Re: [petsc-users] PETSc :: FEM Help
On Fri, Aug 4, 2023 at 10:31 AM Brandon Denton wrote: > Good Morning Prof. Knepley, > > Thank you for the update. I am now able to run the code. However, it does > not appear to solve the problem correctly. The only results available are > the initial conditions (temp = 100). In the problem, one face is set to > 1400 and another face is set to 100. Since the faces are at opposite ends > of the geometry, we would expect a roughly linear temperature profile from > 1400 to 100. What am I missing to get the output to show this proper result. > 1) The inlet/outlet labels where being constructed on dmSurface. I fixed this. 2) The 14/7 faceIDs do not appear to be the ones you want. Here is corrected source. Can you look at the labels? Thanks, Matt > Thank you. > Brandon > > > -- > *From:* Matthew Knepley > *Sent:* Tuesday, August 1, 2023 10:23 AM > *To:* Brandon Denton > *Cc:* petsc-users@mcs.anl.gov > *Subject:* Re: [petsc-users] PETSc :: FEM Help > > 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@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 + > [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/User
Re: [petsc-users] PETSc :: FEM Help
Good Morning Prof. Knepley, Thank you for the update. I am now able to run the code. However, it does not appear to solve the problem correctly. The only results available are the initial conditions (temp = 100). In the problem, one face is set to 1400 and another face is set to 100. Since the faces are at opposite ends of the geometry, we would expect a roughly linear temperature profile from 1400 to 100. What am I missing to get the output to show this proper result. Thank you. Brandon From: Matthew Knepley Sent: Tuesday, August 1, 2023 10:23 AM To: Brandon Denton Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] PETSc :: FEM Help 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 mailto:petsc-users@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 + [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/inter
Re: [petsc-users] PETSc :: FEM Help
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@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 + > [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:
