[petsc-users] PETSc :: FEM Help

Matthew Knepley knepley at gmail.com
Fri Aug 4 11:51:41 CDT 2023 

On Fri, Aug 4, 2023 at 10:31 AM Brandon Denton <bldenton at buffalo.edu> 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 <knepley at gmail.com>
> *Sent:* Tuesday, August 1, 2023 10:23 AM
> *To:* Brandon Denton <bldenton at buffalo.edu>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at 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 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/>
>


-- 
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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