Dear All,
I am trying to execute step-26 (Heat Equation) in parallel with
adaptive mesh. I could execute the code with 1 processor using mpirun and
if more than one processor is used, the program returns the following error
message
--------------------------------------------------------
An error occurred in line <1250> of file
</home/syed/dealii-candi/tmp/unpack/deal.II-v9.3.2/include/deal.II/lac/petsc_vector_base.h>
in function
void
dealii::PETScWrappers::VectorBase::extract_subvector_to(ForwardIterator,
ForwardIterator, OutputIterator) const [with ForwardIterator = const
unsigned int*; OutputIterator = double*]
The violated condition was:
index >= static_cast<unsigned int>(begin) && index <
static_cast<unsigned int>(end)
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 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::PETScWrappers::VectorBase::extract_subvector_to<unsigned int
const*, double*>(unsigned int const*, unsigned int const*, double*) const
#1 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::internal::DoFAccessorImplementation::Implementation::extract_subvector_to<dealii::PETScWrappers::MPI::Vector,
double*>(dealii::PETScWrappers::MPI::Vector const&, unsigned int const*,
unsigned int const*, double*)
#2 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_dof_values<dealii::PETScWrappers::MPI::Vector,
double*>(dealii::PETScWrappers::MPI::Vector const&, double*, double*) const
#3 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_dof_values<dealii::PETScWrappers::MPI::Vector,
double>(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector<double>&)
const
#4 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_interpolated_dof_values<dealii::PETScWrappers::MPI::Vector,
double>(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector<double>&,
unsigned int) const
#5 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::pack_callback(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)
#6 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2,
2>::CellStatus)#1}::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus) const
#7 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::vector<char, std::allocator<char> >
std::__invoke_impl<std::vector<char, std::allocator<char> >,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus>(std::__invoke_other,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulat
--------------------------------------------------------
An error occurred in line <1250> of file
</home/syed/dealii-candi/tmp/unpack/deal.II-v9.3.2/include/deal.II/lac/petsc_vector_base.h>
in function
void
dealii::PETScWrappers::VectorBase::extract_subvector_to(ForwardIterator,
ForwardIterator, OutputIterator) const [with ForwardIterator = const
unsigned int*; OutputIterator = double*]
The violated condition was:
index >= static_cast<unsigned int>(begin) && index <
static_cast<unsigned int>(end)
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 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::PETScWrappers::VectorBase::extract_subvector_to<unsigned int
const*, double*>(unsigned int const*, unsigned int const*, double*) const
#1 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::internal::DoFAccessorImplementation::Implementation::extract_subvector_to<dealii::PETScWrappers::MPI::Vector,
double*>(dealii::PETScWrappers::MPI::Vector const&, unsigned int const*,
unsigned int const*, double*)
#2 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_dof_values<dealii::PETScWrappers::MPI::Vector,
double*>(dealii::PETScWrappers::MPI::Vector const&, double*, double*) const
#3 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_dof_values<dealii::PETScWrappers::MPI::Vector,
double>(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector<double>&)
const
#4 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2: void
dealii::DoFCellAccessor<2, 2,
false>::get_interpolated_dof_values<dealii::PETScWrappers::MPI::Vector,
double>(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector<double>&,
unsigned int) const
#5 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::pack_callback(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)
#6 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2,
2>::CellStatus)#1}::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus) const
#7 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::vector<char, std::allocator<char> >
std::__invoke_impl<std::vector<char, std::allocator<char> >,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus>(std::__invoke_other,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#8 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::enable_if<std::__and_<std::__not_<std::is_void<std::vector<char,
std::allocator<char> > > >,
std::is_convertible<std::__invoke_result<dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus>::type, std::vector<char,
std::allocator<char> > > >::value, std::vector<char, std::allocator<char> >
>::type std::__invoke_r<std::vector<char, std::allocator<char> >,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2,
2>::CellStatus>(dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#9 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::_Function_handler<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus),
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2,
2>::CellStatus)#1}>::_M_invoke(std::_Any_data const&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#10 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2,
2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus) const
#11 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::vector<char, std::allocator<char> >
std::__invoke_impl<std::vector<char, std::allocator<char> >,
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>(std::__invoke_other, std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#12 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::enable_if<std::__and_<std::__not_<std::is_void<std::vector<char,
std::allocator<char> > > >,
std::is_convertible<std::__invoke_result<std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>::type, std::vector<char, std::allocator<char> > > >::value,
std::vector<char, std::allocator<char> > >::type
std::__invoke_r<std::vector<char, std::allocator<char> >,
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>(ion<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#8 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::enable_if<std::__and_<std::__not_<std::is_void<std::vector<char,
std::allocator<char> > > >,
std::is_convertible<std::__invoke_result<dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus>::type, std::vector<char,
std::allocator<char> > > >::value, std::vector<char, std::allocator<char> >
>::type std::__invoke_r<std::vector<char, std::allocator<char> >,
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2,
2>::CellStatus>(dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus)#1}&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#9 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::_Function_handler<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus),
dealii::parallel::distributed::SolutionTransfer<2,
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<2, 2>
>::register_data_attach()::{lambda(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2,
2>::CellStatus)#1}>::_M_invoke(std::_Any_data const&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus&&)
#10 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2,
2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> > const&, dealii::Triangulation<2, 2>::CellStatus) const
#11 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::vector<char, std::allocator<char> >
std::__invoke_impl<std::vector<char, std::allocator<char> >,
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>(std::__invoke_other, std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#12 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::enable_if<std::__and_<std::__not_<std::is_void<std::vector<char,
std::allocator<char> > > >,
std::is_convertible<std::__invoke_result<std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>::type, std::vector<char, std::allocator<char> > > >::value,
std::vector<char, std::allocator<char> > >::type
std::__invoke_r<std::vector<char, std::allocator<char> >,
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >, dealii::Triangulation<2,
2>::CellStatus>(std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#13 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::_Function_handler<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus), std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>
>::_M_invoke(std::_Any_data const&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#14 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2,
2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> >, dealii::Triangulation<2, 2>::CellStatus) const
#15 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::DistributedTriangulationBase<2,
2>::DataTransfer::pack_data(std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<2,
2> >, dealii::Triangulation<2, 2>::CellStatus>,
std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus> > > const&,
std::vector<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)>,
std::allocator<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)> > > const&,
std::vector<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)>,
std::allocator<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)> > > const&)
#16 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::Triangulation<2,
2>::execute_coarsening_and_refinement()
#17 ./step-26_Adpmesh_pv: Step26::HeatEquation<2>::refine_mesh(unsigned
int, unsigned int)
#18 ./step-26_Adpmesh_pv: Step26::HeatEquation<2>::run()
#19 ./step-26_Adpmesh_pv: main
--------------------------------------------------------
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 3 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.
--------------------------------------------------------------------------
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> > const&,
dealii::Triangulation<2, 2>::CellStatus)>&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#13 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::_Function_handler<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus), std::function<std::vector<char,
std::allocator<char> > (dealii::TriaIterator<dealii::CellAccessor<2, 2> >
const&, dealii::Triangulation<2, 2>::CellStatus)>
>::_M_invoke(std::_Any_data const&,
dealii::TriaIterator<dealii::CellAccessor<2, 2> >&&,
dealii::Triangulation<2, 2>::CellStatus&&)
#14 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2,
2>::CellStatus)>::operator()(dealii::TriaIterator<dealii::CellAccessor<2,
2> >, dealii::Triangulation<2, 2>::CellStatus) const
#15 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::DistributedTriangulationBase<2,
2>::DataTransfer::pack_data(std::vector<std::pair<dealii::TriaIterator<dealii::CellAccessor<2,
2> >, dealii::Triangulation<2, 2>::CellStatus>,
std::allocator<std::pair<dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus> > > const&,
std::vector<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)>,
std::allocator<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)> > > const&,
std::vector<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)>,
std::allocator<std::function<std::vector<char, std::allocator<char> >
(dealii::TriaIterator<dealii::CellAccessor<2, 2> >,
dealii::Triangulation<2, 2>::CellStatus)> > > const&)
#16 /home/syed/dealii-candi/deal.II-v9.3.2/lib/libdeal_II.g.so.9.3.2:
dealii::parallel::distributed::Triangulation<2,
2>::execute_coarsening_and_refinement()
#17 ./step-26_Adpmesh_pv: Step26::HeatEquation<2>::refine_mesh(unsigned
int, unsigned int)
#18 ./step-26_Adpmesh_pv: Step26::HeatEquation<2>::run()
#19 ./step-26_Adpmesh_pv: main
--------------------------------------------------------
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
[syed-HP-Pavilion-Laptop-15-eg0xxx:14633] 1 more process has sent help
message help-mpi-api.txt / mpi-abort
I have attached the .cc file for your reference. Kindly help me to resolve
this issue.
Thanks in advance.
Best Regards,
Syed Ansari S.
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/* ---------------------------------------------------------------------
*
* Copyright (C) 2013 - 2021 by the deal.II authors
*
* This file is part of the deal.II library.
*
* The deal.II library is free software; you can use it, redistribute
* it, and/or modify it under the terms of the GNU Lesser General
* Public License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
* The full text of the license can be found in the file LICENSE.md at
* the top level directory of deal.II.
*
* ---------------------------------------------------------------------
*
* Author: Wolfgang Bangerth, Texas A&M University, 2013
*/
#include <deal.II/base/utilities.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/function.h>
#include <deal.II/base/logstream.h>
#include <deal.II/lac/vector.h>
#include <deal.II/lac/full_matrix.h>
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/solver_cg.h>
#include <deal.II/lac/precondition.h>
#include <deal.II/distributed/tria.h> //#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_generator.h>
//#include <deal.II/grid/grid_refinement.h>
#include <deal.II/grid/grid_out.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/numerics/data_out.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/numerics/matrix_tools.h>
//new header files
#include <deal.II/base/index_set.h>//new
#include <deal.II/base/conditional_ostream.h>//new
#include <deal.II/base/timer.h>//new
#include <deal.II/lac/generic_linear_algebra.h>//new
#include <deal.II/lac/sparsity_tools.h>//new
#include <deal.II/dofs/dof_renumbering.h>//new
#include <deal.II/grid/tria_accessor.h>//new
#include <deal.II/grid/tria_iterator.h>//new
#include <deal.II/dofs/dof_accessor.h>//new
#include <deal.II/lac/affine_constraints.h>//new
// grid refine
#include <deal.II/numerics/error_estimator.h>
#include <deal.II/distributed/grid_refinement.h>
#include <deal.II/distributed/solution_transfer.h>
#include <fstream>
#include <iostream>
namespace LA
{
#if defined(DEAL_II_WITH_PETSC) && !defined(DEAL_II_PETSC_WITH_COMPLEX) && \
!(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
using namespace dealii::LinearAlgebraPETSc;
# define USE_PETSC_LA
#elif defined(DEAL_II_WITH_TRILINOS)
using namespace dealii::LinearAlgebraTrilinos;
#else
# error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
#endif
} // namespace LA
namespace Step26
{
using namespace dealii;
template <int dim>
class HeatEquation
{
public:
HeatEquation();
void run();
double time;
double time_step;
unsigned int timestep_number;
const double theta;
private:
void setup_system();
//void setup_system_2();
void solve_time_step();
void output_results() const;
void refine_mesh();void refine_mesh(const unsigned int min_grid_level,
const unsigned int max_grid_level);
MPI_Comm mpi_communicator;
parallel::distributed::Triangulation<dim> triangulation;// Triangulation<dim> triangulation;
FE_Q<dim> fe;
DoFHandler<dim> dof_handler;
IndexSet locally_owned_dofs;
IndexSet locally_relevant_dofs;
AffineConstraints<double> constraints;
//SparsityPattern sparsity_pattern;
LA::MPI::SparseMatrix mass_matrix; //SparseMatrix<double> mass_matrix;
LA::MPI::SparseMatrix laplace_matrix; //SparseMatrix<double> laplace_matrix;
LA::MPI::SparseMatrix system_matrix; //SparseMatrix<double> system_matrix;
LA::MPI::Vector locally_owned_solution; //Vector<double> solution;//current solution
LA::MPI::Vector locally_relevant_solution; //Vector<double> old_solution;
LA::MPI::Vector locally_owned_old_solution; //Vector<double> old_solution;
LA::MPI::Vector system_rhs; //Vector<double> system_rhs;
ConditionalOStream pcout;
TimerOutput computing_timer;
};
template <int dim>
class RightHandSide : public Function<dim>
{
public:
RightHandSide()
: Function<dim>()
, period(0.2)
{}
virtual double value(const Point<dim> & p,
const unsigned int component = 0) const override;
private:
const double period;
};
template <int dim>
double RightHandSide<dim>::value(const Point<dim> & p,
const unsigned int component) const
{
(void)component;
AssertIndexRange(component, 1);
Assert(dim == 2, ExcNotImplemented());
const double time = this->get_time();
const double point_within_period =
(time / period - std::floor(time / period));
if ((point_within_period >= 0.0) && (point_within_period <= 0.2))
{
if ((p[0] > 0.5) && (p[1] > -0.5))
return 1;
else
return 0;
}
else if ((point_within_period >= 0.5) && (point_within_period <= 0.7))
{
if ((p[0] > -0.5) && (p[1] > 0.5))
return 1;
else
return 0;
}
else
return 0;
}
template <int dim>
class BoundaryValues : public Function<dim>
{
public:
virtual double value(const Point<dim> & p,
const unsigned int component = 0) const override;
};
template <int dim>
double BoundaryValues<dim>::value(const Point<dim> & /*p*/,
const unsigned int component) const
{
(void)component;
Assert(component == 0, ExcIndexRange(component, 0, 1));
return 0;
}
template <int dim>
HeatEquation<dim>::HeatEquation()
: mpi_communicator(MPI_COMM_WORLD)
, triangulation(mpi_communicator,
typename Triangulation<dim>::MeshSmoothing(
Triangulation<dim>::smoothing_on_refinement |
Triangulation<dim>::smoothing_on_coarsening))
, fe(1)
, dof_handler(triangulation)
, pcout(std::cout,
(Utilities::MPI::this_mpi_process(mpi_communicator) == 0))
, computing_timer(mpi_communicator,
pcout,
TimerOutput::never,
TimerOutput::wall_times)
, time_step(1. / 500)
, theta(0.5)
{}
template <int dim>
void HeatEquation<dim>::setup_system()
{
TimerOutput::Scope t(computing_timer,"setup_system()");
dof_handler.distribute_dofs(fe);
pcout << std::endl
<< "===========================================" << std::endl
<< "Number of degrees of freedom: " << dof_handler.n_dofs()
<< std::endl;
locally_owned_dofs = dof_handler.locally_owned_dofs() ;
DoFTools::extract_locally_relevant_dofs(dof_handler, locally_relevant_dofs);
// we want to output solution, so here should have ghost cells
locally_relevant_solution.reinit(locally_owned_dofs, locally_relevant_dofs, mpi_communicator);
//locally owned cells
locally_owned_old_solution.reinit(locally_owned_dofs, mpi_communicator);
locally_owned_solution.reinit (locally_owned_dofs, mpi_communicator);
system_rhs.reinit (locally_owned_dofs, mpi_communicator);
constraints.clear();
constraints.reinit(locally_relevant_dofs);
DoFTools::make_hanging_node_constraints(dof_handler, constraints);
VectorTools::interpolate_boundary_values(dof_handler,
0,
Functions::ZeroFunction<dim>(),
constraints);
constraints.close();
DynamicSparsityPattern dsp(locally_relevant_dofs);
DoFTools::make_sparsity_pattern(dof_handler,
dsp,
constraints,/*keep_constrained_dofs =*/ true);
SparsityTools::distribute_sparsity_pattern(dsp, dof_handler.locally_owned_dofs(), mpi_communicator,
locally_relevant_dofs); //sparsity_pattern.copy_from(dsp);
system_matrix.reinit(locally_owned_dofs,
locally_owned_dofs, dsp, mpi_communicator);//system_matrix.reinit(sparsity_pattern);
mass_matrix.reinit(locally_owned_dofs,locally_owned_dofs, dsp, mpi_communicator); //mass_matrix.reinit(sparsity_pattern);
laplace_matrix.reinit(locally_owned_dofs,locally_owned_dofs, dsp, mpi_communicator); //laplace_matrix.reinit(sparsity_pattern);
QGauss<dim> quadrature_formula(2);
FEValues<dim> fe_values (fe, quadrature_formula,
update_values | update_gradients |
update_quadrature_points | update_JxW_values);
const unsigned int dofs_per_cell = fe.dofs_per_cell;
const unsigned int n_q_points = quadrature_formula.size();
FullMatrix<double> local_init_matrix (dofs_per_cell, dofs_per_cell);
Vector<double> local_init_T_rhs (dofs_per_cell);
FullMatrix<double> local_rho_c_T_matrix (dofs_per_cell, dofs_per_cell);
FullMatrix<double> local_sys_int_matrix (dofs_per_cell, dofs_per_cell);
std::vector<types::global_dof_index> local_dof_indices (dofs_per_cell);
system_matrix = 0.0;
mass_matrix = 0.0;
laplace_matrix = 0.0;
system_rhs = 0.0;
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
if(cell->is_locally_owned())
{
fe_values.reinit (cell);
local_init_matrix = 0;
local_rho_c_T_matrix = 0;
local_sys_int_matrix = 0;
local_init_T_rhs = 0;
for (unsigned int q=0; q<n_q_points; ++q)
{
for (unsigned int i=0; i<dofs_per_cell; ++i)
{
const Tensor<1,dim> div_phi_i_u = fe_values.shape_grad (i,q);
const double phi_i_u = fe_values.shape_value (i,q);
for (unsigned int j=0; j<dofs_per_cell; ++j)
{
const Tensor<1,dim> div_phi_j_u = fe_values.shape_grad(j,q);
const double phi_j_u = fe_values.shape_value (j,q);
//initializing system matrix
local_sys_int_matrix(i,j) += (phi_i_u * phi_j_u *
fe_values.JxW (q));
//local_mass_matrix
local_init_matrix(i,j) += (phi_i_u *
phi_j_u *
fe_values.JxW (q));
//local stiffness matrix
local_rho_c_T_matrix(i,j) += (div_phi_i_u *
div_phi_j_u *
fe_values.JxW (q));
}
/*initial_value_func_T.value (fe_values.quadrature_point (q)) function returns the initial temperature 293 at the given quadrature point*/
local_init_T_rhs(i) += (phi_i_u *0.0 *fe_values.JxW (q));
}
}
cell->get_dof_indices (local_dof_indices);
constraints.distribute_local_to_global(local_sys_int_matrix,
local_dof_indices,
system_matrix);
constraints.distribute_local_to_global(local_init_T_rhs,
local_dof_indices,
system_rhs);
constraints.distribute_local_to_global(local_init_matrix,
local_dof_indices,
mass_matrix);
constraints.distribute_local_to_global(local_rho_c_T_matrix,
local_dof_indices,
laplace_matrix);
}
/*
for (const unsigned int i : fe_values.dof_indices())
{
for (const unsigned int j : fe_values.dof_indices())
{
mass_matrix.add(local_dof_indices[i],
local_dof_indices[j],
local_init_matrix(i,j));
laplace_matrix.add(local_dof_indices[i],
local_dof_indices[j],
local_rho_c_T_matrix(i,j));
system_matrix.add(local_dof_indices[i],
local_dof_indices[j],
local_sys_int_matrix(i,j));
}
system_rhs(local_dof_indices[i]) += local_init_T_rhs(i);
}*/
mass_matrix.compress(VectorOperation::add);
laplace_matrix.compress(VectorOperation::add);
system_matrix.compress(VectorOperation::add);
system_rhs.compress(VectorOperation::add);
}
template <int dim>
void HeatEquation<dim>::solve_time_step()
{
TimerOutput::Scope t(computing_timer, "solve");
LA::MPI::Vector completely_distributed_solution(locally_owned_dofs,
mpi_communicator);
SolverControl solver_control(1000, 1e-8 * system_rhs.l2_norm());
#ifdef USE_PETSC_LA
LA::SolverCG solver(solver_control, mpi_communicator);
#else
LA::SolverCG solver(solver_control);
#endif
LA::MPI::PreconditionAMG preconditioner;
LA::MPI::PreconditionAMG::AdditionalData data;
#ifdef USE_PETSC_LA
data.symmetric_operator = true;
#else
/* Trilinos defaults are good */
#endif
/*
SolverCG<Vector<double>> cg(solver_control);
PreconditionSSOR<SparseMatrix<double>> preconditioner;*/
preconditioner.initialize(system_matrix, data);
solver.solve(system_matrix, completely_distributed_solution, system_rhs, preconditioner);
pcout << " Solved in " << solver_control.last_step() << " iterations."
<< std::endl;
constraints.distribute(completely_distributed_solution);
locally_owned_solution = completely_distributed_solution;
}
template <int dim>
void HeatEquation<dim>::output_results() const
{
DataOut<dim> data_out;
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(locally_relevant_solution, "U");
Vector<float> subdomain(triangulation.n_active_cells());
for (unsigned int i = 0; i < subdomain.size(); i++)
subdomain(i) = triangulation.locally_owned_subdomain();
data_out.add_data_vector(subdomain, "subdomain");
data_out.build_patches();
data_out.set_flags(DataOutBase::VtkFlags(time, timestep_number));
/*
const std::string filename =
"solution-" + Utilities::int_to_string(timestep_number, 3) + ".vtk";
std::ofstream output(filename);*/
data_out.write_vtu_with_pvtu_record("./", "solution", timestep_number, mpi_communicator, 2, 8);//data_out.write_vtk(output);
}
template <int dim>
void HeatEquation<dim>::refine_mesh(const unsigned int min_grid_level,
const unsigned int max_grid_level)
{
Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
KellyErrorEstimator<dim>::estimate(
dof_handler,
QGauss<dim - 1>(fe.degree + 1),
std::map<types::boundary_id, const Function<dim> *>(),
locally_relevant_solution,
estimated_error_per_cell);
parallel::distributed::GridRefinement::refine_and_coarsen_fixed_fraction(triangulation,
estimated_error_per_cell,
0.6,
0.4);
if (triangulation.n_levels() > max_grid_level)
for (const auto &cell :
triangulation.active_cell_iterators_on_level(max_grid_level))
cell->clear_refine_flag();
for (const auto &cell :
triangulation.active_cell_iterators_on_level(min_grid_level))
cell->clear_coarsen_flag();
parallel::distributed::SolutionTransfer<dim, LA::MPI::Vector> solution_trans(dof_handler);
LA::MPI::Vector previous_solution;
previous_solution = locally_owned_solution;
triangulation.prepare_coarsening_and_refinement();
solution_trans.prepare_for_coarsening_and_refinement(previous_solution);
triangulation.execute_coarsening_and_refinement();
setup_system();
solution_trans.interpolate(locally_owned_solution);
constraints.distribute(locally_owned_solution);
}
template <int dim>
void HeatEquation<dim>::run()
{
pcout << "Running with "
#ifdef USE_PETSC_LA
<< "PETSc"
#else
<< "Trilinos"
#endif
<< " on " << Utilities::MPI::n_mpi_processes(mpi_communicator)
<< " MPI rank(s)..." << std::endl;
const unsigned int initial_global_refinement = 2;
const unsigned int n_adaptive_pre_refinement_steps = 4;
GridGenerator::hyper_L(triangulation);
triangulation.refine_global(initial_global_refinement);
setup_system();
unsigned int pre_refinement_step = 0;
LA::MPI::Vector tmp; //Vector<double> tmp;
LA::MPI::Vector forcing_terms; //Vector<double> forcing_terms;
//solve_time_step();
start_time_iteration:
//system_rhs = 0.0;
time = 0.0;
timestep_number = 0;
tmp.reinit(locally_owned_solution);
forcing_terms.reinit(locally_owned_solution);
tmp = 0.0;
forcing_terms = 0.0;
VectorTools::interpolate(dof_handler,
Functions::ZeroFunction<dim>(),
locally_owned_old_solution);
locally_relevant_solution = locally_owned_old_solution;
output_results();
while (time <= 0.5)
{
time += time_step;
++timestep_number;
pcout << "Time step " << timestep_number
<< " at t=" << time
<< " time_step = " << time_step
<< std::endl;
system_rhs =0.0;
system_matrix = 0.0;
tmp =0.0;
mass_matrix.vmult(system_rhs, locally_owned_old_solution); //mass_matrix.vmult(system_rhs, old_solution);
laplace_matrix.vmult(tmp, locally_owned_old_solution); //laplace_matrix.vmult(tmp, old_solution);
system_rhs.add(-(1 - theta) * time_step, tmp);
QGauss<dim> quadrature_formula(2);
RightHandSide<dim> rhs_func_T_1;
//rhs_func_T_1.set_time(time);
FEValues<dim> fe_values (fe, quadrature_formula,
update_values | update_gradients |
update_quadrature_points | update_JxW_values);
const unsigned int dofs_per_cell = fe.dofs_per_cell;
const unsigned int n_q_points = quadrature_formula.size();
Vector<double> local_rhs_vector_T (dofs_per_cell);
std::vector<types::global_dof_index> local_dof_indices (dofs_per_cell);
//std::vector<double> Rnp_cal_assemble (n_q_points);
forcing_terms = 0.0 ;
typename DoFHandler<dim>::active_cell_iterator
cell = dof_handler.begin_active(),
endc = dof_handler.end();
for (; cell!=endc; ++cell)
if(cell->is_locally_owned())
{
fe_values.reinit (cell);
local_rhs_vector_T = 0;
for (unsigned int q=0; q<n_q_points; ++q)
{
for (unsigned int i=0; i<dofs_per_cell; ++i)
{
const double phi_i_u = fe_values.shape_value (i,q);
rhs_func_T_1.set_time(time);
local_rhs_vector_T(i) += time_step * theta *
(phi_i_u *
rhs_func_T_1.value (fe_values.quadrature_point (q)) *
fe_values.JxW (q));
}
for (unsigned int i=0; i<dofs_per_cell; ++i)
{
const double phi_i_u = fe_values.shape_value (i,q);
rhs_func_T_1.set_time(time - time_step);
local_rhs_vector_T(i) += time_step * (1.0 - theta) *
(phi_i_u *
rhs_func_T_1.value (fe_values.quadrature_point (q)) *
fe_values.JxW (q));
}
}
cell->get_dof_indices (local_dof_indices);
/*for (const unsigned int i : fe_values.dof_indices())
{
forcing_terms(local_dof_indices[i]) += local_rhs_vector_T(i);
}*/
constraints.distribute_local_to_global(local_rhs_vector_T,
local_dof_indices,
forcing_terms);
}
forcing_terms.compress(VectorOperation::add);
/*
VectorTools::create_right_hand_side(dof_handler,
QGauss<dim>(fe.degree + 1),
rhs_function_1,
tmp);*/
system_rhs.add(1, forcing_terms);
system_matrix.copy_from(mass_matrix);
system_matrix.add(theta * time_step, laplace_matrix);
{
BoundaryValues<dim> boundary_values_function;
boundary_values_function.set_time(time);
std::map<types::global_dof_index, double> boundary_values;
VectorTools::interpolate_boundary_values(dof_handler,
0,
boundary_values_function,
boundary_values);
MatrixTools::apply_boundary_values(boundary_values,
system_matrix,
locally_owned_solution,
system_rhs, false);
}
solve_time_step();
if (Utilities::MPI::n_mpi_processes(mpi_communicator) <= 32)
{
TimerOutput::Scope t(computing_timer, "output");
output_results();
}
computing_timer.print_summary();
computing_timer.reset();
pcout << std::endl;
if ((timestep_number == 1) &&
(pre_refinement_step < n_adaptive_pre_refinement_steps))
{
refine_mesh(initial_global_refinement,
initial_global_refinement +
n_adaptive_pre_refinement_steps);
++pre_refinement_step;
tmp.reinit(locally_owned_solution);
forcing_terms.reinit(locally_owned_solution);
std::cout << std::endl;
goto start_time_iteration;
}
else if ((timestep_number > 0) && (timestep_number % 1 == 0))
{
refine_mesh(initial_global_refinement,
initial_global_refinement +
n_adaptive_pre_refinement_steps);
tmp.reinit(locally_owned_solution);
forcing_terms.reinit(locally_owned_solution);
}
locally_relevant_solution = locally_owned_solution; //old_solution = solution;
locally_owned_old_solution = locally_owned_solution;
//setup_system_2();
}
}
} // namespace Step26
int main(int argc, char *argv[])
{
try
{
using namespace dealii;
using namespace Step26;
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
HeatEquation<2> heat_equation_solver;
heat_equation_solver.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;
}
