[petsc-users] PETSc :: FEM Help

Tue Aug 1 09:23:05 CDT 2023

Sorry about this. I signed up for a conference without the work done, with
predictable results. I have just returned home.

There were just a few small problems. First, the labels were attached to
dmSurface, but you wanted them on dm. They got destroyed with dmSurface
before setting the BC. Second, the declarations of the point function were
missing the constant arguments. Third, the PetscFEDestroy() was missing and
extra DM creations were there. I have fixed these and am attaching the new
source. It runs for me but I have not checked the answer.

  Thanks,

     Matt

On Wed, Jun 7, 2023 at 11:05 AM Brandon Denton via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Good Morning,
>
> I'm trying to verify that the CAD -> PETSc/DMPlex methods I've developed
> can be used for FEM analyses using PETSc. Attached is my current attempt
> where I import a CAD STEP file to create a volumetric tetrahedral
> discretization (DMPlex),  designate boundary condition points using
> DMLabels, and solve the Laplace problem (heat) with Dirichlet conditions on
> each end. At command line I indicate the STEP file with the -filename
> option and the dual space degree with -petscspace_degree 2. The run ends
> with either a SEGV Fault or a General MPI Communication Error.
>
> Could you please look over the attached file to tell me if what I'm doing
> to set up the FEM problem is wrong?
>
> Thank you in advance for your time and help.
> -Brandon
>
> TYPICAL ERROR MESSAGE
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: General MPI error
> [0]PETSC ERROR: MPI error 605109765 Invalid communicator, error stack:
>                 PMPI_Comm_get_attr(344): MPI_Comm_get_attr(comm=0x0,
> comm_keyval=-1539309568, attribute_val=0x7ffe75a58848, flag=0x7ffe75a58844)
> failed
>                 MPII_Comm_get_attr(257): MPIR_Comm_get_attr(comm=0x0,
> comm_keyval=-1539309568, attribute_val=0x7ffe75a58848, flag=0x7ffe75a58844)
> failed
>                 MPII_Comm_get_attr(53).: Invalid communicator
> [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:-dm_plex_refine_without_snap_to_geom
> value: 0 source: command line
> [0]PETSC ERROR:   Option left: name:-dm_refine value: 1 source: command
> line
> [0]PETSC ERROR:   Option left: name:-snes_monitor (no value) source:
> command line
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.18.5-1817-gd2497b8de4c
> GIT Date: 2023-05-22 18:44:03 +0000
> [0]PETSC ERROR: ./thermal on a  named XPS. by bdenton Wed Jun  7 11:03:43
> 2023
> [0]PETSC ERROR: Configure options --with-make-np=16
> --prefix=/mnt/c/Users/Brandon/software/libs/petsc/3.19.1-gitlab/gcc/11.2.0/mpich/3.4.2/openblas/0.3.17/opt
> --with-debugging=false --COPTFLAGS="-O3 -mavx" --CXXOPTFLAGS="-O3 -mavx"
> --FOPTFLAGS=-O3 --with-shared-libraries=1
> --with-mpi-dir=/mnt/c/Users/Brandon/software/libs/mpich/3.4.2/gcc/11.2.0
> --with-mumps=true --download-mumps=1 --with-metis=true --download-metis=1
> --with-parmetis=true --download-parmetis=1 --with-superlu=true
> --download-superlu=1 --with-superludir=true --download-superlu_dist=1
> --with-blacs=true --download-blacs=1 --with-scalapack=true
> --download-scalapack=1 --with-hypre=true --download-hypre=1
> --with-hdf5-dir=/mnt/c/Users/Brandon/software/libs/hdf5/1.12.1/gcc/11.2.0
> --with-valgrind-dir=/mnt/c/Users/Brandon/software/apps/valgrind/3.14.0
> --with-blas-lib="[/mnt/c/Users/Brandon/software/libs/openblas/0.3.17/gcc/11.2.0/lib/libopenblas.so]"
> --with-lapack-lib="[/mnt/c/Users/Brandon/software/libs/openblas/0.3.17/gcc/11.2.0/lib/libopenblas.so]"
> --LDFLAGS= --with-tetgen=true --download-tetgen=1 --download-ctetgen=1
> --download-opencascade=1 --download-egads
> [0]PETSC ERROR: #1 PetscObjectName() at
> /mnt/c/Users/Brandon/software/builddir/petsc-3.19.1-gitlab/src/sys/objects/pname.c:119
> [0]PETSC ERROR: #2 PetscObjectGetName() at
> /mnt/c/Users/Brandon/software/builddir/petsc-3.19.1-gitlab/src/sys/objects/pgname.c:27
> [0]PETSC ERROR: #3 PetscDSAddBoundary() at
> /mnt/c/Users/Brandon/software/builddir/petsc-3.19.1-gitlab/src/dm/dt/interface/dtds.c:3404
> [0]PETSC ERROR: #4 DMAddBoundary() at
> /mnt/c/Users/Brandon/software/builddir/petsc-3.19.1-gitlab/src/dm/interface/dm.c:7828
> [0]PETSC ERROR: #5 main() at
> /mnt/c/Users/Brandon/Documents/School/Dissertation/Software/EGADS-dev/thermal_v319/thermal_nozzle.c:173
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -dm_plex_geom_print_model 1 (source: command line)
> [0]PETSC ERROR: -dm_plex_geom_shape_opt 0 (source: command line)
> [0]PETSC ERROR: -dm_plex_refine_without_snap_to_geom 0 (source: command
> line)
> [0]PETSC ERROR: -dm_refine 1 (source: command line)
> [0]PETSC ERROR: -filename ./examples/Nozzle_example.stp (source: command
> line)
> [0]PETSC ERROR: -petscspace_degree 2 (source: command line)
> [0]PETSC ERROR: -snes_monitor (source: command line)
> [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, 98) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=98
> :
> system msg for write_line failure : Bad file descriptor
>

-- 
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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