Re: [petsc-users] DMView and DMLoad

Berend van Wachem Thu, 17 Feb 2022 01:07:00 -0800

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-ma...@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-ma...@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-ma...@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.vanwac...@ovgu.de>
*Sent:* Monday, December 6, 2021 3:39 PM

*To:* Sagiyama, Koki <k.sagiy...@imperial.ac.uk>; Hapla Vaclav <vaclav.ha...@erdw.ethz.ch>; PETSc users list <petsc-users@mcs.anl.gov>; Lawrence Mitchell <we...@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-ma...@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.vanwac...@ovgu.de>
*Sent:* Wednesday, November 17, 2021 3:16 PM
*To:* Hapla Vaclav <vaclav.ha...@erdw.ethz.ch>; PETSc users list <petsc-users@mcs.anl.gov>; Lawrence Mitchell <we...@gmx.li>; Sagiyama, Koki <k.sagiy...@imperial.ac.uk>
*Subject:* Re: [petsc-users] DMView and DMLoad

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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 <we...@gmx.li <mailto:we...@gmx.li <mailto:we...@gmx.li <mailto:we...@gmx.li>>>> wrote:
Hi Berend,
On 14 Sep 2021, at 12:23, Matthew Knepley <knep...@gmail.com <mailto:knep...@gmail.com <mailto:knep...@gmail.com

<mailto:knep...@gmail.com>>>> wrote:

On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem <berend.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de

<mailto:berend.vanwac...@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

restart-periodic.tar.gz
Description: application/gzip

#include "petsc.h"
#include "petscdmplex.h"
#include "petscdm.h"
#include "petscdmlabel.h"
#include "petscviewerhdf5.h"
#include "petscds.h"
#include "petscvec.h"
#include <time.h>
#include <stdlib.h>

int main(int argc, char **argv)
{

/**** Generate Periodic DM ******/
const PetscBool  cellSimplex = PETSC_FALSE;
const PetscBool  interpBefore = PETSC_TRUE;
PetscInt 		 dim = 3;
PetscInt 		 iSize[3];
PetscInt         i, numPoints;
PetscInt         overlap = 1, numFields = 1;
PetscScalar 	 Xmin[3], Xmax[3];
PetscScalar     *xVecArray;
DMBoundaryType 	 MeshPeriodicity[3]; /* Periodicity of mesh in each direction */
DM 				 dm, pdm = NULL;
PetscPartitioner part;
PetscErrorCode	 ierr;

srand(time(NULL));   /* Random values initialization */

ierr = PetscInitialize(&argc, &argv, NULL, NULL);
CHKERRQ(ierr);

// Number of cells in each direction
iSize[0] = 10;
iSize[1] = 10;
iSize[2] = 10;

// Dimensions
Xmin[0] = 0.0;
Xmin[1] = 0.0;
Xmin[2] = 0.0;
Xmax[0] = 1.0;
Xmax[1] = 1.0;
Xmax[2] = 1.0;

// Periodicity
MeshPeriodicity[0] = DM_BOUNDARY_PERIODIC;
MeshPeriodicity[1] = DM_BOUNDARY_PERIODIC;
MeshPeriodicity[2] = DM_BOUNDARY_PERIODIC;
//MeshPeriodicity[0] = DM_BOUNDARY_NONE;
//MeshPeriodicity[1] = DM_BOUNDARY_NONE;
//MeshPeriodicity[2] = DM_BOUNDARY_NONE;

// Create Mesh
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,cellSimplex,iSize,Xmin,Xmax,MeshPeriodicity,interpBefore,&dm);
CHKERRQ(ierr);

// Create Partition
ierr = DMPlexGetPartitioner(dm, &part);
CHKERRQ(ierr);
if (part)
{
  ierr = PetscPartitionerSetType(part, PETSCPARTITIONERPARMETIS);
  CHKERRQ(ierr);
  ierr = PetscPartitionerSetFromOptions(part);
  CHKERRQ(ierr);
}

// Distribute
ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);
CHKERRQ(ierr);
if (pdm)
{
	  ierr = DMDestroy(&dm);
	  CHKERRQ(ierr);
	  dm = pdm;
	  ierr = PetscObjectSetName((PetscObject) dm, "Distributed Mesh");
	  CHKERRQ(ierr);
 }

ierr = DMLocalizeCoordinates(dm);
CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);
CHKERRQ(ierr);

// Create Section on DM
PetscSection section;
PetscInt *numComp;
PetscInt *numDof;

ierr = PetscCalloc2(numFields, &numComp, numFields * (dim + 1), &numDof);
CHKERRQ(ierr);

for (i = 0; i < numFields; i++)
{
  numComp[i] = 1;
  numDof[i * (dim + 1) + dim] = 1;
}

ierr = DMSetNumFields(dm, numFields);
CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, NULL, numComp, numDof, 0, NULL, NULL, NULL, NULL, &section);
CHKERRQ(ierr);

// Push section onto the DM
ierr = DMSetLocalSection(dm, section);
CHKERRQ(ierr);
ierr = PetscFree2(numComp, numDof);
CHKERRQ(ierr);
ierr = PetscSectionDestroy(&section);
CHKERRQ(ierr);

/**** Create Vector Field => xGlobalVector *********/
Vec xGlobalVector;

ierr = DMCreateGlobalVector(dm, &xGlobalVector);
CHKERRQ(ierr);

// Initialize the Vec to 0
ierr = VecSet(xGlobalVector,0.0);
CHKERRQ(ierr);

// Fill the Vector with random values
ierr = VecGetArray(xGlobalVector, &xVecArray);
CHKERRQ(ierr);
ierr = VecGetLocalSize(xGlobalVector, &numPoints);
CHKERRQ(ierr);

for (i = 0; i < numPoints; i++) /* Loop over all internal cells */
{
	 xVecArray[i] = rand() % 20;
}

ierr = VecRestoreArray(xGlobalVector, &xVecArray);
CHKERRQ(ierr);

/**** Write DM + associated Vec ****/
PetscViewer H5Viewer;
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "periodic_box.h5", FILE_MODE_WRITE, &H5Viewer);
CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm, "plexA");
CHKERRQ(ierr);
ierr = PetscViewerPushFormat(H5Viewer, PETSC_VIEWER_HDF5_PETSC);
CHKERRQ(ierr);
ierr = DMPlexTopologyView(dm, H5Viewer);
CHKERRQ(ierr);
ierr = DMPlexLabelsView(dm, H5Viewer);
CHKERRQ(ierr);
ierr = DMPlexCoordinatesView(dm, H5Viewer);
CHKERRQ(ierr);
ierr = PetscViewerPopFormat(H5Viewer);
CHKERRQ(ierr);

DM sdm;
PetscSection s;

ierr = DMClone(dm, &sdm);
CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)sdm, "dmA");
CHKERRQ(ierr);
ierr = DMGetGlobalSection(dm, &s);
CHKERRQ(ierr);
ierr = DMSetGlobalSection(sdm, s);
CHKERRQ(ierr);
ierr = DMPlexSectionView(dm, H5Viewer, sdm);
CHKERRQ(ierr);

Vec  vec;
PetscScalar *array;

ierr = DMGetGlobalVector(sdm, &vec);
CHKERRQ(ierr);

/*** Fill the vector xGlobalVector ***/
ierr = VecGetArray(vec, &array);
CHKERRQ(ierr);
ierr = VecGetLocalSize(xGlobalVector, &numPoints);
CHKERRQ(ierr);
ierr = VecGetArray(xGlobalVector, &xVecArray);
CHKERRQ(ierr);

for (i = 0; i < numPoints; i++) /* Loop over all internal cells */
{
      array[i] = xVecArray[i];
}

ierr = VecRestoreArray(vec, &array);
CHKERRQ(ierr);
ierr = VecRestoreArray(xGlobalVector, &xVecArray);
CHKERRQ(ierr);

ierr = PetscObjectSetName((PetscObject)vec, "vecA");
CHKERRQ(ierr);
ierr = DMPlexGlobalVectorView(dm, H5Viewer, sdm, vec);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&H5Viewer);
CHKERRQ(ierr);
/*** End of writing ****/

/*** Wait for all CPUs to end ***/
ierr = MPI_Barrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);

/*** Load ***/
ierr = DMDestroy(&dm);
CHKERRQ(ierr);
ierr = DMDestroy(&sdm);
CHKERRQ(ierr);

Vec Restart_xGlobalVector;
PetscSF sfO, sf, sfDist, globalDataSF, localDataSF;
DM distributedDM;

ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "periodic_box.h5", FILE_MODE_READ, &H5Viewer);
CHKERRQ(ierr);
ierr = DMCreate(PETSC_COMM_WORLD, &dm);
CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);
CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm, "plexA");
CHKERRQ(ierr);
ierr = PetscViewerPushFormat(H5Viewer, PETSC_VIEWER_HDF5_PETSC);
CHKERRQ(ierr);
ierr = DMPlexTopologyLoad(dm, H5Viewer, &sfO);
CHKERRQ(ierr);
ierr = DMPlexLabelsLoad(dm, H5Viewer);
CHKERRQ(ierr);
ierr = DMPlexCoordinatesLoad(dm, H5Viewer, sfO);
CHKERRQ(ierr);
ierr = PetscViewerPopFormat(H5Viewer);
CHKERRQ(ierr);

ierr = DMPlexDistribute(dm, overlap, &sfDist, &distributedDM);
CHKERRQ(ierr);
if (distributedDM) {
      ierr = DMDestroy(&dm);
      CHKERRQ(ierr);
      dm = distributedDM;
      ierr = PetscObjectSetName((PetscObject)dm, "plexA");
      CHKERRQ(ierr);
}

ierr = PetscSFCompose(sfO, sfDist, &sf);
CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfO);
CHKERRQ(ierr);
ierr = PetscSFDestroy(&sfDist);
CHKERRQ(ierr);

ierr = DMClone(dm, &sdm);
CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)sdm, "dmA");
CHKERRQ(ierr);
ierr = DMPlexSectionLoad(dm, H5Viewer, sdm, sf, &globalDataSF, &localDataSF);
CHKERRQ(ierr);

/*** Load the Vector to Restart_xGlobalVector ***/
ierr = DMGetGlobalVector(sdm, &Restart_xGlobalVector);
CHKERRQ(ierr);
ierr = VecSet(Restart_xGlobalVector,0.0);
CHKERRQ(ierr);

ierr = PetscObjectSetName((PetscObject)Restart_xGlobalVector, "vecA");
CHKERRQ(ierr);
ierr = DMPlexGlobalVectorLoad(dm, H5Viewer, sdm,globalDataSF,Restart_xGlobalVector);
CHKERRQ(ierr);

ierr = PetscViewerDestroy(&H5Viewer);
CHKERRQ(ierr);

PetscEnd();
}

// *************** Write ***************
//PetscInt rank;
//ierr = MPI_Comm_rank(MPI_COMM_WORLD, &rank);
//CHKERRQ(ierr);
//
//if(rank == 0)
//{
//	for (i = 0; i < numPoints; i++)
//	{
//		printf(" Write %e %i, %i \n", xVecArray[i],i, rank);
//	}
//}
//
//ierr = MPI_Barrier(PETSC_COMM_WORLD);
//CHKERRQ(ierr);
//
//if(rank == 1)
//{
//	for (i = 0; i < numPoints; i++)
//	{
//		printf(" Write %e %i, %i \n", xVecArray[i],i, rank);
//	}
//}

// ***************** LOAD *******************
//ierr = VecGetArray(Restart_xGlobalVector, &xVecArray);
//CHKERRQ(ierr);
//ierr = VecGetLocalSize(Restart_xGlobalVector, &numPoints);
//CHKERRQ(ierr);
//
//if(rank == 0)
//{
//	for (i = 0; i < numPoints; i++)
//	{
//		printf(" LOAD %e %i, %i \n", xVecArray[i],i, rank);
//	}
//}
//
//ierr = MPI_Barrier(PETSC_COMM_WORLD);
//CHKERRQ(ierr);
//
//if(rank == 1)
//{
//	for (i = 0; i < numPoints; i++)
//	{
//		printf(" LOAD %e %i, %i \n", xVecArray[i],i, rank);
//	}
//}
//ierr = VecRestoreArray(Restart_xGlobalVector, &xVecArray);
//CHKERRQ(ierr);

Re: [petsc-users] DMView and DMLoad

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