[petsc-users] DMPlex: Mapping cells before and after partitioning

Matthew Knepley knepley at gmail.com
Tue Jan 28 05:12:23 CST 2020 

On Mon, Jan 27, 2020 at 9:57 PM 'Bisht, Gautam' via tdycores-dev <
tdycores-dev at googlegroups.com> wrote:

> Hi Matt,
>
> Could you issue MR to get changes from knepley/fix-dm-g2n-serial into
> PETSc master? I’m having some trouble during PETSc installation
> withexodusii using your branch, but the master seems fine.
>

Yep, just submitted the MR. Should be in soon.

  Thanks,

     Matt


> Thanks,
> -Gautam.
>
> On Jan 18, 2020, at 11:19 AM, 'Bisht, Gautam' via tdycores-dev <
> tdycores-dev at googlegroups.com> wrote:
>
> Hi Matt,
>
> Thanks for the fixes to the example.
>
> -Gautam
>
> On Jan 15, 2020, at 7:05 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Wed, Jan 15, 2020 at 4:08 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Wed, Jan 15, 2020 at 3:47 PM 'Bisht, Gautam' via tdycores-dev <
>> tdycores-dev at googlegroups.com> wrote:
>>
>>> Hi Matt,
>>>
>>> I’m running into error while using DMPlexNaturalToGlobalBegin/End and am
>>> hoping you have some insights in what I’m doing incorrectly. I create a
>>> 2x2x2 grid and distribute it across processors (N=1,2). I create a natural
>>> and a global vector; and then call DMPlexNaturalToGlobalBegin/End. Here are
>>> the two issues:
>>>
>>> - When N = 1, PETSc complains about DMSetUseNatural() not being called
>>> before DMPlexDistribute(), which is certainly not the case.
>>> - For N=1 and 2, global vector doesn’t have valid entries.
>>>
>>> I’m not sure how to create the natural vector and have used
>>> DMCreateGlobalVector() to create the natural vector, which could be the
>>> issue.
>>>
>>> Attached is the sample code to reproduce the error and below is the
>>> screen output.
>>>
>>
>> Cool. I will run it and figure out the problem.
>>
>
> 1) There was bad error reporting there. I am putting the fix in a new
> branch. It did not check for being on one process. If you run with
>
>        knepley/fix-dm-g2n-serial
>
>     It will work correctly in serial.
>
> 2) The G2N needs a serial data layout to work, so you have to make a
> Section _before_ distributing. I need to put that in the docs. I have
>      fixed your example to do this and attached it. I run it with
>
>      master *:~/Downloads/tmp/Gautam$ /PETSc3/petsc/bin/mpiexec -n 1
> ./ex_test -dm_plex_box_faces 2,2,2 -dm_view
> DM Object: 1 MPI processes
>   type: plex
> DM_0x84000000_0 in 3 dimensions:
>   0-cells: 27
>   1-cells: 54
>   2-cells: 36
>   3-cells: 8
> Labels:
>   marker: 1 strata with value/size (1 (72))
>   Face Sets: 6 strata with value/size (6 (4), 5 (4), 3 (4), 4 (4), 1 (4),
> 2 (4))
>   depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))
> Field p:
>   adjacency FVM++
> Natural vector:
>
> Vec Object: 1 MPI processes
>   type: seq
> 0.
> 1.
> 2.
> 3.
> 4.
> 5.
> 6.
> 7.
>
> Global vector:
>
> Vec Object: 1 MPI processes
>   type: seq
> 0.
> 1.
> 2.
> 3.
> 4.
> 5.
> 6.
> 7.
>
> Information about the mesh:
> [0] cell = 00; (0.250000, 0.250000, 0.250000); is_local = 1
> [0] cell = 01; (0.750000, 0.250000, 0.250000); is_local = 1
> [0] cell = 02; (0.250000, 0.750000, 0.250000); is_local = 1
> [0] cell = 03; (0.750000, 0.750000, 0.250000); is_local = 1
> [0] cell = 04; (0.250000, 0.250000, 0.750000); is_local = 1
> [0] cell = 05; (0.750000, 0.250000, 0.750000); is_local = 1
> [0] cell = 06; (0.250000, 0.750000, 0.750000); is_local = 1
> [0] cell = 07; (0.750000, 0.750000, 0.750000); is_local = 1
>
> master *:~/Downloads/tmp/Gautam$ /PETSc3/petsc/bin/mpiexec -n 2 ./ex_test
> -dm_plex_box_faces 2,2,2 -dm_view
> DM Object: Parallel Mesh 2 MPI processes
>   type: plex
> Parallel Mesh in 3 dimensions:
>   0-cells: 27 27
>   1-cells: 54 54
>   2-cells: 36 36
>   3-cells: 8 8
> Labels:
>   depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))
>   marker: 1 strata with value/size (1 (72))
>   Face Sets: 6 strata with value/size (1 (4), 2 (4), 3 (4), 4 (4), 5 (4),
> 6 (4))
> Field p:
>   adjacency FVM++
> Natural vector:
>
> Vec Object: 2 MPI processes
>   type: mpi
> Process [0]
> 0.
> 1.
> 2.
> 3.
> Process [1]
> 4.
> 5.
> 6.
> 7.
>
> Global vector:
>
> Vec Object: 2 MPI processes
>   type: mpi
> Process [0]
> 2.
> 3.
> 6.
> 7.
> Process [1]
> 0.
> 1.
> 4.
> 5.
>
> Information about the mesh:
> [0] cell = 00; (0.250000, 0.750000, 0.250000); is_local = 1
> [0] cell = 01; (0.750000, 0.750000, 0.250000); is_local = 1
> [0] cell = 02; (0.250000, 0.750000, 0.750000); is_local = 1
> [0] cell = 03; (0.750000, 0.750000, 0.750000); is_local = 1
> [0] cell = 04; (0.250000, 0.250000, 0.250000); is_local = 0
> [0] cell = 05; (0.750000, 0.250000, 0.250000); is_local = 0
> [0] cell = 06; (0.250000, 0.250000, 0.750000); is_local = 0
> [0] cell = 07; (0.750000, 0.250000, 0.750000); is_local = 0
> [1] cell = 00; (0.250000, 0.250000, 0.250000); is_local = 1
> [1] cell = 01; (0.750000, 0.250000, 0.250000); is_local = 1
> [1] cell = 02; (0.250000, 0.250000, 0.750000); is_local = 1
> [1] cell = 03; (0.750000, 0.250000, 0.750000); is_local = 1
> [1] cell = 04; (0.250000, 0.750000, 0.250000); is_local = 0
> [1] cell = 05; (0.750000, 0.750000, 0.250000); is_local = 0
> [1] cell = 06; (0.250000, 0.750000, 0.750000); is_local = 0
>
> [1] cell = 07; (0.750000, 0.750000, 0.750000); is_local = 0
>
> Thanks,
>
>    Matt
>
>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> >make ex_test
>>>
>>>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> >$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -np 1 ./ex_test
>>> Natural vector:
>>>
>>> Vec Object: 1 MPI processes
>>>   type: seq
>>> 0.
>>> 1.
>>> 2.
>>> 3.
>>> 4.
>>> 5.
>>> 6.
>>> 7.
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Object is in wrong state
>>> [0]PETSC ERROR: DM global to natural SF was not created.
>>> You must call DMSetUseNatural() before DMPlexDistribute().
>>>
>>> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
>>> <https://protect2.fireeye.com/v1/url?k=49ab253e-151e1a87-49ab0f2b-0cc47adc5fce-24c0c8c46a909b39&q=1&e=e8c1de75-1fa2-4cdd-a1a0-86a8a8811e0a&u=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fdocumentation%2Ffaq.html>
>>>  for trouble shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.12.2-537-g5f77d1e0e5
>>>  GIT Date: 2019-12-21 14:33:27 -0600
>>> [0]PETSC ERROR: ./ex_test on a darwin-gcc8 named WE37411 by bish218 Wed
>>> Jan 15 12:34:03 2020
>>> [0]PETSC ERROR: Configure options
>>> --with-blaslapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate
>>> --download-parmetis=yes --download-metis=yes --with-hdf5-dir=/opt/local
>>> --download-zlib --download-exodusii=yes --download-hdf5=yes
>>> --download-netcdf=yes --download-pnetcdf=yes --download-hypre=yes
>>> --download-mpich=yes --download-mumps=yes --download-scalapack=yes
>>> --with-cc=/opt/local/bin/gcc-mp-8 --with-cxx=/opt/local/bin/g++-mp-8
>>> --with-fc=/opt/local/bin/gfortran-mp-8 --download-sowing=1
>>> PETSC_ARCH=darwin-gcc8
>>> [0]PETSC ERROR: #1 DMPlexNaturalToGlobalBegin() line 289 in
>>> /Users/bish218/projects/petsc/petsc_v3.12.2/src/dm/impls/plex/plexnatural.c
>>>
>>> Global vector:
>>>
>>> Vec Object: 1 MPI processes
>>>   type: seq
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>>
>>> Information about the mesh:
>>>
>>> Rank = 0
>>> local_id = 00; (0.250000, 0.250000, 0.250000); is_local = 1
>>> local_id = 01; (0.750000, 0.250000, 0.250000); is_local = 1
>>> local_id = 02; (0.250000, 0.750000, 0.250000); is_local = 1
>>> local_id = 03; (0.750000, 0.750000, 0.250000); is_local = 1
>>> local_id = 04; (0.250000, 0.250000, 0.750000); is_local = 1
>>> local_id = 05; (0.750000, 0.250000, 0.750000); is_local = 1
>>> local_id = 06; (0.250000, 0.750000, 0.750000); is_local = 1
>>> local_id = 07; (0.750000, 0.750000, 0.750000); is_local = 1
>>>
>>>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>
>>> >$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -np 2 ./ex_test
>>> Natural vector:
>>>
>>> Vec Object: 2 MPI processes
>>>   type: mpi
>>> Process [0]
>>> 0.
>>> 1.
>>> 2.
>>> 3.
>>> Process [1]
>>> 4.
>>> 5.
>>> 6.
>>> 7.
>>>
>>> Global vector:
>>>
>>> Vec Object: 2 MPI processes
>>>   type: mpi
>>> Process [0]
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>> Process [1]
>>> 0.
>>> 0.
>>> 0.
>>> 0.
>>>
>>> Information about the mesh:
>>>
>>> Rank = 0
>>> local_id = 00; (0.250000, 0.750000, 0.250000); is_local = 1
>>> local_id = 01; (0.750000, 0.750000, 0.250000); is_local = 1
>>> local_id = 02; (0.250000, 0.750000, 0.750000); is_local = 1
>>> local_id = 03; (0.750000, 0.750000, 0.750000); is_local = 1
>>> local_id = 04; (0.250000, 0.250000, 0.250000); is_local = 0
>>> local_id = 05; (0.750000, 0.250000, 0.250000); is_local = 0
>>> local_id = 06; (0.250000, 0.250000, 0.750000); is_local = 0
>>> local_id = 07; (0.750000, 0.250000, 0.750000); is_local = 0
>>>
>>> Rank = 1
>>> local_id = 00; (0.250000, 0.250000, 0.250000); is_local = 1
>>> local_id = 01; (0.750000, 0.250000, 0.250000); is_local = 1
>>> local_id = 02; (0.250000, 0.250000, 0.750000); is_local = 1
>>> local_id = 03; (0.750000, 0.250000, 0.750000); is_local = 1
>>> local_id = 04; (0.250000, 0.750000, 0.250000); is_local = 0
>>> local_id = 05; (0.750000, 0.750000, 0.250000); is_local = 0
>>> local_id = 06; (0.250000, 0.750000, 0.750000); is_local = 0
>>> local_id = 07; (0.750000, 0.750000, 0.750000); is_local = 0
>>>
>>>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>
>>>
>>> -Gautam
>>>
>>>
>>>
>>>
>>> On Jan 9, 2020, at 4:57 PM, 'Bisht, Gautam' via tdycores-dev <
>>> tdycores-dev at googlegroups.com> wrote:
>>>
>>>
>>>
>>> On Jan 9, 2020, at 4:25 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>> On Thu, Jan 9, 2020 at 1:35 PM 'Bisht, Gautam' via tdycores-dev <
>>> tdycores-dev at googlegroups.com> wrote:
>>>
>>>
>>> > On Jan 9, 2020, at 2:58 PM, Jed Brown <jed at jedbrown.org> wrote:
>>> >
>>> > "'Bisht, Gautam' via tdycores-dev" <tdycores-dev at googlegroups.com>
>>> writes:
>>> >
>>> >>> Do you need to rely on the element number, or would coordinates (of a
>>> >>> centroid?) be sufficient for your purposes?
>>> >>
>>> >> I do need to rely on the element number.  In my case, I have a
>>> mapping file that remaps data from one grid onto another grid. Though I’m
>>> currently creating a hexahedron mesh, in the future I would be reading in
>>> an unstructured grid from a file for which I cannot rely on coordinates.
>>> >
>>> > How does the mapping file work and how is it generated?
>>>
>>> In CESM/E3SM, the mapping file is used to map fluxes or states between
>>> grids of two components (e.g. land & atmosphere). The mapping method can be
>>> conservative, nearest neighbor, bilinear, etc. While CESM/E3SM uses
>>> ESMF_RegridWeightGen to generate the mapping file, I’m using by own MATLAB
>>> script to create the mapping file.
>>>
>>> I’m surprised that this is not an issue for other codes that are using
>>> DMPlex. E.g In PFLOTRAN, when a user creates a custom unstructured grid,
>>> they can specify material property for each grid cell. So, there should be
>>> a way to create a vectorscatter that will scatter material property read in
>>> the “application”-order (i.e. order before calling DMPlexDistribute() ) to
>>> ghosted-order (i.e. order after calling DMPlexDistribute()).
>>>
>>>
>>> We did build something specific for this because some people wanted it.
>>> I wish I could purge this from all simulations. Its
>>> definitely destructive, but this is the way the world currently is.
>>>
>>> You want this:
>>>
>>>
>>> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexNaturalToGlobalBegin.html
>>> <https://protect2.fireeye.com/v1/url?k=5fd6bd0b-036383c4-5fd6971e-0cc47adc5e60-2156f2075f6da02c&q=1&e=986b333d-b320-4f42-9c3c-fd4c4b3e0e40&u=https%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-current%2Fdocs%2Fmanualpages%2FDMPLEX%2FDMPlexNaturalToGlobalBegin.html>
>>>
>>>
>>> Perfect.
>>>
>>> Thanks.
>>> -Gautam
>>>
>>>
>>>
>>>     Thanks,
>>>
>>>      Matt
>>>
>>>
>>> > We can locate points and create interpolation with unstructured grids.
>>> >
>>> > --
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>>> .
>>>
>>> --
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>>> .
>>>
>>>
>>>
>>> --
>>> 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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>>> <https://protect2.fireeye.com/v1/url?k=ce43b754-92f6899b-ce439d41-0cc47adc5e60-0a864c0f80b4c75d&q=1&e=4ec2bd09-0f1d-461c-bde7-4a0d8446ce3d&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2FCAMYG4Gm%253DSY%253DyDiYOdBm1j_KZO5NYhu80ZhbFTV23O%252Bv-zVvFnA%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter>
>>> .
>>>
>>>
>>>
>>> --
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>>> .
>>>
>>>
>>>
>>> --
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>>> .
>>>
>>
>>
>> --
>> 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/>
>
> --
> You received this message because you are subscribed to the Google Groups
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> .
> <ex_test.c>
>
>
>
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> .
>
>
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> .
>


-- 
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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