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 < [email protected]> 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 [email protected] 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/>