[petsc-users] Creating a 3D dmplex mesh with cell list and distributing it
Swarnava Ghosh
swarnava89 at gmail.com
Wed Aug 14 23:50:42 CDT 2019
Hi Matthew,
Thank you for your response. It works right now.
dmplex before distribution
DM Object: 3 MPI processes
type: plex
DM_0x84000004_0 in 3 dimensions:
0-cells: 7 0 0
1-cells: 17 0 0
2-cells: 17 0 0
3-cells: 6 0 0
Labels:
depth: 4 strata with value/size (0 (7), 1 (17), 2 (17), 3 (6))
dmplex after distribution
DM Object: Parallel Mesh 3 MPI processes
type: plex
Parallel Mesh in 3 dimensions:
0-cells: 5 5 5
1-cells: 9 9 9
2-cells: 7 7 7
3-cells: 2 2 2
Labels:
depth: 4 strata with value/size (0 (5), 1 (9), 2 (7), 3 (2))
Thanks,
Swarnava
On Wed, Aug 14, 2019 at 8:47 PM Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Aug 14, 2019 at 10:48 PM Swarnava Ghosh <swarnava89 at gmail.com>
> wrote:
>
>> Hi Matthew,
>>
>> "It looks like you are running things with the wrong 'mpirun' ", Could
>> you please elaborate on this? I have another DMDA in my code, which is
>> correctly being parallelized.
>>
>
> Ah, I see it now. You are feeding in the initial mesh on every process.
> Normally one process generates the mesh
> and the other ones just give 0 for num cells and vertices.
>
> Thanks,
>
> Matt
>
>
>> Thanks,
>> SG
>>
>> On Wed, Aug 14, 2019 at 7:35 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Wed, Aug 14, 2019 at 10:23 PM Swarnava Ghosh <swarnava89 at gmail.com>
>>> wrote:
>>>
>>>> Hi Matthew,
>>>>
>>>> I added DMView(pCgdft->dmplex,PETSC_VIEWER_STDOUT_WORLD); before and
>>>> after distribution, and I get the following:
>>>>
>>>
>>> It looks like you are running things with the wrong 'mpirun'
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> dmplex before distribution
>>>> DM Object: 3 MPI processes
>>>> type: plex
>>>> DM_0x84000004_0 in 3 dimensions:
>>>> 0-cells: 7 7 7
>>>> 1-cells: 17 17 17
>>>> 2-cells: 17 17 17
>>>> 3-cells: 6 6 6
>>>> Labels:
>>>> depth: 4 strata with value/size (0 (7), 1 (17), 2 (17), 3 (6))
>>>> dmplex after distribution
>>>> DM Object: Parallel Mesh 3 MPI processes
>>>> type: plex
>>>> Parallel Mesh in 3 dimensions:
>>>> 0-cells: 7 7 7
>>>> 1-cells: 17 17 17
>>>> 2-cells: 17 17 17
>>>> 3-cells: 6 6 6
>>>> Labels:
>>>> depth: 4 strata with value/size (0 (7), 1 (17), 2 (17), 3 (6))
>>>>
>>>> Thanks,
>>>> SG
>>>>
>>>> On Wed, Aug 14, 2019 at 6:48 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> DMView() the mesh before and after distribution, so we can see what we
>>>>> have.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>> On Wed, Aug 14, 2019 at 5:30 PM Swarnava Ghosh via petsc-users <
>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>
>>>>>> Hi PETSc team and users,
>>>>>>
>>>>>> I am trying to create a 3D dmplex mesh
>>>>>> using DMPlexCreateFromCellList, then distribute it, and find out the
>>>>>> coordinates of the vertices owned by each process.
>>>>>> My cell list is as follows:
>>>>>> numCells: 6
>>>>>> numVertices: 7
>>>>>> numCorners: 4
>>>>>> cells:
>>>>>> 0
>>>>>> 3
>>>>>> 2
>>>>>> 1
>>>>>> 4
>>>>>> 0
>>>>>> 2
>>>>>> 1
>>>>>> 6
>>>>>> 4
>>>>>> 2
>>>>>> 1
>>>>>> 3
>>>>>> 6
>>>>>> 2
>>>>>> 1
>>>>>> 5
>>>>>> 4
>>>>>> 6
>>>>>> 1
>>>>>> 3
>>>>>> 5
>>>>>> 6
>>>>>> 1
>>>>>> vertexCoords:
>>>>>> -6.043000
>>>>>> -5.233392
>>>>>> -4.924000
>>>>>> -3.021500
>>>>>> 0.000000
>>>>>> -4.924000
>>>>>> -3.021500
>>>>>> -3.488928
>>>>>> 0.000000
>>>>>> -6.043000
>>>>>> 1.744464
>>>>>> 0.000000
>>>>>> 0.000000
>>>>>> -5.233392
>>>>>> -4.924000
>>>>>> 3.021500
>>>>>> 0.000000
>>>>>> -4.924000
>>>>>> 3.021500
>>>>>> -3.488928
>>>>>> 0.000000
>>>>>>
>>>>>> After reading this information, I do
>>>>>> ierr=
>>>>>> DMPlexCreateFromCellList(PETSC_COMM_WORLD,3,pCgdft->numCellsESP,pCgdft->NESP,pCgdft->numCornersESP,interpolate,pCgdft->cellsESP,3,pCgdft->vertexCoordsESP,&pCgdft->dmplex);
>>>>>>
>>>>>> ierr = DMPlexDistribute(pCgdft->dmplex,0,&pCgdft->dmplexSF,
>>>>>> &distributedMesh);CHKERRQ(ierr);
>>>>>>
>>>>>> if (distributedMesh) {
>>>>>> printf("mesh is distributed \n");
>>>>>> ierr = DMDestroy(&pCgdft->dmplex);CHKERRQ(ierr);
>>>>>> pCgdft->dmplex = distributedMesh;
>>>>>> }
>>>>>>
>>>>>> DMGetCoordinates(pCgdft->dmplex,&VC);
>>>>>> VecView(VC,PETSC_VIEWER_STDOUT_WORLD);
>>>>>>
>>>>>> On running this with 3 mpi processes, From VecView, I see that all
>>>>>> the processes own all the vertices. Why is the dmplex not being
>>>>>> distributed?
>>>>>>
>>>>>> The VecView is :
>>>>>> Process [0]
>>>>>> -6.043
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>> -6.043
>>>>>> 1.74446
>>>>>> 0.
>>>>>> 0.
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>> Process [1]
>>>>>> -6.043
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>> -6.043
>>>>>> 1.74446
>>>>>> 0.
>>>>>> 0.
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>> Process [2]
>>>>>> -6.043
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> -3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>> -6.043
>>>>>> 1.74446
>>>>>> 0.
>>>>>> 0.
>>>>>> -5.23339
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> 0.
>>>>>> -4.924
>>>>>> 3.0215
>>>>>> -3.48893
>>>>>> 0.
>>>>>>
>>>>>> Thanks,
>>>>>> SG
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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/>
>>>
>>
>
> --
> 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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