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 <[email protected]> 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;
> }
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
For more options, visit https://groups.google.com/d/optout.
