File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6676ms, 85.64% of 7795ms total Dropped 574 nodes (cum <= 38.98ms) flat flat% sum% cum cum% 0 0% 0% 7759ms 99.54% __libc_start_call_main 0 0% 0% 7759ms 99.54% __libc_start_main_impl 0 0% 0% 7759ms 99.54% _start 0 0% 0% 7741ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7741ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7741ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7741ms 99.31% main 0 0% 0% 7700ms 98.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7700ms 98.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7700ms 98.78% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7696ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3383ms 43.40% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2925ms 37.52% MeshBasedCellPopulation::Update 0 0% 0% 2694ms 34.56% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 1614ms 20.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0% 1488ms 19.09% MutableMesh::ReMesh 0 0% 0% 1448ms 18.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.09% 0.09% 1396ms 17.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.09% 1384ms 17.75% MeshBasedCellPopulation::UpdateNodePairs 22ms 0.28% 0.37% 1217ms 15.61% MeshBasedCellPopulation::SpringIterator::operator++ 295ms 3.78% 4.16% 989ms 12.69% __dynamic_cast 120ms 1.54% 5.70% 979ms 12.56% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 5.72% 953ms 12.23% AbstractTwoBodyInteractionForce::AddForceContribution 438ms 5.62% 11.34% 927ms 11.89% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.064% 11.40% 918ms 11.78% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 6ms 0.077% 11.48% 910ms 11.67% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.12% 11.60% 860ms 11.03% CellPopulationElementWriter::Visit 38ms 0.49% 12.08% 847ms 10.87% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 9ms 0.12% 12.20% 766ms 9.83% MeshBasedCellPopulation::AcceptCellWriter 3ms 0.038% 12.24% 754ms 9.67% AbstractCellProperty::IsSubType (inline) 37ms 0.47% 12.71% 749ms 9.61% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.064% 12.78% 736ms 9.44% TetrahedralMesh::ImportFromMesher 41ms 0.53% 13.30% 616ms 7.90% operator new 42ms 0.54% 13.84% 586ms 7.52% std::map::operator[] (partial-inline) 187ms 2.40% 16.24% 576ms 7.39% __GI___libc_malloc 1ms 0.013% 16.25% 575ms 7.38% std::ostream::operator<< (inline) 2ms 0.026% 16.28% 573ms 7.35% triangulate 101ms 1.30% 17.58% 571ms 7.33% std::ostream::_M_insert 7ms 0.09% 17.67% 544ms 6.98% std::set::insert (inline) 14ms 0.18% 17.84% 537ms 6.89% std::_Rb_tree::_M_insert_unique 24ms 0.31% 18.15% 530ms 6.80% std::__new_allocator::allocate (inline) 2ms 0.026% 18.18% 528ms 6.77% Cell::GetCellProliferativeType 259ms 3.32% 21.50% 527ms 6.76% __cxxabiv1::__si_class_type_info::__do_dyncast 525ms 6.74% 28.24% 525ms 6.74% __strcmp_avx2 0 0% 28.24% 524ms 6.72% std::allocator_traits::allocate (inline) 0 0% 28.24% 500ms 6.41% delaunay 1ms 0.013% 28.25% 499ms 6.40% divconqdelaunay 7ms 0.09% 28.34% 492ms 6.31% LegacyCellProliferativeTypesWriter::VisitCell 36ms 0.46% 28.80% 492ms 6.31% std::_Rb_tree::find (inline) 0 0% 28.80% 486ms 6.23% std::_Rb_tree::lower_bound (inline) 0 0% 28.80% 486ms 6.23% std::map::lower_bound (inline) 5ms 0.064% 28.86% 447ms 5.73% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.86% 443ms 5.68% std::set::count (inline) 38ms 0.49% 29.35% 441ms 5.66% std::_Rb_tree::~_Rb_tree (inline) 0 0% 29.35% 421ms 5.40% std::_Rb_tree::_M_create_node (inline) 0 0% 29.35% 407ms 5.22% std::set::~set (inline) 97ms 1.24% 30.60% 400ms 5.13% std::_Rb_tree::_M_erase 0 0% 30.60% 398ms 5.11% std::_Rb_tree::_M_get_node (inline) 0 0% 30.60% 383ms 4.91% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.013% 30.61% 375ms 4.81% Cell::GetMutationState 3ms 0.038% 30.65% 370ms 4.75% NodeLocationWriter::Visit 3ms 0.038% 30.69% 340ms 4.36% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 30.74% 337ms 4.32% AbstractCentreBasedCellPopulation::GetDampingConstant 23ms 0.3% 31.03% 330ms 4.23% std::_Rb_tree::_Rb_tree (partial-inline) 12ms 0.15% 31.19% 327ms 4.19% std::less::operator() (inline) 28ms 0.36% 31.55% 325ms 4.17% std::num_put::_M_insert_float 71ms 0.91% 32.46% 321ms 4.12% __GI___libc_free 8ms 0.1% 32.56% 320ms 4.11% Element::Element 18ms 0.23% 32.79% 320ms 4.11% std::_Rb_tree::_M_insert_ (inline) 315ms 4.04% 36.83% 315ms 4.04% std::operator< (inline) 6ms 0.077% 36.91% 310ms 3.98% Cell::ReadyToDivide 307ms 3.94% 40.85% 307ms 3.94% std::_Rb_tree::_S_right (inline) 198ms 2.54% 43.39% 297ms 3.81% _int_malloc 4ms 0.051% 43.44% 295ms 3.78% std::set::set (inline) 0 0% 43.44% 290ms 3.72% std::_Rb_tree::_M_drop_node (inline) 8ms 0.1% 43.54% 287ms 3.68% std::__new_allocator::deallocate (inline) 0 0% 43.54% 283ms 3.63% std::allocator_traits::deallocate (inline) 12ms 0.15% 43.69% 275ms 3.53% divconqrecurse 7ms 0.09% 43.78% 273ms 3.50% AbstractCellPopulation::IsCellAttachedToLocationIndex 27ms 0.35% 44.13% 261ms 3.35% std::_Rb_tree::_M_copy (inline) 6ms 0.077% 44.21% 260ms 3.34% std::__cxx11::collate::do_transform 211ms 2.71% 46.91% 250ms 3.21% _int_free 73ms 0.94% 47.85% 249ms 3.19% mergehulls 3ms 0.038% 47.89% 243ms 3.12% ___vsnprintf 0 0% 47.89% 240ms 3.08% __vsnprintf_internal (inline) 0 0% 47.89% 237ms 3.04% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 47.93% 236ms 3.03% AbstractCellProperty::IsType (inline) 40ms 0.51% 48.44% 234ms 3.00% __printf_buffer 3ms 0.038% 48.48% 230ms 2.95% CellProliferativeTypesWriter::VisitCell 63ms 0.81% 49.29% 228ms 2.92% std::_Rb_tree::_M_clone_node (inline) 5ms 0.064% 49.35% 222ms 2.85% AbstractPhaseBasedCellCycleModel::ReadyToDivide 1ms 0.013% 49.36% 221ms 2.84% CellPropertyCollection::HasProperty 0 0% 49.36% 220ms 2.82% Cell::HasCellProperty (inline) 7ms 0.09% 49.45% 215ms 2.76% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.038% 49.49% 207ms 2.66% Element::RegisterWithNodes (inline) 17ms 0.22% 49.71% 206ms 2.64% TetrahedralMesh::Clear 64ms 0.82% 50.53% 203ms 2.60% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.038% 50.57% 200ms 2.57% Node::AddElement 9ms 0.12% 50.69% 197ms 2.53% MeshBasedCellPopulation::SpringsEnd (inline) 8ms 0.1% 50.79% 185ms 2.37% __printf_fp_l_buffer 0 0% 50.79% 185ms 2.37% __printf_fp_spec (inline) 46ms 0.59% 51.38% 183ms 2.35% AbstractCellProperty::IsSame 87ms 1.12% 52.50% 172ms 2.21% __printf_fp_buffer_1 1ms 0.013% 52.51% 162ms 2.08% OutputFileHandler::CommonConstructor 0 0% 52.51% 162ms 2.08% OutputFileHandler::OutputFileHandler 1ms 0.013% 52.52% 159ms 2.04% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 13ms 0.17% 52.69% 159ms 2.04% AbstractTetrahedralElement::CalculateJacobian 0 0% 52.69% 159ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 0 0% 52.69% 156ms 2.00% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 52.70% 155ms 1.99% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 52.70% 155ms 1.99% OutputFileHandler::OpenOutputFile 0 0% 52.70% 155ms 1.99% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 52.71% 150ms 1.92% std::basic_filebuf::open 0 0% 52.71% 150ms 1.92% std::basic_ofstream::open (inline) 0 0% 52.71% 147ms 1.89% AbstractCellPopulation::CloseRoundRobinWritersFiles 3ms 0.038% 52.75% 147ms 1.89% alternateaxes 1ms 0.013% 52.76% 146ms 1.87% AbstractCellBasedWriter::CloseFile 36ms 0.46% 53.23% 146ms 1.87% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 53.23% 145ms 1.86% std::basic_filebuf::close 0 0% 53.23% 145ms 1.86% std::basic_ofstream::close (inline) 10ms 0.13% 53.35% 143ms 1.83% AbstractTetrahedralElement::CalculateInverseJacobian 47ms 0.6% 53.96% 143ms 1.83% std::__ostream_insert 137ms 1.76% 55.72% 142ms 1.82% vertexmedian 37ms 0.47% 56.19% 137ms 1.76% std::type_info::operator== (inline) 11ms 0.14% 56.33% 130ms 1.67% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.064% 56.40% 129ms 1.65% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 56.40% 128ms 1.64% boost::numeric::ublas::vector_assign (inline) 0 0% 56.40% 126ms 1.62% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 56.41% 121ms 1.55% std::operator<< (inline) 14ms 0.18% 56.59% 119ms 1.53% boost::detail::shared_count::~shared_count (inline) 0 0% 56.59% 119ms 1.53% boost::shared_ptr::~shared_ptr (inline) 119ms 1.53% 58.11% 119ms 1.53% incircle 5ms 0.064% 58.18% 118ms 1.51% Node::~Node 1ms 0.013% 58.19% 115ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 15ms 0.19% 58.38% 115ms 1.48% AbstractTetrahedralElement::RefreshJacobian 22ms 0.28% 58.67% 113ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.013% 58.68% 113ms 1.45% std::__basic_file::open 1ms 0.013% 58.69% 112ms 1.44% std::basic_filebuf::_M_terminate_output 0 0% 58.69% 111ms 1.42% _IO_new_fopen 0 0% 58.69% 111ms 1.42% __fopen_internal (inline) 1ms 0.013% 58.70% 110ms 1.41% _IO_new_file_fopen 1ms 0.013% 58.72% 110ms 1.41% std::basic_filebuf::overflow 73ms 0.94% 59.65% 109ms 1.40% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 59.67% 109ms 1.40% __GI__IO_file_open 1ms 0.013% 59.68% 109ms 1.40% std::basic_filebuf::_M_convert_to_external 4ms 0.051% 59.73% 109ms 1.40% std::vector::push_back (inline) 4ms 0.051% 59.78% 108ms 1.39% AbstractTetrahedralElement::AbstractTetrahedralElement 108ms 1.39% 61.17% 108ms 1.39% __GI___libc_write 0 0% 61.17% 108ms 1.39% std::__basic_file::xsputn 10ms 0.13% 61.30% 102ms 1.31% std::vector::_M_realloc_insert 96ms 1.23% 62.53% 96ms 1.23% __libc_open64 95ms 1.22% 63.75% 95ms 1.22% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 90ms 1.15% 64.90% 95ms 1.22% boost::detail::sp_counted_base::release 46ms 0.59% 65.49% 95ms 1.22% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 65.53% 93ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 93ms 1.19% 66.72% 93ms 1.19% [libchaste_cell_based.so] 67ms 0.86% 67.58% 90ms 1.15% malloc_consolidate 20ms 0.26% 67.84% 90ms 1.15% std::num_put::_M_insert_int 8ms 0.1% 67.94% 89ms 1.14% std::_Rb_tree_const_iterator::operator++ (inline) 63ms 0.81% 68.75% 89ms 1.14% std::basic_filebuf::xsputn 29ms 0.37% 69.12% 88ms 1.13% boost::numeric::ublas::indexing_vector_assign 87ms 1.12% 70.24% 87ms 1.12% std::_Rb_tree_insert_and_rebalance 86ms 1.10% 71.34% 86ms 1.10% __GI___fstatat64 37ms 0.47% 71.82% 85ms 1.09% AbstractElement::GetNodeLocation 0 0% 71.82% 85ms 1.09% tcache_get (inline) 85ms 1.09% 72.91% 85ms 1.09% tcache_get_n (inline) 1ms 0.013% 72.92% 84ms 1.08% std::filesystem::status 2ms 0.026% 72.94% 83ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 72.96% 80ms 1.03% Cell::GetCellId 80ms 1.03% 73.98% 80ms 1.03% std::_Rb_tree_increment 0 0% 73.98% 80ms 1.03% std::filesystem::create_directory 0 0% 73.98% 79ms 1.01% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.98% 73ms 0.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.98% 73ms 0.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 69ms 0.89% 74.87% 69ms 0.89% std::vector::size (inline) 64ms 0.82% 75.69% 68ms 0.87% vertexsort 45ms 0.58% 76.27% 67ms 0.86% AbstractElement::GetNodeGlobalIndex 65ms 0.83% 77.10% 65ms 0.83% __memcpy_avx_unaligned_erms 9ms 0.12% 77.22% 64ms 0.82% CellPropertyCollection::AddProperty 0 0% 77.22% 64ms 0.82% std::vector::vector (inline) 44ms 0.56% 77.78% 61ms 0.78% std::basic_streambuf::xsputn 2ms 0.026% 77.81% 60ms 0.77% TetrahedralMesh::EdgeIterator::GetNodeB 59ms 0.76% 78.56% 59ms 0.76% counterclockwise 1ms 0.013% 78.58% 58ms 0.74% Node::ClearAppliedForce 2ms 0.026% 78.60% 58ms 0.74% Node::ConstructNodeAttributes (inline) 1ms 0.013% 78.61% 58ms 0.74% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.026% 78.64% 58ms 0.74% std::_Vector_base::_M_create_storage (inline) 0 0% 78.64% 58ms 0.74% std::_Vector_base::_Vector_base (inline) 35ms 0.45% 79.09% 57ms 0.73% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.09% 56ms 0.72% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 43ms 0.55% 79.64% 55ms 0.71% std::num_put::do_put 0 0% 79.64% 53ms 0.68% boost::numeric::ublas::norm_2 (inline) 21ms 0.27% 79.91% 53ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 79.91% 53ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.91% 53ms 0.68% std::__new_allocator::destroy (inline) 0 0% 79.91% 53ms 0.68% std::allocator_traits::destroy (inline) 1ms 0.013% 79.92% 52ms 0.67% AbstractCentreBasedCellPopulation::CreateCellPair 52ms 0.67% 80.59% 52ms 0.67% Node::GetIndex 35ms 0.45% 81.04% 52ms 0.67% hack_digit 0 0% 81.04% 51ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 6ms 0.077% 81.12% 50ms 0.64% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 81.12% 49ms 0.63% BoundaryNodeWriter::Visit 47ms 0.6% 81.72% 49ms 0.63% boost::detail::shared_count::shared_count (inline) 23ms 0.3% 82.01% 48ms 0.62% AbstractTetrahedralMesh::GetElement 4ms 0.051% 82.07% 48ms 0.62% std::_Vector_base::_M_deallocate (inline) 14ms 0.18% 82.25% 47ms 0.6% Determinant (inline) 47ms 0.6% 82.85% 47ms 0.6% Node::rGetLocation 31ms 0.4% 83.25% 45ms 0.58% writeedges 44ms 0.56% 83.81% 44ms 0.56% [libstdc++.so.6.0.33] 43ms 0.55% 84.36% 43ms 0.55% boost::numeric::ublas::c_vector::operator() 0 0% 84.36% 43ms 0.55% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.038% 84.40% 43ms 0.55% std::_Rb_tree_header::_Rb_tree_header (inline) 9ms 0.12% 84.52% 42ms 0.54% Inverse 0 0% 84.52% 42ms 0.54% std::map::find (inline) 1ms 0.013% 84.53% 41ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 2ms 0.026% 84.55% 41ms 0.53% NodeAttributes::NodeAttributes 0 0% 84.55% 40ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.026% 84.58% 40ms 0.51% Element::~Element 40ms 0.51% 85.09% 40ms 0.51% boost::shared_ptr::operator-> (inline) 40ms 0.51% 85.61% 40ms 0.51% std::_Rb_tree_header::_M_reset (inline) 3ms 0.038% 85.64% 40ms 0.51% std::__copy_move::__copy_m (inline) 0 0% 85.64% 40ms 0.51% std::__copy_move_a (inline) 0 0% 85.64% 40ms 0.51% std::__copy_move_a1 (inline) 0 0% 85.64% 40ms 0.51% std::__copy_move_a2 (inline) 0 0% 85.64% 40ms 0.51% std::copy (inline) 0 0% 85.64% 39ms 0.5% std::map::map (inline)