[petsc-users] DMPlex: Mapping cells before and after partitioning
Matthew Knepley
knepley at gmail.com
Wed Jan 29 07:52:15 CST 2020
On Tue, Jan 28, 2020 at 6:12 AM Matthew Knepley <knepley at gmail.com> wrote:
> 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.
>
I forgot to say, this is now merged.
Thanks,
Matt
> 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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>>>> To unsubscribe from this group and stop receiving emails from it, send
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>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/tdycores-dev/9AB001AF-8857-446A-AE69-E8D6A25CB8FA%40pnnl.gov
>>>> <https://protect2.fireeye.com/v1/url?k=711264f2-2da75a3d-71124ee7-0cc47adc5e60-a1731ca51d9b5203&q=1&e=4ec2bd09-0f1d-461c-bde7-4a0d8446ce3d&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F9AB001AF-8857-446A-AE69-E8D6A25CB8FA%2540pnnl.gov>
>>>> .
>>>>
>>>>
>>>>
>>>> --
>>>> 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>
>>>> .
>>>>
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
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>>>> an email to tdycores-dev+unsubscribe at googlegroups.com.
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>>>> <https://protect2.fireeye.com/v1/url?k=365c6512-6ae95bdd-365c4f07-0cc47adc5e60-f9b3b6f5e8918ac5&q=1&e=986b333d-b320-4f42-9c3c-fd4c4b3e0e40&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F7C23ABBA-2F76-4EAB-9834-9391AD77E18B%2540pnnl.gov%3Futm_medium%3Demail%26utm_source%3Dfooter>
>>>> .
>>>>
>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
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>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to tdycores-dev+unsubscribe at googlegroups.com.
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>>>> <https://protect2.fireeye.com/v1/url?k=d941301d-85f40fa4-d9411a08-0cc47adc5fce-ae3accbb18dd8e05&q=1&e=e8c1de75-1fa2-4cdd-a1a0-86a8a8811e0a&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2F8A7925AE-08F5-4F81-AAA5-B2FDC3D833B0%2540pnnl.gov%3Futm_medium%3Demail%26utm_source%3Dfooter>
>>>> .
>>>>
>>>
>>>
>>> --
>>> 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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>> To unsubscribe from this group and stop receiving emails from it, send an
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>> <https://protect2.fireeye.com/v1/url?k=bae87786-e65d483f-bae85d93-0cc47adc5fce-c50576531e121267&q=1&e=e8c1de75-1fa2-4cdd-a1a0-86a8a8811e0a&u=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Ftdycores-dev%2FCAMYG4Gn%253DxsVjjN8sX6km8ub%253Djkk8vxiU2DZVEi-4Kpbi_rM-0w%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter>
>> .
>> <ex_test.c>
>>
>>
>>
>> --
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>> .
>>
>>
>> --
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>> <https://groups.google.com/d/msgid/tdycores-dev/042A2165-BACC-41C0-8603-C4319C1A5176%40pnnl.gov?utm_medium=email&utm_source=footer>
>> .
>>
>
>
> --
> 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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