[petsc-users] Is the results of `DMAdaptLabel` as expected in `src/dm/impls/plex/tests/ex20.c`
Zongze Yang
yangzongze at gmail.com
Wed Oct 5 01:39:57 CDT 2022
Matthew Knepley <knepley at gmail.com> 于2022年10月5日周三 00:33写道：
> On Tue, Oct 4, 2022 at 3:19 PM Zongze Yang <yangzongze at gmail.com> wrote:
>
>> Hi everyone,
>>
>> I am learning how to use the `DMAdaptLabel` for `DMPlex`, and found the
>> example `src/dm/impls/plex/tests/ex20.c` which label one cell to refine.
>>
>> 1. This example is just a uniform refinement when using the following
>> command. (see attached pdfs for the results).
>> ```
>> [real-int32-gcc] z2yang at ws5:~/opt/firedrake/real-int32-gcc/petsc/src/dm/impls/plex/tests$
>> ./ex20 -dm_plex_box_faces 3,3 -dm_coord_space 0 -pre_adapt_dm_view
>> ascii::ascii_info -post_adapt_dm_view draw:tikz:figure2.tex
>> ```
>> Is this expected for this example?
>>
>
> Hi Zongze,
>
> Yes, I agree this is not easy to see. If you give -dm_plex_transform_view,
> you can see the kind of transform being used
>
> knepley/pylith $:/PETSc3/petsc/petsc-pylith$ PETSC_ARCH=arch-pylith-opt
> make -j8 -f ./gmakefile test search="dm_impls_plex_tests-ex20_
> 2d" TIMEOUT=5000 EXTRA_OPTIONS="-dm_plex_transform_view"
> Using MAKEFLAGS: --jobserver-fds=3,4 -j --
> EXTRA_OPTIONS=-dm_plex_transform_view TIMEOUT=5000
> search=dm_impls_plex_tests-ex20_2d
> TEST
> arch-pylith-opt/tests/counts/dm_impls_plex_tests-ex20_2d.counts
> ok dm_impls_plex_tests-ex20_2d
> not ok diff-dm_impls_plex_tests-ex20_2d # Error code: 1
> # 11a12,14
> # > DMPlexTransform Object: 1 MPI process
> # > type: refine_regular
> # > Regular refinement DMPlexTransform_0x84000000_1
>
> You can see that it is regular refinement, so it ignores the input and
> refines everything. If you change it, you can get adaptive refinement,
>
> knepley/pylith $:/PETSc3/petsc/petsc-pylith$ PETSC_ARCH=arch-pylith-opt
> make -j8 -f ./gmakefile test search="dm_impls_plex_tests-ex20_
> 2d" TIMEOUT=5000 EXTRA_OPTIONS="-pre_adapt_dm_view draw
> -post_adapt_dm_view draw -draw_pause -1 -dm_plex_transform_type refine_sbr"
>
> I attached the plot.
>
>
Hi Matt,
Thanks for your clear explanation. Now, I see that by setting different
transform types I can refine the mesh by different algorithms. But why the
refinement algorithms are classified as transform?
2. I found there is a function named `DMAdaptLabel_Plex`, and
>> `DMAdaptLabel` did not call that function when the type of the dm is
>> `DMPlex`. Is the function `DMAdaptLabel_Plex` still in use?
>>
>
> No. I rewrote all the transformations last year. I think the new form is
> much smaller, cleaner, and more performant. I should delete this function,
> but I am finishing
> up the review of all adaptive refinement with Joe Wallwork at Imperial.
>
>
>> 3. `DMAdaptLabel` seems to lack some useful information when I use the
>> wrong adaptor. For example, if I set `-dm_adaptor mmg`, then the process
>> will give a segment fault because the `metric` passed to
>> `DMAdaptMetric_Mmg_Plex` is NULL, see the output below:
>> ```
>> [real-int32-gcc] z2yang at ws5:~/opt/firedrake/real-int32-gcc/petsc/src/dm/impls/plex/tests$
>> ./ex20 -dm_plex_box_faces 3,3 -dm_coord_space 0 -pre_adapt_dm_view
>> draw:tikz:figure1.tex -post_adapt_dm_view draw:tikz:figure2.tex -dm_adaptor
>> mmg
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
>> https://petsc.org/release/faq/
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is
>> causing the crash.
>> Abort(59) on node 0 (rank 0 in comm 0): application called
>> MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> ```
>>
>
> Hmm, I at least get an error message:
>
> # [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> # [0]PETSC ERROR: Null argument, when expecting valid pointer
> # [0]PETSC ERROR: Null Pointer: Parameter # 1
> # [0]PETSC ERROR: WARNING! There are option(s) set that were not
> used! Could be the program crashed before they were used or a spelling
> mistake, etc!
> # [0]PETSC ERROR: Option left: name:-post_adapt_dm_view value:
> ascii::ascii_info
> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
> shooting.
> # [0]PETSC ERROR: Petsc Development GIT revision:
> v3.17.4-1472-ga50e2f9f007 GIT Date: 2022-09-23 13:01:31 +0000
> # [0]PETSC ERROR: ../ex20 on a arch-master-debug named
> MacBook-Pro.local by knepley Tue Oct 4 17:29:20 2022
> # [0]PETSC ERROR: Configure options --PETSC_ARCH=arch-master-debug
> --download-bamg --download-bison --download-chaco --download-ctetgen
> --download-egads --download-eigen --download-exodusii --download-fftw
> --download-hpddm --download-ks --download-libceed --download-libpng
> --download-metis --download-ml --download-mmg --download-mumps
> --download-netcdf --download-opencascade --download-p4est
> --download-parmetis --download-parmmg --download-pnetcdf
> --download-pragmatic --download-ptscotch --download-scalapack
> --download-slepc --download-suitesparse --download-superlu_dist
> --download-tetgen --download-triangle
> --with-cmake-exec=/PETSc3/petsc/apple/bin/cmake
> --with-ctest-exec=/PETSc3/petsc/apple/bin/ctest
> --with-hdf5-dir=/PETSc3/petsc/apple --with-mpi-dir=/PETSc3/petsc/apple
> --with-petsc4py=1 --with-shared-libraries --with-slepc --with-zlib
> --download-muparser
> # [0]PETSC ERROR: #1 VecViewFromOptions() at
> /PETSc3/petsc/petsc-dev/src/vec/vec/interface/vector.c:627
> # [0]PETSC ERROR: #2 DMAdaptMetric_Mmg_Plex() at
> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/adaptors/mmg/mmgadapt.c:130
> # [0]PETSC ERROR: #3 DMAdaptLabel() at
> /PETSc3/petsc/petsc-dev/src/dm/interface/dmgenerate.c:179
> # [0]PETSC ERROR: #4 main() at
> /PETSc3/petsc/petsc-dev/src/dm/impls/plex/tests/ex20.c:24
> # [0]PETSC ERROR: PETSc Option Table entries:
> # [0]PETSC ERROR: -dm_adaptor mmg
> # [0]PETSC ERROR: -dm_coord_space 0
> # [0]PETSC ERROR: -dm_plex_box_faces 3,3
> # [0]PETSC ERROR: -post_adapt_dm_view ascii::ascii_info
> # [0]PETSC ERROR: -pre_adapt_dm_view ascii::ascii_info
> # [0]PETSC ERROR: ----------------End of Error Message -------send
> entire error message to petsc-maint at mcs.anl.gov----------
> # application called MPI_Abort(MPI_COMM_SELF, 85) - process 0
> ok dm_impls_plex_tests-ex20_2d # SKIP Command failed so no diff
>
I should use `--with-debugging=yes` when configuring petsc for more
information.
> I agree that it would be nice to segregate the adaptors into those that
> work with labels and those that work with metrics, but I thought we could
> have an automated system to convert between metrics and labels. However, I
> have not implemented it yet, since I am still trying to figure out exactly
> how everything should work.
>
That would be really nice!
Thanks,
Zongze
Thanks,
>
> Matt
>
>
>> Thanks,
>> Zongze Yang
>>
>
>
> --
> 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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20221005/151c70a8/attachment.html>
More information about the petsc-users
mailing list