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

Wed Jan 15 15:08:42 CST 2020

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.

  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
> 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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>
> --
> 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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-- 
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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