Thanks Wolfgang for your kind and fast response.
I simplified my code and use gdb as you suggested.
Now, it uses only one color, the idea being that the copier task is
executed in multithread.
I still get the same random crash when using two or more MPI procs with two
or more threads, respectively.
Is the implementation of the (colored) WorkStream::run() compatible with a
hybrid parallel code-architecture?
Here is the simplified code (also attached):
#include <deal.II/fe/fe_dgq.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/meshworker/loop.h>
#include <deal.II/meshworker/simple.h>
#include <deal.II/distributed/tria.h>
#include <deal.II/lac/trilinos_vector.h>
#include <vector>
int main(int argc,char **argv)
{
dealii::Utilities::MPI::MPI_InitFinalize mpi_initialization(argc,argv,2);
typedef dealii::MeshWorker::DoFInfo<2> DOFINFO ;
typedef dealii::MeshWorker::IntegrationInfoBox<2> INFOBOX ;
typedef dealii::MeshWorker::Assembler::ResidualSimple<dealii::
TrilinosWrappers::MPI::Vector> ASSEMBLER ;
typedef typename dealii::DoFHandler<2>::active_cell_iterator ITERATOR ;
dealii::parallel::distributed::Triangulation<2> tr(MPI_COMM_WORLD);
const dealii::FE_DGQ<2> fe{1};
dealii::DoFHandler<2> dof_handler{tr};
dealii::GridGenerator::hyper_cube (tr,0.,1.);
tr.refine_global(6);
dof_handler.distribute_dofs(fe);
std::vector<std::vector<ITERATOR> > colored_iterators{1} ;
for (auto cell = dof_handler.begin_active();cell != dof_handler.end(); ++
cell)
colored_iterators[0].push_back(cell);
const dealii::IndexSet locally_owned_dofs = dof_handler.locally_owned_dofs
();
dealii::TrilinosWrappers::MPI::Vector dst(locally_owned_dofs,
MPI_COMM_WORLD);
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::
MPI::Vector> assembler;
dealii::AnyData dst_data;
dst_data.add<dealii::TrilinosWrappers::MPI::Vector* >(&dst, "dst");
assembler.initialize(dst_data);
DOFINFO dof_info(dof_handler);
dealii::MeshWorker::DoFInfoBox<2, DOFINFO> dinfo_box(dof_info);
assembler.initialize_info(dinfo_box.cell, false);
for (unsigned int i=0; i<dealii::GeometryInfo<2>::faces_per_cell; ++i){
assembler.initialize_info(dinfo_box.interior[i], true);
assembler.initialize_info(dinfo_box.exterior[i], true);}
dealii::WorkStream::run(colored_iterators,
dealii::std_cxx11::bind(&dealii::MeshWorker::
cell_action<INFOBOX, DOFINFO, 2, 2, ITERATOR>,
dealii::std_cxx11::_1,
dealii::std_cxx11::_3, dealii::std_cxx11::_2,
nullptr, nullptr, nullptr,
dealii::MeshWorker::LoopControl{}),
dealii::std_cxx11::bind(&dealii::internal::
assemble<2,DOFINFO,ASSEMBLER>,
dealii::std_cxx11::_1, &
assembler),
INFOBOX{}, dinfo_box);
}
The gdb-backtrace (also attached) shows some problem with
memcopy using ssse3 in frame #0 (I checked my cpuinfo and I have ssse3).
It is very difficult for me to point out the issue just by looking to the
backtrace, particularly of its randomness.
I wonder if anybody has had problems with colorized iterators in a hybrid
parallel environment?
Thanks in advance, here is the backtrace:
#0 __memmove_ssse3_back ()
> at ../sysdeps/x86_64/multiarch/memcpy-ssse3-back.S:1629
> #1 0x00007ffff07358d1 in __copy_m<int> (__result=<optimized out>,
> __last=<optimized out>, __first=0x8f2424)
> at /usr/include/c++/4.8/bits/stl_algobase.h:372
> #2 __copy_move_a<true, int*, int*> (__result=<optimized out>,
> __last=<optimized out>, __first=0x8f2424)
> at /usr/include/c++/4.8/bits/stl_algobase.h:390
> #3 __copy_move_a2<true, int*, int*> (__result=<optimized out>,
> __last=<optimized out>, __first=0x8f2424)
> at /usr/include/c++/4.8/bits/stl_algobase.h:428
> #4 copy<std::move_iterator<int*>, int*> (__result=<optimized out>,
> __last=..., __first=...) at
> /usr/include/c++/4.8/bits/stl_algobase.h:460
> #5 __uninit_copy<std::move_iterator<int*>, int*> (__result=<optimized
> out>,
> __last=..., __first=...)
> at /usr/include/c++/4.8/bits/stl_uninitialized.h:93
> #6 uninitialized_copy<std::move_iterator<int*>, int*> (
> __result=<optimized out>, __last=..., __first=...)
> at /usr/include/c++/4.8/bits/stl_uninitialized.h:117
> #7 __uninitialized_copy_a<std::move_iterator<int*>, int*, int> (
> __result=<optimized out>, __last=..., __first=...)
> at /usr/include/c++/4.8/bits/stl_uninitialized.h:258
> #8 __uninitialized_move_if_noexcept_a<int*, int*, std::allocator<int> > (
> __alloc=..., __result=<optimized out>, __last=<optimized out>,
> __first=0x8f2424) at /usr/include/c++/4.8/bits/stl_uninitialized.h:281
> #9 std::vector<int, std::allocator<int> >::_M_insert_aux<int const&> (
> this=0x8ecb40, __position=0) at
> /usr/include/c++/4.8/bits/vector.tcc:369
> #10 0x00007ffff0735a05 in std::vector<int, std::allocator<int> >::insert (
> this=this@entry=0x8ecb40, __position=..., __x=@0x7fffda9c85f8: 1)
> at /usr/include/c++/4.8/bits/vector.tcc:127
> #11 0x00007ffff077ff62 in Epetra_FEVector::inputNonlocalValues<int> (
> this=this@entry=0x8eca40, GID=771, numValues=numValues@entry=1,
> values=values@entry=0x7fffda9c8680, suminto=suminto@entry=true,
> vectorIndex=vectorIndex@entry=0)
> at
> /export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:427
> #12 0x00007ffff077db5d in inputNonlocalValue<int> (vectorIndex=0,
> suminto=true, value=0, GID=<optimized out>, this=0x8eca40)
> at
> /export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:371
> #13 Epetra_FEVector::inputValues<int> (this=0x8eca40,
> numIDs=numIDs@entry=1,
> GIDs=GIDs@entry=0x7fffda9c870c, values=values@entry=0x7fffd0002b58,
> vectorIndex=vectorIndex@entry=0, suminto=true)
> at
> /export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:296
> #14 0x00007ffff077dcc5 in Epetra_FEVector::SumIntoGlobalValues (
> this=<optimized out>, numIDs=numIDs@entry=1,
> GIDs=GIDs@entry=0x7fffda9c870c, values=values@entry=0x7fffd0002b58,
> vectorIndex=vectorIndex@entry=0)
> at
> /export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:168
> #15 0x00000000004307be in dealii::TrilinosWrappers::VectorBase::add (
> this=this@entry=0x7fffffffb7d0, n_elements=4, indices=0x7fffd00029d0,
> values=0x7fffd0002b40)
> at
> /mnt/data/jwitte/dealii/install/include/deal.II/lac/trilinos_vector_base.h:1375
> #16 0x0000000000430b28 in dealii::TrilinosWrappers::VectorBase::add (
> this=this@entry=0x7fffffffb7d0,
> indices=std::vector of length -1073741823, capacity -1073741823 =
> {...},
> values=...)
> at
> /mnt/data/jwitte/dealii/install/include/deal.II/lac/trilinos_vector_base.h:1343
> #17 0x0000000000439a4a in
> dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>::assemble<dealii::MeshWorker::DoFInfo<2,
>
> 2, double> > (this=this@entry=0x7fffffffb8c0, info=...)
> at
> /mnt/data/jwitte/dealii/install/include/deal.II/meshworker/simple.h:530
> #18 0x0000000000439aac in
> assemble<dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>
>
> > (assembler=..., this=0x7fffd0001030)
> at
> /mnt/data/jwitte/dealii/install/include/deal.II/meshworker/dof_info.h:458---Type
>
> <return> to continue, or q <return> to quit---
>
> #19 dealii::internal::assemble<2, dealii::MeshWorker::DoFInfo<2, 2,
> double>,
> dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>
>
> > (dinfo=..., assembler=0x7fffffffb8c0)
> at /mnt/data/jwitte/dealii/install/include/deal.II/meshworker/loop.h:63
> #20 0x0000000000437ed9 in __call<void, dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > const&, 0ul, 1ul> (
> __args=<unknown type in /export/home/jwitte/test-colored/build/myloop,
> CU 0x0, DIE 0xb1296>, this=0x8efd10) at /usr/include/c++/4.8/functional:1296
> #21 operator()<const dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> >&, void> (this=0x8efd10)
> at /usr/include/c++/4.8/functional:1355
> #22 std::_Function_handler<void (dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > const&), std::_Bind<void
> (*(std::_Placeholder<1>,
> dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>*))(dealii::MeshWorker::DoFInfoBox<2,
>
> dealii::MeshWorker::DoFInfo<2, 2, double> > const&,
> dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>*)>
>
> >::_M_invoke(std::_Any_data const&, dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > const&) (
> __functor=..., __args#0=...) at /usr/include/c++/4.8/functional:2071
> #23 0x0000000000433686 in std::function<void
> (dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2,
> double> > const&)>::operator()(dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > const&) const (
> this=this@entry=0x7fffffffb6c0, __args#0=...)
> at /usr/include/c++/4.8/functional:2471
> #24 0x0000000000440db0 in
> dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
> dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double>
> > >::operator() (
> this=0x7fffffffb640, range=...)
> at
> /mnt/data/jwitte/dealii/install/include/deal.II/base/work_stream.h:847
> #25 0x000000000043c8a1 in
> operator()<tbb::blocked_range<__gnu_cxx::__normal_iterator<const
> dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> 2>, false> >*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >&, void> (
> __object=..., this=0x7fffdea03d60) at
> /usr/include/c++/4.8/functional:588
> #26 __call_c<void,
> tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >&, 0ul, 1ul> (
> __args=<unknown type in /export/home/jwitte/test-colored/build/myloop,
> CU 0x0, DIE 0xb9fd1>, this=0x7fffdea03d60) at
> /usr/include/c++/4.8/functional:1305
> #27 operator()<tbb::blocked_range<__gnu_cxx::__normal_iterator<const
> dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> 2>, false> >*, std---Type <return> to continue, or q <return> to quit---
> ::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >&, void> (this=0x7fffdea03d60)
> at /usr/include/c++/4.8/functional:1369
> #28 run_body (r=..., this=0x7fffdea03d40)
> at /usr/include/tbb/parallel_for.h:110
> #29
> tbb::interface6::internal::partition_type_base<tbb::interface6::internal::auto_partition_type>::execute<tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
> (dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
> dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double>
> >
> >::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> >
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > > const&)>
> (std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::I---Type <return> to continue, or q
> <return> to quit---
> ntegrationInfoBox<2, 2>, dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>,
> tbb::auto_partitioner const>,
> tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >
> >(tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> >
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
> (dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
> dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double>
> >
> >::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> >
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > > const&)>
> (std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
> dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWor---Type <return> to
> continue, or q <return> to quit---
> ker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>,
> tbb::auto_partitioner const>&,
> tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >&) (this=0x7fffdea03d78, start=...,
> range=...) at /usr/include/tbb/partitioner.h:277
> #30 0x000000000043c98f in
> tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
> (dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
> dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double>
> >
> >::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
> >
> 2>, false> > const*,
> std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >,
> std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> > > > > > const&)>
> (std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
>
> 2>, false> >, dealii::MeshWorker::Int---Type <return> to continue, or q
> <return> to quit---
> egrationInfoBox<2, 2>, dealii::MeshWorker::DoFInfoBox<2,
> dealii::MeshWorker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>,
> tbb::auto_partitioner const>::execute() (this=<optimized out>) at
> /usr/include/tbb/parallel_for.h:116
> #31 0x00007ffff0a3cb3a in
> tbb::internal::custom_scheduler<tbb::internal::IntelSchedulerTraits>::local_wait_for_all
>
> (this=0x7fffde9ffe00, parent=...,
> child=<optimized out>) at ../../src/tbb/custom_scheduler.h:455
> #32 0x00007ffff0a38816 in tbb::internal::arena::process
> (this=0x7fffdea17300,
> s=...) at ../../src/tbb/arena.cpp:106
> #33 0x00007ffff0a37f4b in tbb::internal::market::process
> (this=0x7fffdea17900,
> j=...) at ../../src/tbb/market.cpp:479
> #34 0x00007ffff0a340ff in tbb::internal::rml::private_worker::run (
> this=0x7fffde839000) at ../../src/tbb/private_server.cpp:283
> #35 0x00007ffff0a342f9 in
> tbb::internal::rml::private_worker::thread_routine (
> arg=<optimized out>) at ../../src/tbb/private_server.cpp:240
> #36 0x00007fffe83d8182 in start_thread (arg=0x7fffda9c9700)
> at pthread_create.c:312
> #37 0x00007fffefb4747d in clone ()
> at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
>
Am Dienstag, 24. Mai 2016 22:23:57 UTC+2 schrieb bangerth:
>
>
> Julius,
>
> > the current MeshWorker::loop() uses the WorkStream::run() which copies
> in serial.
> > I tried to use the WorkStream::run() version which uses colored
> iterators and
> > therefore assembles in parallel, in the sense of a tbb::parallel_for().
> >
> > My code runs without using MPI as well as using an arbitrary amount of
> MPI
> > procs with a single thread each. If I use 2 MPI procs with 2 threads
> each, it
> > crashes due to a segmentation fault.
> > For the construction of the colored iterators I am using the
> > make_graph_coloring() in such a way that two cells sharing a face have
> > different colors.
> >
> > The segmentation fault always appears while calling assemble() of the
> > ResidualSimple in simple.h.
> >
> > Does anybody have a clue why I get a segmentation fault after adding
> local
> > data to the global dst vector inside assemble(), although I avoid write
> > conflicts by colored iterators?
>
> Nothing particularly obvious comes to mind, without having tried to debug
> this
> in more detail.
>
> Have you tried running the program under a debugger? Segmentation faults
> are
> often relatively easy to debug because something is accessing an invalid
> address, and the debugger can tell you what object this address
> corresponds
> to, and how this address got into the current function. Try the approach
> outlined here, for example:
>
>
> https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#how-do-i-debug-mpi-programs
>
>
> using the `mpirun -np 4 xterm -e gdb ./my_executable` approach.
>
> Best
> W.
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth email: [email protected]
> <javascript:>
> www: http://www.math.tamu.edu/~bangerth/
>
>
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#0 __memmove_ssse3_back ()
at ../sysdeps/x86_64/multiarch/memcpy-ssse3-back.S:1629
#1 0x00007ffff07358d1 in __copy_m<int> (__result=<optimized out>,
__last=<optimized out>, __first=0x8f2424)
at /usr/include/c++/4.8/bits/stl_algobase.h:372
#2 __copy_move_a<true, int*, int*> (__result=<optimized out>,
__last=<optimized out>, __first=0x8f2424)
at /usr/include/c++/4.8/bits/stl_algobase.h:390
#3 __copy_move_a2<true, int*, int*> (__result=<optimized out>,
__last=<optimized out>, __first=0x8f2424)
at /usr/include/c++/4.8/bits/stl_algobase.h:428
#4 copy<std::move_iterator<int*>, int*> (__result=<optimized out>,
__last=..., __first=...) at /usr/include/c++/4.8/bits/stl_algobase.h:460
#5 __uninit_copy<std::move_iterator<int*>, int*> (__result=<optimized out>,
__last=..., __first=...)
at /usr/include/c++/4.8/bits/stl_uninitialized.h:93
#6 uninitialized_copy<std::move_iterator<int*>, int*> (
__result=<optimized out>, __last=..., __first=...)
at /usr/include/c++/4.8/bits/stl_uninitialized.h:117
#7 __uninitialized_copy_a<std::move_iterator<int*>, int*, int> (
__result=<optimized out>, __last=..., __first=...)
at /usr/include/c++/4.8/bits/stl_uninitialized.h:258
#8 __uninitialized_move_if_noexcept_a<int*, int*, std::allocator<int> > (
__alloc=..., __result=<optimized out>, __last=<optimized out>,
__first=0x8f2424) at /usr/include/c++/4.8/bits/stl_uninitialized.h:281
#9 std::vector<int, std::allocator<int> >::_M_insert_aux<int const&> (
this=0x8ecb40, __position=0) at /usr/include/c++/4.8/bits/vector.tcc:369
#10 0x00007ffff0735a05 in std::vector<int, std::allocator<int> >::insert (
this=this@entry=0x8ecb40, __position=..., __x=@0x7fffda9c85f8: 1)
at /usr/include/c++/4.8/bits/vector.tcc:127
#11 0x00007ffff077ff62 in Epetra_FEVector::inputNonlocalValues<int> (
this=this@entry=0x8eca40, GID=771, numValues=numValues@entry=1,
values=values@entry=0x7fffda9c8680, suminto=suminto@entry=true,
vectorIndex=vectorIndex@entry=0)
at
/export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:427
#12 0x00007ffff077db5d in inputNonlocalValue<int> (vectorIndex=0,
suminto=true, value=0, GID=<optimized out>, this=0x8eca40)
at
/export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:371
#13 Epetra_FEVector::inputValues<int> (this=0x8eca40, numIDs=numIDs@entry=1,
GIDs=GIDs@entry=0x7fffda9c870c, values=values@entry=0x7fffd0002b58,
vectorIndex=vectorIndex@entry=0, suminto=true)
at
/export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:296
#14 0x00007ffff077dcc5 in Epetra_FEVector::SumIntoGlobalValues (
this=<optimized out>, numIDs=numIDs@entry=1,
GIDs=GIDs@entry=0x7fffda9c870c, values=values@entry=0x7fffd0002b58,
vectorIndex=vectorIndex@entry=0)
at
/export/home/jwitte/trilinos-12.6.1-Source/packages/epetra/src/Epetra_FEVector.cpp:168
#15 0x00000000004307be in dealii::TrilinosWrappers::VectorBase::add (
this=this@entry=0x7fffffffb7d0, n_elements=4, indices=0x7fffd00029d0,
values=0x7fffd0002b40)
at
/mnt/data/jwitte/dealii/install/include/deal.II/lac/trilinos_vector_base.h:1375
#16 0x0000000000430b28 in dealii::TrilinosWrappers::VectorBase::add (
this=this@entry=0x7fffffffb7d0,
indices=std::vector of length -1073741823, capacity -1073741823 = {...},
values=...)
at
/mnt/data/jwitte/dealii/install/include/deal.II/lac/trilinos_vector_base.h:1343
#17 0x0000000000439a4a in
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>::assemble<dealii::MeshWorker::DoFInfo<2,
2, double> > (this=this@entry=0x7fffffffb8c0, info=...)
at /mnt/data/jwitte/dealii/install/include/deal.II/meshworker/simple.h:530
#18 0x0000000000439aac in
assemble<dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>
> (assembler=..., this=0x7fffd0001030)
at
/mnt/data/jwitte/dealii/install/include/deal.II/meshworker/dof_info.h:458---Type
<return> to continue, or q <return> to quit---
#19 dealii::internal::assemble<2, dealii::MeshWorker::DoFInfo<2, 2, double>,
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>
> (dinfo=..., assembler=0x7fffffffb8c0)
at /mnt/data/jwitte/dealii/install/include/deal.II/meshworker/loop.h:63
#20 0x0000000000437ed9 in __call<void, dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > const&, 0ul, 1ul> (
__args=<unknown type in /export/home/jwitte/test-colored/build/myloop, CU
0x0, DIE 0xb1296>, this=0x8efd10) at /usr/include/c++/4.8/functional:1296
#21 operator()<const dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> >&, void> (this=0x8efd10)
at /usr/include/c++/4.8/functional:1355
#22 std::_Function_handler<void (dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > const&), std::_Bind<void
(*(std::_Placeholder<1>,
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>*))(dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > const&,
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector>*)>
>::_M_invoke(std::_Any_data const&, dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > const&) (
__functor=..., __args#0=...) at /usr/include/c++/4.8/functional:2071
#23 0x0000000000433686 in std::function<void (dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> >
const&)>::operator()(dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > const&) const (
this=this@entry=0x7fffffffb6c0, __args#0=...)
at /usr/include/c++/4.8/functional:2471
#24 0x0000000000440db0 in
dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double> >
>::operator() (
this=0x7fffffffb640, range=...)
at /mnt/data/jwitte/dealii/install/include/deal.II/base/work_stream.h:847
#25 0x000000000043c8a1 in
operator()<tbb::blocked_range<__gnu_cxx::__normal_iterator<const
dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2, 2>,
false> >*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >&, void> (
__object=..., this=0x7fffdea03d60) at /usr/include/c++/4.8/functional:588
#26 __call_c<void,
tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >&, 0ul, 1ul> (
__args=<unknown type in /export/home/jwitte/test-colored/build/myloop, CU
0x0, DIE 0xb9fd1>, this=0x7fffdea03d60) at /usr/include/c++/4.8/functional:1305
#27 operator()<tbb::blocked_range<__gnu_cxx::__normal_iterator<const
dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2, 2>,
false> >*, std---Type <return> to continue, or q <return> to quit---
::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >&, void> (this=0x7fffdea03d60)
at /usr/include/c++/4.8/functional:1369
#28 run_body (r=..., this=0x7fffdea03d40)
at /usr/include/tbb/parallel_for.h:110
#29
tbb::interface6::internal::partition_type_base<tbb::interface6::internal::auto_partition_type>::execute<tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
(dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double> >
>::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > > const&)>
(std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::I---Type <return> to continue, or q <return>
to quit---
ntegrationInfoBox<2, 2>, dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>,
tbb::auto_partitioner const>,
tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >
>(tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
(dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double> >
>::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > > const&)>
(std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWor---Type <return> to continue,
or q <return> to quit---
ker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>, tbb::auto_partitioner
const>&,
tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >&) (this=0x7fffdea03d78, start=...,
range=...) at /usr/include/tbb/partitioner.h:277
#30 0x000000000043c98f in
tbb::interface6::internal::start_for<tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > >, std::_Bind<std::_Mem_fn<void
(dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::IntegrationInfoBox<2, 2>,
dealii::MeshWorker::DoFInfoBox<2, dealii::MeshWorker::DoFInfo<2, 2, double> >
>::*)(tbb::blocked_range<__gnu_cxx::__normal_iterator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > const*,
std::vector<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >,
std::allocator<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> > > > > > const&)>
(std::reference_wrapper<dealii::WorkStream::internal::Implementation3::WorkerAndCopier<dealii::TriaActiveIterator<dealii::DoFCellAccessor<dealii::DoFHandler<2,
2>, false> >, dealii::MeshWorker::Int---Type <return> to continue, or q
<return> to quit---
egrationInfoBox<2, 2>, dealii::MeshWorker::DoFInfoBox<2,
dealii::MeshWorker::DoFInfo<2, 2, double> > > >, std::_Placeholder<1>)>,
tbb::auto_partitioner const>::execute() (this=<optimized out>) at
/usr/include/tbb/parallel_for.h:116
#31 0x00007ffff0a3cb3a in
tbb::internal::custom_scheduler<tbb::internal::IntelSchedulerTraits>::local_wait_for_all
(this=0x7fffde9ffe00, parent=...,
child=<optimized out>) at ../../src/tbb/custom_scheduler.h:455
#32 0x00007ffff0a38816 in tbb::internal::arena::process (this=0x7fffdea17300,
s=...) at ../../src/tbb/arena.cpp:106
#33 0x00007ffff0a37f4b in tbb::internal::market::process (this=0x7fffdea17900,
j=...) at ../../src/tbb/market.cpp:479
#34 0x00007ffff0a340ff in tbb::internal::rml::private_worker::run (
this=0x7fffde839000) at ../../src/tbb/private_server.cpp:283
#35 0x00007ffff0a342f9 in tbb::internal::rml::private_worker::thread_routine (
arg=<optimized out>) at ../../src/tbb/private_server.cpp:240
#36 0x00007fffe83d8182 in start_thread (arg=0x7fffda9c9700)
at pthread_create.c:312
#37 0x00007fffefb4747d in clone ()
at ../sysdeps/unix/sysv/linux/x86_64/clone.S:111
#include <deal.II/fe/fe_dgq.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/meshworker/loop.h>
#include <deal.II/meshworker/simple.h>
#include <deal.II/distributed/tria.h>
#include <deal.II/lac/trilinos_vector.h>
#include <vector>
int main(int argc,char **argv)
{
dealii::Utilities::MPI::MPI_InitFinalize mpi_initialization(argc,argv,2);
typedef dealii::MeshWorker::DoFInfo<2> DOFINFO ;
typedef dealii::MeshWorker::IntegrationInfoBox<2> INFOBOX ;
typedef dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector> ASSEMBLER ;
typedef typename dealii::DoFHandler<2>::active_cell_iterator ITERATOR ;
dealii::parallel::distributed::Triangulation<2> tr(MPI_COMM_WORLD);
const dealii::FE_DGQ<2> fe{1};
dealii::DoFHandler<2> dof_handler{tr};
dealii::GridGenerator::hyper_cube (tr,0.,1.);
tr.refine_global(6);
dof_handler.distribute_dofs(fe);
std::vector<std::vector<ITERATOR> > colored_iterators{1} ;
for (auto cell = dof_handler.begin_active();cell != dof_handler.end(); ++cell)
colored_iterators[0].push_back(cell);
const dealii::IndexSet locally_owned_dofs = dof_handler.locally_owned_dofs();
dealii::TrilinosWrappers::MPI::Vector dst(locally_owned_dofs,MPI_COMM_WORLD);
dealii::MeshWorker::Assembler::ResidualSimple<dealii::TrilinosWrappers::MPI::Vector> assembler;
dealii::AnyData dst_data;
dst_data.add<dealii::TrilinosWrappers::MPI::Vector* >(&dst, "dst");
assembler.initialize(dst_data);
DOFINFO dof_info(dof_handler);
dealii::MeshWorker::DoFInfoBox<2, DOFINFO> dinfo_box(dof_info);
assembler.initialize_info(dinfo_box.cell, false);
for (unsigned int i=0; i<dealii::GeometryInfo<2>::faces_per_cell; ++i)
{
assembler.initialize_info(dinfo_box.interior[i], true);
assembler.initialize_info(dinfo_box.exterior[i], true);
}
dealii::WorkStream::run(colored_iterators,
dealii::std_cxx11::bind(&dealii::MeshWorker::cell_action<INFOBOX, DOFINFO, 2, 2, ITERATOR>,
dealii::std_cxx11::_1, dealii::std_cxx11::_3, dealii::std_cxx11::_2,
nullptr, nullptr, nullptr, dealii::MeshWorker::LoopControl{}),
dealii::std_cxx11::bind(&dealii::internal::assemble<2,DOFINFO,ASSEMBLER>,
dealii::std_cxx11::_1, &assembler),
INFOBOX{}, dinfo_box);
}
