File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 4713ms, 85.89% of 5487ms total Dropped 508 nodes (cum <= 27.43ms) flat flat% sum% cum cum% 0 0% 0% 5458ms 99.47% __libc_start_call_main 0 0% 0% 5458ms 99.47% __libc_start_main_impl 0 0% 0% 5458ms 99.47% _start 0 0% 0% 5442ms 99.18% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 5442ms 99.18% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 5442ms 99.18% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 5442ms 99.18% main 0 0% 0% 5402ms 98.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 5402ms 98.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 5402ms 98.45% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 5400ms 98.41% AbstractCellBasedSimulation::Solve 0 0% 0% 2561ms 46.67% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.036% 0.036% 2250ms 41.01% MeshBasedCellPopulation::Update 1ms 0.018% 0.055% 1769ms 32.24% AbstractCellPopulation::WriteResultsToFiles 1ms 0.018% 0.073% 1180ms 21.51% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.073% 1064ms 19.39% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.35% 0.42% 1034ms 18.84% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 0.42% 1032ms 18.81% MutableMesh::ReMesh 1ms 0.018% 0.44% 915ms 16.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.44% 879ms 16.02% AbstractNumericalMethod::ComputeForcesIncludingDamping 81ms 1.48% 1.91% 843ms 15.36% TetrahedralMesh::EdgeIterator::operator++ 331ms 6.03% 7.95% 685ms 12.48% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.091% 8.04% 679ms 12.37% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.24% 8.27% 657ms 11.97% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 22ms 0.4% 8.68% 612ms 11.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 5ms 0.091% 8.77% 606ms 11.04% CellPopulationElementWriter::Visit 124ms 2.26% 11.03% 579ms 10.55% __dynamic_cast 8ms 0.15% 11.17% 559ms 10.19% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.15% 11.32% 537ms 9.79% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.055% 11.37% 530ms 9.66% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.055% 11.43% 526ms 9.59% TetrahedralMesh::ImportFromMesher 38ms 0.69% 12.12% 482ms 8.78% operator new 7ms 0.13% 12.25% 459ms 8.37% std::set::insert (inline) 6ms 0.11% 12.36% 452ms 8.24% std::_Rb_tree::_M_insert_unique 3ms 0.055% 12.41% 446ms 8.13% AbstractCellProperty::IsSubType (inline) 20ms 0.36% 12.78% 439ms 8.00% std::__new_allocator::allocate (inline) 141ms 2.57% 15.35% 436ms 7.95% __GI___libc_malloc 7ms 0.13% 15.47% 436ms 7.95% std::_Rb_tree::find (inline) 0 0% 15.47% 433ms 7.89% std::allocator_traits::allocate (inline) 0 0% 15.47% 413ms 7.53% std::set::count (inline) 59ms 1.08% 16.55% 399ms 7.27% std::_Rb_tree::~_Rb_tree (inline) 53ms 0.97% 17.51% 389ms 7.09% std::map::operator[] (partial-inline) 2ms 0.036% 17.55% 389ms 7.09% triangulate 0 0% 17.55% 388ms 7.07% std::ostream::operator<< (inline) 50ms 0.91% 18.46% 387ms 7.05% std::ostream::_M_insert 0 0% 18.46% 369ms 6.72% std::set::~set (inline) 1ms 0.018% 18.48% 367ms 6.69% LegacyCellProliferativeTypesWriter::VisitCell 3ms 0.055% 18.53% 359ms 6.54% Cell::GetCellProliferativeType 350ms 6.38% 24.91% 350ms 6.38% __strcmp_evex 1ms 0.018% 24.93% 349ms 6.36% delaunay 2ms 0.036% 24.97% 347ms 6.32% divconqdelaunay 0 0% 24.97% 347ms 6.32% std::_Rb_tree::_M_create_node (inline) 37ms 0.67% 25.64% 338ms 6.16% std::_Rb_tree::_M_erase 0 0% 25.64% 335ms 6.11% std::_Rb_tree::_M_get_node (inline) 0 0% 25.64% 323ms 5.89% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.036% 25.68% 306ms 5.58% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.68% 296ms 5.39% std::_Rb_tree::_M_drop_node (inline) 11ms 0.2% 25.88% 289ms 5.27% std::_Rb_tree::_Rb_tree (partial-inline) 151ms 2.75% 28.63% 288ms 5.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.63% 283ms 5.16% std::_Rb_tree::lower_bound (inline) 0 0% 28.63% 283ms 5.16% std::map::lower_bound (inline) 17ms 0.31% 28.94% 272ms 4.96% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.94% 265ms 4.83% std::set::set (inline) 7ms 0.13% 29.07% 258ms 4.70% boost::detail::shared_count::~shared_count (inline) 0 0% 29.07% 258ms 4.70% boost::shared_ptr::~shared_ptr (inline) 27ms 0.49% 29.56% 257ms 4.68% std::_Rb_tree::_M_copy (inline) 2ms 0.036% 29.60% 255ms 4.65% NodeLocationWriter::Visit 58ms 1.06% 30.65% 251ms 4.57% __GI___libc_free 4ms 0.073% 30.73% 247ms 4.50% Element::Element 246ms 4.48% 35.21% 246ms 4.48% boost::detail::sp_counted_base::release 161ms 2.93% 38.14% 228ms 4.16% _int_malloc 98ms 1.79% 39.93% 226ms 4.12% std::_Rb_tree::_M_clone_node (inline) 18ms 0.33% 40.26% 224ms 4.08% std::num_put::_M_insert_float 4ms 0.073% 40.33% 219ms 3.99% std::__new_allocator::deallocate (inline) 217ms 3.95% 44.29% 217ms 3.95% std::_Rb_tree::_S_right (inline) 0 0% 44.29% 216ms 3.94% std::allocator_traits::deallocate (inline) 4ms 0.073% 44.36% 215ms 3.92% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.11% 44.47% 215ms 3.92% std::less::operator() (inline) 209ms 3.81% 48.28% 209ms 3.81% std::operator< (inline) 0 0% 48.28% 205ms 3.74% Cell::GetMutationState 174ms 3.17% 51.45% 192ms 3.50% _int_free 9ms 0.16% 51.61% 189ms 3.44% divconqrecurse 5ms 0.091% 51.70% 184ms 3.35% std::__cxx11::collate::do_transform 4ms 0.073% 51.78% 181ms 3.30% Cell::ReadyToDivide 5ms 0.091% 51.87% 180ms 3.28% Element::RegisterWithNodes (inline) 0 0% 51.87% 179ms 3.26% std::_Rb_tree::_M_put_node (inline) 52ms 0.95% 52.82% 174ms 3.17% std::_Rb_tree::_M_get_insert_unique_pos (inline) 9ms 0.16% 52.98% 171ms 3.12% Node::AddElement 55ms 1.00% 53.98% 169ms 3.08% mergehulls 0 0% 53.98% 168ms 3.06% ___vsnprintf 0 0% 53.98% 168ms 3.06% __vsnprintf_internal (inline) 16ms 0.29% 54.27% 164ms 2.99% __printf_buffer 6ms 0.11% 54.38% 155ms 2.82% MeshBasedCellPopulation::SpringsEnd (inline) 155ms 2.82% 57.21% 155ms 2.82% [libchaste_cell_based.so] 2ms 0.036% 57.24% 152ms 2.77% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 57.24% 152ms 2.77% MeshBasedCellPopulation::GetDampingConstant 1ms 0.018% 57.26% 143ms 2.61% CellProliferativeTypesWriter::VisitCell 5ms 0.091% 57.35% 137ms 2.50% AbstractCellProperty::IsType (inline) 3ms 0.055% 57.41% 137ms 2.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.036% 57.44% 133ms 2.42% CellPropertyCollection::HasProperty 0 0% 57.44% 132ms 2.41% Cell::HasCellProperty (inline) 4ms 0.073% 57.52% 127ms 2.31% __printf_fp_l_buffer 0 0% 57.52% 127ms 2.31% __printf_fp_spec (inline) 3ms 0.055% 57.57% 126ms 2.30% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.13% 57.70% 119ms 2.17% AbstractTetrahedralElement::CalculateJacobian 17ms 0.31% 58.01% 119ms 2.17% TetrahedralMesh::EdgesEnd (partial-inline) 67ms 1.22% 59.23% 119ms 2.17% __printf_fp_buffer_1 0 0% 59.23% 117ms 2.13% std::_Rb_tree::_M_destroy_node (inline) 0 0% 59.23% 117ms 2.13% std::__new_allocator::destroy (inline) 0 0% 59.23% 117ms 2.13% std::allocator_traits::destroy (inline) 0 0% 59.23% 110ms 2.00% TetrahedralMesh::Clear 0 0% 59.23% 107ms 1.95% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 59.23% 107ms 1.95% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.018% 59.25% 105ms 1.91% OutputFileHandler::OpenOutputFile 0 0% 59.25% 105ms 1.91% TetrahedralMesh::RefreshJacobianCachedData 104ms 1.90% 61.14% 104ms 1.90% [libchaste_mesh.so] 17ms 0.31% 61.45% 102ms 1.86% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.036% 61.49% 99ms 1.80% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 61.49% 98ms 1.79% std::_Vector_base::_M_allocate (inline) 6ms 0.11% 61.60% 95ms 1.73% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.018% 61.62% 95ms 1.73% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.036% 61.65% 95ms 1.73% alternateaxes 16ms 0.29% 61.95% 94ms 1.71% AbstractCellProperty::IsSame 80ms 1.46% 63.40% 94ms 1.71% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 24ms 0.44% 63.84% 92ms 1.68% std::num_put::_M_insert_int 2ms 0.036% 63.88% 92ms 1.68% std::vector::push_back (inline) 82ms 1.49% 65.37% 91ms 1.66% vertexmedian 0 0% 65.37% 87ms 1.59% boost::numeric::ublas::vector_assign (inline) 2ms 0.036% 65.41% 85ms 1.55% boost::numeric::ublas::c_vector::c_vector (inline) 4ms 0.073% 65.48% 85ms 1.55% std::vector::_M_realloc_insert 16ms 0.29% 65.77% 84ms 1.53% AbstractTetrahedralElement::RefreshJacobian 36ms 0.66% 66.43% 78ms 1.42% std::__ostream_insert 3ms 0.055% 66.48% 78ms 1.42% std::type_info::operator== (inline) 1ms 0.018% 66.50% 72ms 1.31% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 9ms 0.16% 66.67% 69ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 69ms 1.26% 67.92% 69ms 1.26% incircle 0 0% 67.92% 68ms 1.24% Node::~Node 2ms 0.036% 67.96% 67ms 1.22% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 67.96% 65ms 1.18% std::operator<< (inline) 64ms 1.17% 69.13% 64ms 1.17% std::_Rb_tree_insert_and_rebalance 23ms 0.42% 69.55% 63ms 1.15% AbstractElement::GetNodeLocation 54ms 0.98% 70.53% 61ms 1.11% vertexsort 58ms 1.06% 71.59% 58ms 1.06% [libstdc++.so.6.0.33] 39ms 0.71% 72.30% 58ms 1.06% malloc_consolidate 57ms 1.04% 73.34% 57ms 1.04% __memcpy_avx512_unaligned_erms 32ms 0.58% 73.92% 57ms 1.04% std::basic_streambuf::xsputn 0 0% 73.92% 57ms 1.04% tcache_get (inline) 57ms 1.04% 74.96% 57ms 1.04% tcache_get_n (inline) 56ms 1.02% 75.98% 56ms 1.02% std::_Rb_tree::_S_left (inline) 20ms 0.36% 76.34% 55ms 1.00% boost::numeric::ublas::indexing_vector_assign 2ms 0.036% 76.38% 54ms 0.98% CellPropertyCollection::AddProperty 54ms 0.98% 77.36% 54ms 0.98% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 4ms 0.073% 77.44% 53ms 0.97% std::_Rb_tree::_M_emplace_hint_unique 0 0% 77.44% 53ms 0.97% std::basic_ofstream::basic_ofstream (inline) 0 0% 77.44% 52ms 0.95% Cell::GetCellId 7ms 0.13% 77.57% 51ms 0.93% TetrahedralMesh::EdgeIterator::GetNodeB 51ms 0.93% 78.49% 51ms 0.93% std::vector::size (inline) 0 0% 78.49% 50ms 0.91% std::basic_filebuf::open 0 0% 78.49% 50ms 0.91% std::basic_ofstream::open (inline) 0 0% 78.49% 49ms 0.89% OutputFileHandler::CommonConstructor 0 0% 78.49% 49ms 0.89% OutputFileHandler::OutputFileHandler 4ms 0.073% 78.57% 47ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.57% 45ms 0.82% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 78.57% 45ms 0.82% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.57% 45ms 0.82% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.57% 44ms 0.8% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 78.57% 43ms 0.78% AbstractCellBasedWriter::CloseFile 0 0% 78.57% 43ms 0.78% Node::ClearAppliedForce 1ms 0.018% 78.59% 43ms 0.78% Node::ConstructNodeAttributes (inline) 0 0% 78.59% 43ms 0.78% std::basic_filebuf::close 0 0% 78.59% 43ms 0.78% std::basic_ofstream::close (inline) 2ms 0.036% 78.62% 42ms 0.77% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 78.62% 42ms 0.77% CellPropertyCollection::~CellPropertyCollection (inline) 26ms 0.47% 79.10% 41ms 0.75% boost::shared_ptr::shared_ptr (inline) 41ms 0.75% 79.84% 41ms 0.75% counterclockwise 0 0% 79.84% 40ms 0.73% std::vector::vector (inline) 0 0% 79.84% 38ms 0.69% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 30ms 0.55% 80.39% 37ms 0.67% CellPropertyCollection::GetProperty 0 0% 80.39% 37ms 0.67% CxxTest::RealWorldDescription::setUp 0 0% 80.39% 37ms 0.67% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 80.39% 37ms 0.67% PMPI_Init_thread 0 0% 80.39% 37ms 0.67% PetscInitialize 0 0% 80.39% 37ms 0.67% PetscSetup::setUpWorld 0 0% 80.39% 37ms 0.67% PetscSetupUtils::CommonSetup 0 0% 80.39% 37ms 0.67% PetscSetupUtils::InitialisePetsc 0 0% 80.39% 37ms 0.67% ompi_mpi_init 35ms 0.64% 81.03% 35ms 0.64% __GI___libc_write 17ms 0.31% 81.34% 35ms 0.64% hack_digit 27ms 0.49% 81.83% 35ms 0.64% std::num_put::do_put 0 0% 81.83% 34ms 0.62% 12ms 0.22% 82.05% 34ms 0.62% AbstractElement::GetNodeGlobalIndex 0 0% 82.05% 34ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 34ms 0.62% 82.67% 34ms 0.62% Node::GetIndex 0 0% 82.67% 34ms 0.62% std::_Vector_base::_M_deallocate (inline) 1ms 0.018% 82.69% 34ms 0.62% std::basic_filebuf::_M_convert_to_external 0 0% 82.69% 34ms 0.62% std::basic_filebuf::_M_terminate_output 0 0% 82.69% 34ms 0.62% std::basic_filebuf::overflow 0 0% 82.69% 33ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 5ms 0.091% 82.78% 33ms 0.6% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.78% 33ms 0.6% std::_Vector_base::_M_create_storage (inline) 0 0% 82.78% 33ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 82.78% 33ms 0.6% std::__basic_file::xsputn 0 0% 82.78% 32ms 0.58% BoundaryNodeWriter::Visit 13ms 0.24% 83.01% 32ms 0.58% Determinant (inline) 20ms 0.36% 83.38% 31ms 0.56% AbstractTetrahedralMesh::GetElement 0 0% 83.38% 31ms 0.56% _IO_new_file_fopen 0 0% 83.38% 31ms 0.56% _IO_new_fopen 0 0% 83.38% 31ms 0.56% __GI__IO_file_open 0 0% 83.38% 31ms 0.56% __fopen_internal (inline) 0 0% 83.38% 31ms 0.56% std::__basic_file::open 3ms 0.055% 83.43% 31ms 0.56% std::__copy_move::__copy_m (inline) 0 0% 83.43% 31ms 0.56% std::__copy_move_a (inline) 0 0% 83.43% 31ms 0.56% std::__copy_move_a1 (inline) 0 0% 83.43% 31ms 0.56% std::__copy_move_a2 (inline) 0 0% 83.43% 31ms 0.56% std::copy (inline) 0 0% 83.43% 30ms 0.55% _dl_init 0 0% 83.43% 30ms 0.55% call_init (inline) 0 0% 83.43% 30ms 0.55% std::map::map (inline) 0 0% 83.43% 30ms 0.55% std::map::~map (inline) 29ms 0.53% 83.96% 29ms 0.53% Node::rGetLocation 0 0% 83.96% 29ms 0.53% boost::numeric::ublas::norm_2 (inline) 11ms 0.2% 84.16% 29ms 0.53% boost::numeric::ublas::vector_norm_2::apply (inline) 15ms 0.27% 84.44% 29ms 0.53% std::basic_filebuf::xsputn 0 0% 84.44% 28ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 21ms 0.38% 84.82% 28ms 0.51% boost::numeric::ublas::c_matrix::operator() 28ms 0.51% 85.33% 28ms 0.51% std::_Rb_tree_increment 3ms 0.055% 85.38% 28ms 0.51% std::_Rb_tree_iterator::operator-- (inline) 28ms 0.51% 85.89% 28ms 0.51% unlink_chunk