[petsc-users] reading and writing periodic DMPlex to file
Matthew Knepley
knepley at gmail.com
Tue Jan 24 10:26:05 CST 2023
On Tue, Jan 24, 2023 at 10:39 AM Berend van Wachem <berend.vanwachem at ovgu.de>
wrote:
> Dear Matt,
>
> I have been working on this now with Petsc-3.18.3
>
> 1) I can confirm that enforcing periodicity works for a single core
> simulation.
>
> 2) However, when using multiple cores, the code still hangs. Is there
> something I should do to fix this? Or should this be fixed in the next
> Petsc version?
>
Dang dang dang. I forgot to merge this fix. Thanks for reminding me. It is
now here:
https://gitlab.com/petsc/petsc/-/merge_requests/6001
> 3) This is strange, as it works fine for me.
>
Will try again with current main.
Thanks
Matt
> Thanks, best, Berend.
>
>
> On 12/15/22 18:56, Matthew Knepley wrote:
> > On Wed, Dec 14, 2022 at 3:58 AM Berend van Wachem
> > <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>> wrote:
> >
> >
> > Dear PETSc team and users,
> >
> > I have asked a few times about this before, but we haven't really
> > gotten
> > this to work yet.
> >
> > In our code, we use the DMPlex framework and are also interested in
> > periodic geometries.
> >
> > As our simulations typically require many time-steps, we would like
> to
> > be able to save the DM to file and to read it again to resume the
> > simulation (a restart).
> >
> > Although this works for a non-periodic DM, we haven't been able to
> get
> > this to work for a periodic one. To illustrate this, I have made a
> > working example, consisting of 2 files, createandwrite.c and
> > readandcreate.c. I have attached these 2 working examples. We are
> using
> > Petsc-3.18.2.
> >
> > In the first file (createandwrite.c) a DMPlex is created and written
> to
> > a file. Periodicity is activated on lines 52-55 of the code.
> >
> > In the second file (readandcreate.c) a DMPlex is read from the file.
> > When a periodic DM is read, this does not work. Also, trying to
> > 'enforce' periodicity, lines 55 - 66, does not work if the number of
> > processes is larger than 1 - the code "hangs" without producing an
> > error.
> >
> > Could you indicate what I am missing? I have really tried many
> > different
> > options, without finding a solution.
> >
> >
> > Hi Berend,
> >
> > There are several problems. I will eventually fix all of them, but I
> > think we can get this working quickly.
> >
> > 1) Periodicity information is not saved. I will fix this, but forcing it
> > should work.
> >
> > 2) You were getting a hang because the blocksize on the local
> > coordinates was not set correctly after loading
> > since the vector had zero length. This does not happen in any test
> > because HDF5 loads a global vector, but
> > most other things create local coordinates. I have a fix for this,
> > which I will get in an MR, Also, I moved DMLocalizeCoordinates()
> > after distribution, since this is where it belongs.
> >
> > knepley/fix-plex-periodic-faces *$:/PETSc3/petsc/petsc-dev$ git diff
> > diff --git a/src/dm/interface/dmcoordinates.c
> > b/src/dm/interface/dmcoordinates.c
> > index a922348f95b..6437e9f7259 100644
> > --- a/src/dm/interface/dmcoordinates.c
> > +++ b/src/dm/interface/dmcoordinates.c
> > @@ -551,10 +551,14 @@ PetscErrorCode DMGetCoordinatesLocalSetUp(DM dm)
> > PetscFunctionBegin;
> > PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
> > if (!dm->coordinates[0].xl && dm->coordinates[0].x) {
> > - DM cdm = NULL;
> > + DM cdm = NULL;
> > + PetscInt bs;
> >
> > PetscCall(DMGetCoordinateDM(dm, &cdm));
> > PetscCall(DMCreateLocalVector(cdm, &dm->coordinates[0].xl));
> > + // If the size of the vector is 0, it will not get the right block
> size
> > + PetscCall(VecGetBlockSize(dm->coordinates[0].x, &bs));
> > + PetscCall(VecSetBlockSize(dm->coordinates[0].xl, bs));
> > PetscCall(PetscObjectSetName((PetscObject)dm->coordinates[0].xl,
> > "coordinates"));
> > PetscCall(DMGlobalToLocalBegin(cdm, dm->coordinates[0].x,
> > INSERT_VALUES, dm->coordinates[0].xl));
> > PetscCall(DMGlobalToLocalEnd(cdm, dm->coordinates[0].x,
> > INSERT_VALUES, dm->coordinates[0].xl));
> >
> > 3) If I comment out forcing the periodicity, your example does not run
> > for me. I will try to figure it out
> >
> > [0]PETSC ERROR: --------------------- Error Message
> > --------------------------------------------------------------
> > [0]PETSC ERROR: Nonconforming object sizes
> > [0]PETSC ERROR: SF roots 4400 < pEnd 6000
> > [1]PETSC ERROR: --------------------- Error Message
> > --------------------------------------------------------------
> > [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!
> > [1]PETSC ERROR: Nonconforming object sizes
> > [0]PETSC ERROR: Option left: name:-start_in_debugger_no (no value)
> > source: command line
> > [1]PETSC ERROR: SF roots 4400 < pEnd 6000
> > [0]PETSC ERROR: See https://petsc.org/release/faq/
> > <https://petsc.org/release/faq/> for trouble shooting.
> > [0]PETSC ERROR: Petsc Development GIT revision: v3.18.1-494-g16200351da0
> > GIT Date: 2022-12-12 23:42:20 +0000
> > [1]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!
> > [1]PETSC ERROR: Option left: name:-start_in_debugger_no (no value)
> > source: command line
> > [0]PETSC ERROR: ./readandcreate on a arch-master-debug named
> > MacBook-Pro.cable.rcn.com <http://MacBook-Pro.cable.rcn.com> by knepley
> > Thu Dec 15 12:50:26 2022
> > [1]PETSC ERROR: See https://petsc.org/release/faq/
> > <https://petsc.org/release/faq/> for trouble shooting.
> > [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-mumps --download-muparser
> > --download-netcdf --download-opencascade --download-p4est
> > --download-parmetis --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
> > [1]PETSC ERROR: Petsc Development GIT revision: v3.18.1-494-g16200351da0
> > GIT Date: 2022-12-12 23:42:20 +0000
> > [0]PETSC ERROR: #1 PetscSectionCreateGlobalSection() at
> > /PETSc3/petsc/petsc-dev/src/vec/is/section/interface/section.c:1322
> > [1]PETSC ERROR: ./readandcreate on a arch-master-debug named
> > MacBook-Pro.cable.rcn.com <http://MacBook-Pro.cable.rcn.com> by knepley
> > Thu Dec 15 12:50:26 2022
> > [0]PETSC ERROR: #2 DMGetGlobalSection() at
> > /PETSc3/petsc/petsc-dev/src/dm/interface/dm.c:4527
> > [1]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-mumps --download-muparser
> > --download-netcdf --download-opencascade --download-p4est
> > --download-parmetis --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
> > [0]PETSC ERROR: #3 DMPlexSectionLoad_HDF5_Internal() at
> > /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plexhdf5.c:2750
> > [1]PETSC ERROR: #1 PetscSectionCreateGlobalSection() at
> > /PETSc3/petsc/petsc-dev/src/vec/is/section/interface/section.c:1322
> > [0]PETSC ERROR: #4 DMPlexSectionLoad() at
> > /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plex.c:2364
> > [1]PETSC ERROR: #2 DMGetGlobalSection() at
> > /PETSc3/petsc/petsc-dev/src/dm/interface/dm.c:4527
> > [0]PETSC ERROR: #5 main() at
> > /Users/knepley/Downloads/tmp/Berend/readandcreate.c:85
> > [1]PETSC ERROR: #3 DMPlexSectionLoad_HDF5_Internal() at
> > /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plexhdf5.c:2750
> > [0]PETSC ERROR: PETSc Option Table entries:
> > [0]PETSC ERROR: -malloc_debug (source: environment)
> > [1]PETSC ERROR: #4 DMPlexSectionLoad() at
> > /PETSc3/petsc/petsc-dev/src/dm/impls/plex/plex.c:2364
> > [1]PETSC ERROR: #5 main() at
> > /Users/knepley/Downloads/tmp/Berend/readandcreate.c:85
> > [0]PETSC ERROR: -start_in_debugger_no (source: command line)
> > [1]PETSC ERROR: PETSc Option Table entries:
> > [0]PETSC ERROR: ----------------End of Error Message -------send entire
> > error message to petsc-maint at mcs.anl.gov----------
> > [1]PETSC ERROR: -malloc_debug (source: environment)
> > application called MPI_Abort(MPI_COMM_SELF, 60) - process 0
> > [1]PETSC ERROR: -start_in_debugger_no (source: command line)
> > [1]PETSC ERROR: ----------------End of Error Message -------send entire
> > error message to petsc-maint at mcs.anl.gov----------
> > application called MPI_Abort(MPI_COMM_SELF, 60) - process 0
> > 4) We now have parallel HDF5 loading, so you should not have to manually
> > distribute. I will change your example to use it
> > and send it back when I am done.
> >
> > Thanks!
> >
> > Matt
> >
> > Many thanks and kind regards,
> > Berend.
> >
> >
> >
> > --
> > 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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