[petsc-users] DMView and DMLoad
Sagiyama, Koki
k.sagiyama at imperial.ac.uk
Thu Feb 24 05:07:29 CST 2022
Dear Berend,
DMClone() on a DMPlex object does not clone the PetscSection that that DMPlex object carries (https://petsc.org/main/docs/manualpages/DM/DMClone.html). I think you intended to do something like the following:
```
DMClone(dm, &sdm);
PetscObjectSetName((PetscObject)sdm, "dmA");
DMSetLocalSection(sdm, section);
...
DMCreateGlobalVector(sdm, &xGlobalVector);
...
```
Regarding save/load, current default I/O seems not working for some reason for periodic meshes as you reported. The latest implementation, however, seems working, so you can try using `-dm_plex_view_hdf5_storage_version 2.0.0` option when saving and see if it works.
Thanks,
Koki
________________________________
From: Berend van Wachem <berend.vanwachem at ovgu.de>
Sent: Thursday, February 17, 2022 9:06 AM
To: Sagiyama, Koki <k.sagiyama at imperial.ac.uk>; Hapla Vaclav <vaclav.hapla at erdw.ethz.ch>; PETSc users list <petsc-users at mcs.anl.gov>; Lawrence Mitchell <wence at gmx.li>
Subject: Re: [petsc-users] DMView and DMLoad
Dear Koki,
Many thanks for your help and sorry for the slow reply.
I haven't been able to get it to work successfully. I have attached a
small example that replicates the main features of our code. In this
example a Box with one random field is generated, saved and loaded. The
case works for non-periodic domains and fails for periodic ones. I've
also included the error output at the bottom of this email.
To switch between periodic and non-periodic, please comment/uncomment
lines 47 to 52 in src/main.c. To compile, the files "compile" and
"CMakeLists.txt" are included in a separate tar file, if you want to use
this. Your library paths should be updated in the latter file. The PETSc
main distribution is used.
Many thanks for your help!
Thanks and best regards,
Berend.
The error message with --with-debugging=no --with-errorchecking=no:
[0]PETSC ERROR: --------------------- Error Message
------------------------------------------------
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: Number of coordinates loaded 3168 does not match number
of vertices 1000
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.16.2-499-g9039b796d1
GIT Date: 2021-12-24 23:23:09 +0000
[0]PETSC ERROR: ./bin/restart_periodic on a arch-linux-c-opt named james
by serbenlo Thu Dec 30 20:53:22 2021
[0]PETSC ERROR: Configure options --with-debugging=no
--with-errorchecking=no --with-clean --download-metis=yes
--download-parmetis=yes --download-hdf5 --download-p4est
--download-triangle --download-tetgen
--with-zlib-lib=/usr/lib/x86_64-linux-gnu/libz.a
--with-zlib-include=/usr/include --with-mpi=yes --with-mpi-dir=/usr
--with-mpiexec=/usr/bin/mpiexec
[0]PETSC ERROR: #1 DMPlexCoordinatesLoad_HDF5_V0_Private() at
/usr/local/petsc_main/src/dm/impls/plex/plexhdf5.c:1387
[0]PETSC ERROR: #2 DMPlexCoordinatesLoad_HDF5_Internal() at
/usr/local/petsc_main/src/dm/impls/plex/plexhdf5.c:1419
[0]PETSC ERROR: #3 DMPlexCoordinatesLoad() at
/usr/local/petsc_main/src/dm/impls/plex/plex.c:2070
[0]PETSC ERROR: #4 main() at
/media/MANNHEIM/Arbeit/OvGU_PostDoc_2021/Projects/MF_Restart/Periodic_DM/restart-periodic/src/main.c:229
[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----------
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
The error message with --with-debugging=yes --with-errorchecking=yes:
[0]PETSC ERROR: --------------------- Error Message
-------------------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer
[1]PETSC ERROR: --------------------- Error Message
-------------------------------------------------
[1]PETSC ERROR: Null argument, when expecting valid pointer
[1]PETSC ERROR: Null Object: Parameter # 1
[1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[1]PETSC ERROR: Petsc Development GIT revision: v3.16.2-499-g9039b796d1
GIT Date: 2021-12-24 23:23:09 +0000
[1]PETSC ERROR: ./bin/restart_periodic on a arch-linux-c-opt named james
by serbenlo Thu Dec 30 20:17:22 2021
[1]PETSC ERROR: Configure options --with-debugging=yes
--with-errorchecking=yes --with-clean --download-metis=yes
--download-parmetis=yes --download-hdf5 --download-p4est
--download-triangle --download-tetgen
--with-zlib-lib=/usr/lib/x86_64-linux-gnu/libz.a
--with-zlib-include=/usr/include --with-mpi=yes --with-mpi-dir=/usr
--with-mpiexec=/usr/bin/mpiexec
[1]PETSC ERROR: #1 PetscSectionGetDof() at
/usr/local/petsc_main/src/vec/is/section/interface/section.c:807
[1]PETSC ERROR: [0]PETSC ERROR: Null Object: Parameter # 1
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.16.2-499-g9039b796d1
GIT Date: 2021-12-24 23:23:09 +0000
[0]PETSC ERROR: ./bin/restart_periodic on a arch-linux-c-opt named james
by serbenlo Thu Dec 30 20:17:22 2021
[0]PETSC ERROR: Configure options --with-debugging=yes
--with-errorchecking=yes --with-clean --download-metis=yes
--download-parmetis=yes --download-hdf5 --download-p4est
--download-triangle --download-tetgen
--with-zlib-lib=/usr/lib/x86_64-linux-gnu/libz.a
--with-zlib-include=/usr/include --with-mpi=yes --with-mpi-dir=/usr
--with-mpiexec=/usr/bin/mpiexec
#2 DMDefaultSectionCheckConsistency_Internal() at
/usr/local/petsc_main/src/dm/interface/dm.c:4489
[1]PETSC ERROR: #3 DMSetGlobalSection() at
/usr/local/petsc_main/src/dm/interface/dm.c:4583
[1]PETSC ERROR: [0]PETSC ERROR: #1 PetscSectionGetDof() at
/usr/local/petsc_main/src/vec/is/section/interface/section.c:807
[0]PETSC ERROR: #4 main() at
/media/MANNHEIM/Arbeit/OvGU_PostDoc_2021/Projects/MF_Restart/Periodic_DM/restart-periodic/src/main.c:164
[1]PETSC ERROR: No PETSc Option Table entries
[1]PETSC ERROR: #2 DMDefaultSectionCheckConsistency_Internal() at
/usr/local/petsc_main/src/dm/interface/dm.c:4489
[0]PETSC ERROR: #3 DMSetGlobalSection() at
/usr/local/petsc_main/src/dm/interface/dm.c:4583
----------------End of Error Message -------send entire error message to
petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_WORLD, 85) - process 1
[0]PETSC ERROR: #4 main() at
/media/MANNHEIM/Arbeit/OvGU_PostDoc_2021/Projects/MF_Restart/Periodic_DM/restart-periodic/src/main.c:164
[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----------
application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0
On 12/7/21 16:50, Sagiyama, Koki wrote:
> Hi Berend,
>
> I made some small changes to your code to successfully compile it and
> defined a periodic dm using DMPlexCreateBoxMesh(), but otherwise your
> code worked fine.
> I think we would like to see a complete minimal failing example. Can you
> make the working example that I pasted in earlier email fail just by
> modifying the dm(i.e., using the periodic mesh you are actually using)?
>
> Thanks,
> Koki
> ------------------------------------------------------------------------
> *From:* Berend van Wachem <berend.vanwachem at ovgu.de>
> *Sent:* Monday, December 6, 2021 3:39 PM
> *To:* Sagiyama, Koki <k.sagiyama at imperial.ac.uk>; Hapla Vaclav
> <vaclav.hapla at erdw.ethz.ch>; PETSc users list <petsc-users at mcs.anl.gov>;
> Lawrence Mitchell <wence at gmx.li>
> *Subject:* Re: [petsc-users] DMView and DMLoad
> Dear Koki,
>
> Thanks for your email. In the example of your last email
> DMPlexCoordinatesLoad() takes sF0 (PetscSF) as a third argument. In our
> code this modification does not fix the error when loading a periodic
> dm. Are we doing something wrong? I've included an example code at the
> bottom of this email, including the error output.
>
> Thanks and best regards,
> Berend
>
>
> /**** Write DM + Vec restart ****/
> PetscViewerHDF5Open(PETSC_COMM_WORLD, "result", FILE_MODE_WRITE, &H5Viewer);
> PetscObjectSetName((PetscObject)dm, "plexA");
> PetscViewerPushFormat(H5Viewer, PETSC_VIEWER_HDF5_PETSC);
> DMPlexTopologyView(dm, H5Viewer);
> DMPlexLabelsView(dm, H5Viewer);
> DMPlexCoordinatesView(dm, H5Viewer);
> PetscViewerPopFormat(H5Viewer);
>
> DM sdm;
> PetscSection s;
>
> DMClone(dm, &sdm);
> PetscObjectSetName((PetscObject)sdm, "dmA");
> DMGetGlobalSection(dm, &s);
> DMSetGlobalSection(sdm, s);
> DMPlexSectionView(dm, H5Viewer, sdm);
>
> Vec vec, vecOld;
> PetscScalar *array, *arrayOld, *xVecArray, *xVecArrayOld;
> PetscInt numPoints;
>
> DMGetGlobalVector(sdm, &vec);
> DMGetGlobalVector(sdm, &vecOld);
>
> /*** Fill the vectors vec and vecOld ***/
> VecGetArray(vec, &array);
> VecGetArray(vecOld, &arrayOld);
> VecGetLocalSize(xGlobalVector, &numPoints);
> VecGetArray(xGlobalVector, &xVecArray);
> VecGetArray(xOldGlobalVector, &xVecArrayOld);
>
> for (i = 0; i < numPoints; i++) /* Loop over all internal mesh points */
> {
> array[i] = xVecArray[i];
> arrayOld[i] = xVecArrayOld[i];
> }
>
> VecRestoreArray(vec, &array);
> VecRestoreArray(vecOld, &arrayOld);
> VecRestoreArray(xGlobalVector, &xVecArray);
> VecRestoreArray(xOldGlobalVector, &xVecArrayOld);
>
> PetscObjectSetName((PetscObject)vec, "vecA");
> PetscObjectSetName((PetscObject)vecOld, "vecB");
> DMPlexGlobalVectorView(dm, H5Viewer, sdm, vec);
> DMPlexGlobalVectorView(dm, H5Viewer, sdm, vecOld);
> PetscViewerDestroy(&H5Viewer);
> /*** end of writing ****/
>
> /*** Load ***/
> PetscViewerHDF5Open(PETSC_COMM_WORLD, "result", FILE_MODE_READ, &H5Viewer);
> DMCreate(PETSC_COMM_WORLD, &dm);
> DMSetType(dm, DMPLEX);
> PetscObjectSetName((PetscObject)dm, "plexA");
> PetscViewerPushFormat(H5Viewer, PETSC_VIEWER_HDF5_PETSC);
> DMPlexTopologyLoad(dm, H5Viewer, &sfO);
> DMPlexLabelsLoad(dm, H5Viewer);
> DMPlexCoordinatesLoad(dm, H5Viewer, sfO);
> PetscViewerPopFormat(H5Viewer);
>
> DMPlexDistribute(dm, Options->Mesh.overlap, &sfDist, &distributedDM);
> if (distributedDM) {
> DMDestroy(&dm);
> dm = distributedDM;
> PetscObjectSetName((PetscObject)dm, "plexA");
> }
>
> PetscSFCompose(sfO, sfDist, &sf);
> PetscSFDestroy(&sfO);
> PetscSFDestroy(&sfDist);
>
> DMClone(dm, &sdm);
> PetscObjectSetName((PetscObject)sdm, "dmA");
> DMPlexSectionLoad(dm, H5Viewer, sdm, sf, &globalDataSF, &localDataSF);
>
> /** Load the Vectors **/
> DMGetGlobalVector(sdm, &Restart_xGlobalVector);
> VecSet(Restart_xGlobalVector,0.0);
>
> PetscObjectSetName((PetscObject)Restart_xGlobalVector, "vecA");
> DMPlexGlobalVectorLoad(dm, H5Viewer, sdm,
> globalDataSF,Restart_xGlobalVector);
> DMGetGlobalVector(sdm, &Restart_xOldGlobalVector);
> VecSet(Restart_xOldGlobalVector,0.0);
>
> PetscObjectSetName((PetscObject)Restart_xOldGlobalVector, "vecB");
> DMPlexGlobalVectorLoad(dm, H5Viewer, sdm, globalDataSF,
> Restart_xOldGlobalVector);
>
> PetscViewerDestroy(&H5Viewer);
>
>
> /**** The error message when loading is the following ************/
>
> Creating and distributing mesh
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------
> [0]PETSC ERROR: Invalid argument
> [0]PETSC ERROR: Number of coordinates loaded 17128 does not match number
> of vertices 8000
> [0]PETSC ERROR: See https://petsc.org/release/faq/
> <https://petsc.org/release/faq/> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.16.1-435-g007f11b901
> GIT Date: 2021-12-01 14:31:21 +0000
> [0]PETSC ERROR: ./MF3 on a linux-gcc-openmpi-opt named
> ivt24.ads.uni-magdeburg.de by berend Mon Dec 6 16:11:21 2021
> [0]PETSC ERROR: Configure options --with-p4est=yes --with-partemis
> --with-metis --with-debugging=no --download-metis=yes
> --download-parmetis=yes --with-errorchecking=no --download-hdf5
> --download-zlib --download-p4est
> [0]PETSC ERROR: #1 DMPlexCoordinatesLoad_HDF5_V0_Private() at
> /home/berend/src/petsc_main/src/dm/impls/plex/plexhdf5.c:1387
> [0]PETSC ERROR: #2 DMPlexCoordinatesLoad_HDF5_Internal() at
> /home/berend/src/petsc_main/src/dm/impls/plex/plexhdf5.c:1419
> [0]PETSC ERROR: #3 DMPlexCoordinatesLoad() at
> /home/berend/src/petsc_main/src/dm/impls/plex/plex.c:2070
> [0]PETSC ERROR: #4 RestartMeshDM() at
> /home/berend/src/eclipseworkspace/multiflow/src/io/restartmesh.c:81
> [0]PETSC ERROR: #5 CreateMeshDM() at
> /home/berend/src/eclipseworkspace/multiflow/src/mesh/createmesh.c:61
> [0]PETSC ERROR: #6 main() at
> /home/berend/src/eclipseworkspace/multiflow/src/general/main.c:132
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: --download-hdf5
> [0]PETSC ERROR: --download-metis=yes
> [0]PETSC ERROR: --download-p4est
> [0]PETSC ERROR: --download-parmetis=yes
> [0]PETSC ERROR: --download-zlib
> [0]PETSC ERROR: --with-debugging=no
> [0]PETSC ERROR: --with-errorchecking=no
> [0]PETSC ERROR: --with-metis
> [0]PETSC ERROR: --with-p4est=yes
> [0]PETSC ERROR: --with-partemis
> [0]PETSC ERROR: -d results
> [0]PETSC ERROR: -o run.mf
> [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_WORLD
> with errorcode 62.
>
> 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.
> --------------------------------------------------------------------------
>
>
>
>
>
> On 11/19/21 00:26, Sagiyama, Koki wrote:
>> Hi Berend,
>>
>> I was not able to reproduce the issue you are having, but the following
>> 1D example (and similar 2D examples) worked fine for me using the latest
>> PETSc. Please note that DMPlexCoordinatesLoad() now takes a PetscSF
>> object as the third argument, but the default behavior is unchanged.
>>
>> /* test_periodic_io.c */
>>
>> #include <petscdmplex.h>
>> #include <petscsf.h>
>> #include <petsclayouthdf5.h>
>>
>> int main(int argc, char **argv)
>> {
>> DM dm;
>> Vec coordinates;
>> PetscViewer viewer;
>> PetscViewerFormat format = PETSC_VIEWER_HDF5_PETSC;
>> PetscSF sfO;
>> PetscErrorCode ierr;
>>
>> ierr = PetscInitialize(&argc, &argv, NULL, NULL); if (ierr) return ierr;
>> /* Save */
>> ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "periodic_example.h5",
>> FILE_MODE_WRITE, &viewer);CHKERRQ(ierr);
>> {
>> DM pdm;
>> PetscInt dim = 1;
>> const PetscInt faces[1] = {4};
>> DMBoundaryType periodicity[] = {DM_BOUNDARY_PERIODIC};
>> PetscInt overlap = 1;
>>
>> ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_FALSE,
>> faces, NULL, NULL, periodicity, PETSC_TRUE, &dm);CHKERRQ(ierr);
>> ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr);
>> ierr = DMDestroy(&dm);CHKERRQ(ierr);
>> dm = pdm;
>> ierr = PetscObjectSetName((PetscObject)dm, "periodicDM");CHKERRQ(ierr);
>> }
>> ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr);
>> ierr = PetscPrintf(PETSC_COMM_WORLD, "Coordinates before
>> saving:\n");CHKERRQ(ierr);
>> ierr = VecView(coordinates, NULL);CHKERRQ(ierr);
>> ierr = PetscViewerPushFormat(viewer, format);CHKERRQ(ierr);
>> ierr = DMPlexTopologyView(dm, viewer);CHKERRQ(ierr);
>> ierr = DMPlexCoordinatesView(dm, viewer);CHKERRQ(ierr);
>> ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
>> ierr = DMDestroy(&dm);CHKERRQ(ierr);
>> ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
>> /* Load */
>> ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "periodic_example.h5",
>> FILE_MODE_READ, &viewer);CHKERRQ(ierr);
>> ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
>> ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
>> ierr = PetscObjectSetName((PetscObject)dm, "periodicDM");CHKERRQ(ierr);
>> ierr = PetscViewerPushFormat(viewer, format);CHKERRQ(ierr);
>> ierr = DMPlexTopologyLoad(dm, viewer, &sfO);CHKERRQ(ierr);
>> ierr = DMPlexCoordinatesLoad(dm, viewer, sfO);CHKERRQ(ierr);
>> ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
>> ierr = DMGetCoordinates(dm, &coordinates);CHKERRQ(ierr);
>> ierr = PetscPrintf(PETSC_COMM_WORLD, "Coordinates after
>> loading:\n");CHKERRQ(ierr);
>> ierr = VecView(coordinates, NULL);CHKERRQ(ierr);
>> ierr = PetscSFDestroy(&sfO);CHKERRQ(ierr);
>> ierr = DMDestroy(&dm);CHKERRQ(ierr);
>> ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
>> ierr = PetscFinalize();
>> return ierr;
>> }
>>
>> mpiexec -n 2 ./test_periodic_io
>>
>> Coordinates before saving:
>> Vec Object: coordinates 2 MPI processes
>> type: mpi
>> Process [0]
>> 0.
>> Process [1]
>> 0.25
>> 0.5
>> 0.75
>> Coordinates after loading:
>> Vec Object: vertices 2 MPI processes
>> type: mpi
>> Process [0]
>> 0.
>> 0.25
>> 0.5
>> 0.75
>> Process [1]
>>
>> I would also like to note that, with the latest update, we can
>> optionally load coordinates directly on the distributed dm as (using
>> your notation):
>>
>> /* Distribute dm */
>> ...
>> PetscSFCompose(sfO, sfDist, &sf);
>> DMPlexCoordinatesLoad(dm, viewer, sf);
>>
>> To use this feature, we need to pass "-dm_plex_view_hdf5_storage_version
>> 2.0.0" option when saving topology/coordinates.
>>
>>
>> Thanks,
>> Koki
>> ------------------------------------------------------------------------
>> *From:* Berend van Wachem <berend.vanwachem at ovgu.de>
>> *Sent:* Wednesday, November 17, 2021 3:16 PM
>> *To:* Hapla Vaclav <vaclav.hapla at erdw.ethz.ch>; PETSc users list
>> <petsc-users at mcs.anl.gov>; Lawrence Mitchell <wence at gmx.li>; Sagiyama,
>> Koki <k.sagiyama at imperial.ac.uk>
>> *Subject:* Re: [petsc-users] DMView and DMLoad
>>
>> *******************
>> This email originates from outside Imperial. Do not click on links and
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>> If you trust the sender, add them to your safe senders list
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> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx>> to disable email
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>> *******************
>> Dear Vaclav, Lawrence, Koki,
>>
>> Thanks for your help! Following your advice and following your example
>> (https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
>
>> <https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
> <https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5>>)
>
>>
>> we are able to save and load the DM with a wrapped Vector in h5 format
>> (PETSC_VIEWER_HDF5_PETSC) successfully.
>>
>> For saving, we use something similar to:
>>
>> DMPlexTopologyView(dm, viewer);
>> DMClone(dm, &sdm);
>> ...
>> DMPlexSectionView(dm, viewer, sdm);
>> DMGetLocalVector(sdm, &vec);
>> ...
>> DMPlexLocalVectorView(dm, viewer, sdm, vec);
>>
>> and for loading:
>>
>> DMCreate(PETSC_COMM_WORLD, &dm);
>> DMSetType(dm, DMPLEX);
>> ...
>> PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_PETSC);
>> DMPlexTopologyLoad(dm, viewer, &sfO);
>> DMPlexLabelsLoad(dm, viewer);
>> DMPlexCoordinatesLoad(dm, viewer);
>> PetscViewerPopFormat(viewer);
>> ...
>> PetscSFCompose(sfO, sfDist, &sf);
>> ...
>> DMClone(dm, &sdm);
>> DMPlexSectionLoad(dm, viewer, sdm, sf, &globalDataSF, &localDataSF);
>> DMGetLocalVector(sdm, &vec);
>> ...
>> DMPlexLocalVectorLoad(dm, viewer, sdm, localDataSF, vec);
>>
>>
>> This works fine for non-periodic DMs but for periodic cases the line:
>>
>> DMPlexCoordinatesLoad(dm, H5Viewer);
>>
>> delivers the error message: invalid argument and the number of loaded
>> coordinates does not match the number of vertices.
>>
>> Is this a known shortcoming, or have we forgotten something to load
>> periodic DMs?
>>
>> Best regards,
>>
>> Berend.
>>
>>
>>
>> On 9/22/21 20:59, Hapla Vaclav wrote:
>>> To avoid confusions here, Berend seems to be specifically demanding XDMF
>>> (PETSC_VIEWER_HDF5_XDMF). The stuff we are now working on is parallel
>>> checkpointing in our own HDF5 format (PETSC_VIEWER_HDF5_PETSC), I will
>>> make a series of MRs on this topic in the following days.
>>>
>>> For XDMF, we are specifically missing the ability to write/load DMLabels
>>> properly. XDMF uses specific cell-local numbering for faces for
>>> specification of face sets, and face-local numbering for specification
>>> of edge sets, which is not great wrt DMPlex design. And ParaView doesn't
>>> show any of these properly so it's hard to debug. Matt, we should talk
>>> about this soon.
>>>
>>> Berend, for now, could you just load the mesh initially from XDMF and
>>> then use our PETSC_VIEWER_HDF5_PETSC format for subsequent saving/loading?
>>>
>>> Thanks,
>>>
>>> Vaclav
>>>
>>>> On 17 Sep 2021, at 15:46, Lawrence Mitchell <wence at gmx.li
>>>> <mailto:wence at gmx.li <mailto:wence at gmx.li <mailto:wence at gmx.li>>>> wrote:
>>>>
>>>> Hi Berend,
>>>>
>>>>> On 14 Sep 2021, at 12:23, Matthew Knepley <knepley at gmail.com
>>>>> <mailto:knepley at gmail.com <mailto:knepley at gmail.com
> <mailto:knepley at gmail.com>>>> wrote:
>>>>>
>>>>> On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem
>>>>> <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de
> <mailto:berend.vanwachem at ovgu.de>>>> wrote:
>>>>> Dear PETSc-team,
>>>>>
>>>>> We are trying to save and load distributed DMPlex and its associated
>>>>> physical fields (created with DMCreateGlobalVector) (Uvelocity,
>>>>> VVelocity, ...) in HDF5_XDMF format. To achieve this, we do the
>>>>> following:
>>>>>
>>>>> 1) save in the same xdmf.h5 file:
>>>>> DMView( DM , H5_XDMF_Viewer );
>>>>> VecView( UVelocity, H5_XDMF_Viewer );
>>>>>
>>>>> 2) load the dm:
>>>>> DMPlexCreateFromfile(PETSC_COMM_WORLD, Filename, PETSC_TRUE, DM);
>>>>>
>>>>> 3) load the physical field:
>>>>> VecLoad( UVelocity, H5_XDMF_Viewer );
>>>>>
>>>>> There are no errors in the execution, but the loaded DM is distributed
>>>>> differently to the original one, which results in the incorrect
>>>>> placement of the values of the physical fields (UVelocity etc.) in the
>>>>> domain.
>>>>>
>>>>> This approach is used to restart the simulation with the last saved DM.
>>>>> Is there something we are missing, or there exists alternative routes to
>>>>> this goal? Can we somehow get the IS of the redistribution, so we can
>>>>> re-distribute the vector data as well?
>>>>>
>>>>> Many thanks, best regards,
>>>>>
>>>>> Hi Berend,
>>>>>
>>>>> We are in the midst of rewriting this. We want to support saving
>>>>> multiple meshes, with fields attached to each,
>>>>> and preserving the discretization (section) information, and allowing
>>>>> us to load up on a different number of
>>>>> processes. We plan to be done by October. Vaclav and I are doing this
>>>>> in collaboration with Koki Sagiyama,
>>>>> David Ham, and Lawrence Mitchell from the Firedrake team.
>>>>
>>>> The core load/save cycle functionality is now in PETSc main. So if
>>>> you're using main rather than a release, you can get access to it now.
>>>> This section of the manual shows an example of how to do
>>>> thingshttps://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
>>>> <https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
>
>> <https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
> <https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5>>>
>>>>
>>>> Let us know if things aren't clear!
>>>>
>>>> Thanks,
>>>>
>>>> Lawrence
>>>
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