Thank you, Praveen!
So, what should I do? I cannot use that kind of mesh with MPI? Could you
please suggest other solution?
Best,
Ki-Tae
On Wednesday, November 7, 2018 at 12:26:20 PM UTC-5, Praveen C wrote:
>
> Running your code in debug mode gives an error, says error is in the
> library not your code
>
> $ mpirun -np 4 ./step-1
> Cycle 0:
> Number of active cells: 24
> Number of degrees of freedom: 889
> =====================================
>
> Cycle 1:
> Number of active cells: 192
> Number of degrees of freedom: 6097
> =====================================
>
>
> --------------------------------------------------------
> An error occurred in line <3610> of file
> </Users/praveen/Applications/deal.II/git/source/dofs/dof_handler_policy.cc>
> in function
> auto dealii::internal::DoFHandlerImplementation::Policy::(anonymous
> namespace)::communicate_dof_indices_on_marked_cells(const
> dealii::DoFHandler<3, 3> &, const std::map<unsigned int,
> std::set<dealii::types::subdomain_id> > &, const
> std::vector<dealii::types::global_dof_index> &, const
> std::vector<dealii::types::global_dof_index> &)::(anonymous
> class)::operator()(const typename DoFHandlerType::active_cell_iterator &,
> const std::vector<types::global_dof_index> &) const
> The violated condition was:
> (received_dof_indices[i] == numbers::invalid_dof_index) ||
> (received_dof_indices[i] == local_dof_indices[i])
> Additional information:
> This exception -- which is used in many places in the library --
> usually indicates that some condition which the author of the code thought
> must be satisfied at a certain point in an algorithm, is not fulfilled. An
> example would be that the first part of an algorithm sorts elements of an
> array in ascending order, and a second part of the algorithm later
> encounters an element that is not larger than the previous one.
>
> There is usually not very much you can do if you encounter such an
> exception since it indicates an error in deal.II, not in your own program.
> Try to come up with the smallest possible program that still demonstrates
> the error and contact the deal.II mailing lists with it to obtain help.
>
> Stacktrace:
> -----------
> #0 2 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0b80a3
> _ZZN6dealii8internal24DoFHandlerImplementation6Policy12_GLOBAL__N_139communicate_dof_indices_on_marked_cellsINS_10DoFHandlerILi3ELi3EEEEEvRKT_RKNSt3__13mapIjNSA_3setIjNSA_4lessIjEENSA_9allocatorIjEEEESE_NSF_INSA_4pairIKjSH_EEEEEERKNSA_6vectorIjSG_EESS_ENKUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorIS6_Lb0EEEEESS_E_clESY_SS_
>
> + 419: 2 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0b80a3
> _ZZN6dealii8internal24DoFHandlerImplementation6Policy12_GLOBAL__N_139communicate_dof_indices_on_marked_cellsINS_10DoFHandlerILi3ELi3EEEEEvRKT_RKNSt3__13mapIjNSA_3setIjNSA_4lessIjEENSA_9allocatorIjEEEESE_NSF_INSA_4pairIKjSH_EEEEEERKNSA_6vectorIjSG_EESS_ENKUlRKNS_18TriaActiveIteratorINS_15DoFCellAccessorIS6_Lb0EEEEESS_E_clESY_SS_
>
> #1 3 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0b6bed
> _ZN6dealii9GridTools28exchange_cell_data_to_ghostsINSt3__16vectorIjNS2_9allocatorIjEEEENS_10DoFHandlerILi3ELi3EEEEEvRKT0_RKNS2_8functionIFN5boost8optionalIT_EERKNS9_20active_cell_iteratorEEEERKNSC_IFvSJ_RKSF_EEE
>
> + 1725: 3 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0b6bed
> _ZN6dealii9GridTools28exchange_cell_data_to_ghostsINSt3__16vectorIjNS2_9allocatorIjEEEENS_10DoFHandlerILi3ELi3EEEEEvRKT0_RKNS2_8functionIFN5boost8optionalIT_EERKNS9_20active_cell_iteratorEEEERKNSC_IFvSJ_RKSF_EEE
>
> #2 4 libdeal_II.g.9.1.0-pre.dylib 0x000000010f050c97
> _ZN6dealii8internal24DoFHandlerImplementation6Policy12_GLOBAL__N_139communicate_dof_indices_on_marked_cellsINS_10DoFHandlerILi3ELi3EEEEEvRKT_RKNSt3__13mapIjNSA_3setIjNSA_4lessIjEENSA_9allocatorIjEEEESE_NSF_INSA_4pairIKjSH_EEEEEERKNSA_6vectorIjSG_EESS_
>
> + 71: 4 libdeal_II.g.9.1.0-pre.dylib 0x000000010f050c97
> _ZN6dealii8internal24DoFHandlerImplementation6Policy12_GLOBAL__N_139communicate_dof_indices_on_marked_cellsINS_10DoFHandlerILi3ELi3EEEEEvRKT_RKNSt3__13mapIjNSA_3setIjNSA_4lessIjEENSA_9allocatorIjEEEESE_NSF_INSA_4pairIKjSH_EEEEEERKNSA_6vectorIjSG_EESS_
>
> #3 5 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0504f8
> _ZNK6dealii8internal24DoFHandlerImplementation6Policy19ParallelDistributedINS_10DoFHandlerILi3ELi3EEEE15distribute_dofsEv
>
> + 1640: 5 libdeal_II.g.9.1.0-pre.dylib 0x000000010f0504f8
> _ZNK6dealii8internal24DoFHandlerImplementation6Policy19ParallelDistributedINS_10DoFHandlerILi3ELi3EEEE15distribute_dofsEv
>
> #4 6 libdeal_II.g.9.1.0-pre.dylib 0x000000010ecd9e73
> _ZN6dealii10DoFHandlerILi3ELi3EE15distribute_dofsERKNS_13FiniteElementILi3ELi3EEE
>
> + 211: 6 libdeal_II.g.9.1.0-pre.dylib 0x000000010ecd9e73
> _ZN6dealii10DoFHandlerILi3ELi3EE15distribute_dofsERKNS_13FiniteElementILi3ELi3EEE
>
> #5 7 step-1 0x000000010145c2b1
> _ZN7Problem3runEv + 113: 7 step-1
> 0x000000010145c2b1 _ZN7Problem3runEv
> #6 8 step-1 0x000000010145c552 main + 98:
> 8 step-1 0x000000010145c552 main
> #7 9 libdyld.dylib 0x00007fff6795f015 start + 1:
> 9 libdyld.dylib 0x00007fff6795f015 start
> --------------------------------------------------------
>
> Calling MPI_Abort now.
> To break execution in a GDB session, execute 'break MPI_Abort' before
> running. You can also put the following into your ~/.gdbinit:
> set breakpoint pending on
> break MPI_Abort
> set breakpoint pending auto
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 255.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Best
> praveen
>
> On 07-Nov-2018, at 10:42 PM, Ki-Tae Kim <qls...@gmail.com <javascript:>>
> wrote:
>
> #include <iostream>
>
> #include <deal.II/distributed/tria.h>
> #include <deal.II/dofs/dof_handler.h>
> #include <deal.II/fe/fe_q.h>
>
> #include <deal.II/base/mpi.h>
> #include <deal.II/base/utilities.h>
> #include <deal.II/base/conditional_ostream.h>
>
> #include <deal.II/base/index_set.h>
>
> using namespace dealii;
>
> class Problem
> {
> public:
> Problem();
> ~Problem();
>
> void run();
>
> private:
> MPI_Comm mpi_communicator;
>
> parallel::distributed::Triangulation<3> triangulation;
>
> DoFHandler<3> dof_handler;
> FE_Q<3> fe;
>
> ConditionalOStream pcout;
>
> void make_domain_quater_crack();
> };
>
> Problem::Problem() :
> mpi_communicator (MPI_COMM_WORLD),
> triangulation (mpi_communicator,
> typename Triangulation<3>::MeshSmoothing
> (Triangulation<3>::smoothing_on_refinement |
> Triangulation<3>::smoothing_on_coarsening)),
> dof_handler(triangulation),
> fe(3),
> pcout (std::cout,
> (Utilities::MPI::this_mpi_process(mpi_communicator) == 0))
> {}
>
> Problem::~Problem()
> {
> dof_handler.clear();
> }
>
> void Problem::make_domain_quater_crack() {
> std::vector<Point<3>> vertices ={
> {0.0,0.0,0.0},
> {1.0,0.0,0.0},
> {2.0,0.0,0.0},
> {0.0,0.0,1.0},
> {1.0,0.0,1.0},
> {2.0,0.0,1.0},
> {0.0,1.0,0.0},
> {0.0,2.0,0.0},
> {0.0,1.0,1.0},
> {0.0,2.0,1.0},
> {1.0,1.0,0.0},
> {2.0,2.0,0.0},
> {1.0,1.0,1.0},
> {2.0,2.0,1.0},
> };
>
> const std::vector<std::array<int, GeometryInfo<3>::vertices_per_cell>>
> cell_vertices = {
> {0,1,6,10,3,4,8,12},
> {1,2,10,11,4,5,12,13},
> {10,11,6,7,12,13,8,9},
> };
>
> const unsigned int n_cells = cell_vertices.size();
>
> std::vector<CellData<3>> cells(n_cells, CellData<3>());
> for (unsigned int i = 0; i < n_cells; ++i)
> {
> for (unsigned int j = 0; j < GeometryInfo<3>::vertices_per_cell;
> ++j)
> cells[i].vertices[j] = cell_vertices[i][j];
> cells[i].material_id = 0;
> }
>
> triangulation.create_triangulation(vertices, cells, SubCellData());
> }
>
> void Problem::run() {
> make_domain_quater_crack();
>
> unsigned int max_cycle=4;
> for (unsigned int cycle(0); cycle<max_cycle; ++cycle){
> triangulation.refine_global(1);
>
> dof_handler.distribute_dofs (fe);
>
> if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0) {
> const unsigned int n_active_cells =
> triangulation.n_global_active_cells();
> const unsigned int n_dofs = dof_handler.n_dofs();
> pcout << "Cycle " << cycle << ':'
> << std::endl
> << " Number of active cells: "
> << n_active_cells
> << std::endl
> << " Number of degrees of freedom: "
> << n_dofs
> << std::endl;
> }
> pcout << "=====================================" << std::endl;
> pcout << std::endl;
> }
> }
>
> int main(int argc, char *argv[])
> {
> try
> {
> Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
> Problem test;
> test.run ();
> }
> catch (std::exception &exc)
> {
> std::cerr << std::endl << std::endl
> << "----------------------------------------------------"
> << std::endl;
> std::cerr << "Exception on processing: " << std::endl
> << exc.what() << std::endl
> << "Aborting!" << std::endl
> << "----------------------------------------------------"
> << std::endl;
> return 1;
> }
> catch (...)
> {
> std::cerr << std::endl << std::endl
> << "----------------------------------------------------"
> << std::endl;
> std::cerr << "Unknown exception!" << std::endl
> << "Aborting!" << std::endl
> << "----------------------------------------------------"
> << std::endl;
> return 1;
> }
> return 0;
> }
>
>
>
--
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