File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6928ms, 85.28% of 8124ms total Dropped 568 nodes (cum <= 40.62ms) flat flat% sum% cum cum% 0 0% 0% 8084ms 99.51% __libc_start_call_main 0 0% 0% 8084ms 99.51% __libc_start_main_impl 0 0% 0% 8084ms 99.51% _start 0 0% 0% 8066ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 8066ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 8066ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 8066ms 99.29% main 0 0% 0% 8022ms 98.74% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 8022ms 98.74% CxxTest::TestRunner::runTest (inline) 0 0% 0% 8022ms 98.74% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.012% 0.012% 8018ms 98.70% AbstractCellBasedSimulation::Solve 1ms 0.012% 0.025% 3478ms 42.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.025% 2996ms 36.88% MeshBasedCellPopulation::Update 2ms 0.025% 0.049% 2953ms 36.35% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.062% 1577ms 19.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.074% 1479ms 18.21% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.074% 1471ms 18.11% MutableMesh::ReMesh 1ms 0.012% 0.086% 1420ms 17.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.11% 1366ms 16.81% AbstractNumericalMethod::ComputeForcesIncludingDamping 22ms 0.27% 0.38% 1282ms 15.78% MeshBasedCellPopulation::SpringIterator::operator++ 108ms 1.33% 1.71% 1036ms 12.75% TetrahedralMesh::EdgeIterator::operator++ 432ms 5.32% 7.03% 984ms 12.11% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.062% 7.09% 981ms 12.08% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 256ms 3.15% 10.24% 953ms 11.73% __dynamic_cast 2ms 0.025% 10.27% 937ms 11.53% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.15% 10.41% 927ms 11.41% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.11% 10.52% 901ms 11.09% CellPopulationElementWriter::Visit 39ms 0.48% 11.00% 845ms 10.40% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 10ms 0.12% 11.13% 827ms 10.18% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.32% 11.45% 773ms 9.52% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.56% 760ms 9.35% TetrahedralMesh::ImportFromMesher 3ms 0.037% 11.60% 744ms 9.16% AbstractCellProperty::IsSubType (inline) 63ms 0.78% 12.37% 615ms 7.57% std::map::operator[] (partial-inline) 1ms 0.012% 12.38% 583ms 7.18% std::ostream::operator<< (inline) 30ms 0.37% 12.75% 582ms 7.16% operator new 580ms 7.14% 19.89% 580ms 7.14% __strcmp_avx2 116ms 1.43% 21.32% 579ms 7.13% std::ostream::_M_insert 1ms 0.012% 21.33% 558ms 6.87% triangulate 4ms 0.049% 21.38% 557ms 6.86% Cell::GetCellProliferativeType 176ms 2.17% 23.55% 543ms 6.68% __GI___libc_malloc 24ms 0.3% 23.84% 536ms 6.60% std::_Rb_tree::find (inline) 33ms 0.41% 24.25% 536ms 6.60% std::__new_allocator::allocate (inline) 5ms 0.062% 24.31% 529ms 6.51% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.31% 529ms 6.51% std::allocator_traits::allocate (inline) 10ms 0.12% 24.43% 518ms 6.38% std::set::insert (inline) 8ms 0.098% 24.53% 509ms 6.27% std::_Rb_tree::_M_insert_unique 0 0% 24.53% 499ms 6.14% std::_Rb_tree::lower_bound (inline) 0 0% 24.53% 499ms 6.14% std::map::lower_bound (inline) 0 0% 24.53% 492ms 6.06% std::set::count (inline) 0 0% 24.53% 483ms 5.95% delaunay 0 0% 24.53% 483ms 5.95% divconqdelaunay 37ms 0.46% 24.99% 481ms 5.92% std::_Rb_tree::~_Rb_tree (inline) 230ms 2.83% 27.82% 475ms 5.85% __cxxabiv1::__si_class_type_info::__do_dyncast 5ms 0.062% 27.88% 459ms 5.65% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.88% 453ms 5.58% std::set::~set (inline) 84ms 1.03% 28.91% 440ms 5.42% std::_Rb_tree::_M_erase 0 0% 28.91% 417ms 5.13% std::_Rb_tree::_M_create_node (inline) 3ms 0.037% 28.95% 402ms 4.95% Cell::GetMutationState 0 0% 28.95% 390ms 4.80% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.95% 388ms 4.78% std::_Rb_tree::_M_get_node (inline) 10ms 0.12% 29.07% 358ms 4.41% std::less::operator() (inline) 1ms 0.012% 29.09% 348ms 4.28% NodeLocationWriter::Visit 348ms 4.28% 33.37% 348ms 4.28% std::operator< (inline) 340ms 4.19% 37.56% 340ms 4.19% std::_Rb_tree::_S_right (inline) 1ms 0.012% 37.57% 338ms 4.16% MeshBasedCellPopulation::GetDampingConstant 5ms 0.062% 37.63% 337ms 4.15% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.63% 334ms 4.11% std::_Rb_tree::_M_drop_node (inline) 10ms 0.12% 37.75% 333ms 4.10% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 37.75% 328ms 4.04% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.012% 37.76% 326ms 4.01% AbstractCellBasedWriter::OpenOutputFileForAppend 101ms 1.24% 39.01% 324ms 3.99% __GI___libc_free 1ms 0.012% 39.02% 321ms 3.95% OutputFileHandler::OpenOutputFile 2ms 0.025% 39.04% 319ms 3.93% Cell::ReadyToDivide 8ms 0.098% 39.14% 304ms 3.74% std::set::set (inline) 26ms 0.32% 39.46% 302ms 3.72% std::_Rb_tree::_M_insert_ (inline) 10ms 0.12% 39.59% 300ms 3.69% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.049% 39.64% 300ms 3.69% Element::Element 1ms 0.012% 39.65% 299ms 3.68% std::__new_allocator::deallocate (inline) 23ms 0.28% 39.93% 298ms 3.67% std::num_put::_M_insert_float 0 0% 39.93% 297ms 3.66% std::allocator_traits::deallocate (inline) 6ms 0.074% 40.00% 284ms 3.50% divconqrecurse 192ms 2.36% 42.37% 281ms 3.46% _int_malloc 23ms 0.28% 42.65% 281ms 3.46% std::_Rb_tree::_M_copy (inline) 65ms 0.8% 43.45% 267ms 3.29% mergehulls 0 0% 43.45% 266ms 3.27% std::_Rb_tree::_M_put_node (inline) 72ms 0.89% 44.34% 252ms 3.10% std::_Rb_tree::_M_clone_node (inline) 4ms 0.049% 44.39% 251ms 3.09% AbstractCellProperty::IsType (inline) 1ms 0.012% 44.40% 248ms 3.05% CellProliferativeTypesWriter::VisitCell 2ms 0.025% 44.42% 247ms 3.04% CellPropertyCollection::HasProperty 0 0% 44.42% 246ms 3.03% Cell::HasCellProperty (inline) 10ms 0.12% 44.55% 243ms 2.99% std::__cxx11::collate::do_transform 17ms 0.21% 44.76% 225ms 2.77% TetrahedralMesh::Clear 2ms 0.025% 44.78% 224ms 2.76% ___vsnprintf 0 0% 44.78% 222ms 2.73% __vsnprintf_internal (inline) 193ms 2.38% 47.16% 222ms 2.73% _int_free 45ms 0.55% 47.71% 220ms 2.71% __printf_buffer 4ms 0.049% 47.76% 215ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.074% 47.83% 209ms 2.57% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.098% 47.93% 204ms 2.51% MeshBasedCellPopulation::SpringsEnd (inline) 76ms 0.94% 48.87% 200ms 2.46% std::_Rb_tree::_M_get_insert_unique_pos (inline) 44ms 0.54% 49.41% 196ms 2.41% AbstractCellProperty::IsSame 3ms 0.037% 49.45% 191ms 2.35% Element::RegisterWithNodes (inline) 3ms 0.037% 49.48% 184ms 2.26% Node::AddElement 44ms 0.54% 50.02% 166ms 2.04% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.02% 159ms 1.96% AbstractCellBasedWriter::CloseFile 0 0% 50.02% 159ms 1.96% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.012% 50.04% 159ms 1.96% std::basic_filebuf::close 0 0% 50.04% 159ms 1.96% std::basic_ofstream::close (inline) 9ms 0.11% 50.15% 157ms 1.93% AbstractTetrahedralElement::CalculateJacobian 3ms 0.037% 50.18% 157ms 1.93% __printf_fp_l_buffer 0 0% 50.18% 157ms 1.93% __printf_fp_spec (inline) 1ms 0.012% 50.20% 152ms 1.87% OutputFileHandler::OutputFileHandler 0 0% 50.20% 152ms 1.87% std::basic_ofstream::basic_ofstream (inline) 26ms 0.32% 50.52% 152ms 1.87% std::type_info::operator== (inline) 3ms 0.037% 50.55% 151ms 1.86% Node::~Node 0 0% 50.55% 151ms 1.86% OutputFileHandler::CommonConstructor 85ms 1.05% 51.60% 151ms 1.86% __printf_fp_buffer_1 0 0% 51.60% 148ms 1.82% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 51.62% 148ms 1.82% std::basic_filebuf::open 0 0% 51.62% 148ms 1.82% std::basic_ofstream::open (inline) 1ms 0.012% 51.64% 146ms 1.80% boost::numeric::ublas::vector_assign (inline) 20ms 0.25% 51.88% 144ms 1.77% boost::detail::shared_count::~shared_count (inline) 0 0% 51.88% 144ms 1.77% boost::shared_ptr::~shared_ptr (inline) 3ms 0.037% 51.92% 142ms 1.75% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.012% 51.93% 142ms 1.75% std::_Vector_base::_M_allocate (inline) 19ms 0.23% 52.17% 140ms 1.72% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 52.17% 139ms 1.71% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.012% 52.18% 139ms 1.71% std::filesystem::permissions 138ms 1.70% 53.88% 138ms 1.70% __GI_fchmodat 2ms 0.025% 53.90% 136ms 1.67% TetrahedralMesh::RefreshJacobianCachedData 7ms 0.086% 53.99% 131ms 1.61% std::vector::push_back (inline) 51ms 0.63% 54.62% 128ms 1.58% std::__ostream_insert 4ms 0.049% 54.67% 126ms 1.55% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.025% 54.69% 126ms 1.55% alternateaxes 125ms 1.54% 56.23% 125ms 1.54% incircle 89ms 1.10% 57.32% 124ms 1.53% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 57.32% 123ms 1.51% _IO_new_fopen 0 0% 57.32% 123ms 1.51% __fopen_internal (inline) 0 0% 57.32% 123ms 1.51% std::__basic_file::open 111ms 1.37% 58.69% 122ms 1.50% vertexmedian 11ms 0.14% 58.83% 121ms 1.49% std::vector::_M_realloc_insert 1ms 0.012% 58.84% 118ms 1.45% _IO_new_file_fopen 2ms 0.025% 58.86% 118ms 1.45% std::basic_filebuf::overflow 111ms 1.37% 60.23% 117ms 1.44% boost::detail::sp_counted_base::release 0 0% 60.23% 117ms 1.44% std::basic_filebuf::_M_terminate_output 31ms 0.38% 60.61% 117ms 1.44% std::num_put::_M_insert_int 0 0% 60.61% 116ms 1.43% __GI__IO_file_open 0 0% 60.61% 116ms 1.43% std::__basic_file::xsputn 0 0% 60.61% 116ms 1.43% std::basic_filebuf::_M_convert_to_external 112ms 1.38% 61.99% 114ms 1.40% __GI___libc_write 47ms 0.58% 62.57% 111ms 1.37% boost::shared_ptr::shared_ptr (inline) 12ms 0.15% 62.72% 110ms 1.35% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 62.72% 110ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.037% 62.75% 110ms 1.35% AbstractTetrahedralElement::AbstractTetrahedralElement 36ms 0.44% 63.20% 108ms 1.33% boost::numeric::ublas::indexing_vector_assign 17ms 0.21% 63.40% 107ms 1.32% AbstractTetrahedralElement::RefreshJacobian 99ms 1.22% 64.62% 100ms 1.23% __libc_open64 0 0% 64.62% 99ms 1.22% std::operator<< (inline) 8ms 0.098% 64.72% 97ms 1.19% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 64.72% 95ms 1.17% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 64.73% 95ms 1.17% std::filesystem::create_directory 92ms 1.13% 65.87% 92ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 91ms 1.12% 66.99% 91ms 1.12% std::_Rb_tree_increment 2ms 0.025% 67.01% 90ms 1.11% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.012% 67.02% 89ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 2ms 0.025% 67.05% 87ms 1.07% Cell::GetCellId 79ms 0.97% 68.02% 79ms 0.97% [libchaste_cell_based.so] 2ms 0.025% 68.05% 79ms 0.97% std::filesystem::status 78ms 0.96% 69.01% 78ms 0.96% __GI___fstatat64 78ms 0.96% 69.97% 78ms 0.96% std::_Rb_tree_insert_and_rebalance 0 0% 69.97% 78ms 0.96% tcache_get (inline) 78ms 0.96% 70.93% 78ms 0.96% tcache_get_n (inline) 32ms 0.39% 71.32% 77ms 0.95% AbstractElement::GetNodeLocation 77ms 0.95% 72.27% 77ms 0.95% counterclockwise 50ms 0.62% 72.88% 76ms 0.94% std::basic_filebuf::xsputn 2ms 0.025% 72.91% 73ms 0.9% AbstractCellPopulation::GetLocationIndexUsingCell 59ms 0.73% 73.63% 73ms 0.9% AbstractElement::GetNodeGlobalIndex 7ms 0.086% 73.72% 72ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeA 4ms 0.049% 73.77% 72ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 73.77% 70ms 0.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.77% 70ms 0.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 63ms 0.78% 74.54% 70ms 0.86% vertexsort 8ms 0.098% 74.64% 69ms 0.85% CellPropertyCollection::AddProperty 68ms 0.84% 75.48% 68ms 0.84% Node::GetIndex 0 0% 75.48% 68ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 0 0% 75.48% 68ms 0.84% std::__new_allocator::destroy (inline) 0 0% 75.48% 68ms 0.84% std::allocator_traits::destroy (inline) 29ms 0.36% 75.84% 67ms 0.82% AbstractTetrahedralMesh::GetElement 46ms 0.57% 76.40% 67ms 0.82% malloc_consolidate 66ms 0.81% 77.22% 66ms 0.81% __memcpy_avx_unaligned_erms 62ms 0.76% 77.98% 64ms 0.79% boost::detail::shared_count::shared_count (inline) 34ms 0.42% 78.40% 59ms 0.73% std::basic_streambuf::xsputn 59ms 0.73% 79.12% 59ms 0.73% std::vector::size (inline) 42ms 0.52% 79.64% 58ms 0.71% std::num_put::do_put 1ms 0.012% 79.65% 56ms 0.69% Node::ClearAppliedForce 56ms 0.69% 80.34% 56ms 0.69% [libstdc++.so.6.0.33] 0 0% 80.34% 56ms 0.69% std::vector::vector (inline) 29ms 0.36% 80.70% 55ms 0.68% CellPropertyCollection::GetProperty 0 0% 80.70% 55ms 0.68% Node::ConstructNodeAttributes (inline) 37ms 0.46% 81.15% 55ms 0.68% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 81.15% 55ms 0.68% boost::numeric::ublas::norm_2 (inline) 17ms 0.21% 81.36% 55ms 0.68% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 81.36% 54ms 0.66% AbstractCentreBasedCellPopulation::CreateCellPair 54ms 0.66% 82.03% 54ms 0.66% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.03% 53ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.03% 50ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 14ms 0.17% 82.20% 50ms 0.62% Determinant (inline) 0 0% 82.20% 50ms 0.62% std::_Vector_base::_Vector_base (inline) 0 0% 82.20% 49ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 49ms 0.6% 82.80% 49ms 0.6% boost::shared_ptr::operator-> (inline) 1ms 0.012% 82.82% 48ms 0.59% std::_Vector_base::_M_create_storage (inline) 46ms 0.57% 83.38% 46ms 0.57% __GI___mkdir 0 0% 83.38% 45ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 45ms 0.55% 83.94% 45ms 0.55% [libchaste_mesh.so] 0 0% 83.94% 44ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 25ms 0.31% 84.24% 44ms 0.54% hack_digit 39ms 0.48% 84.72% 44ms 0.54% writeedges 43ms 0.53% 85.25% 43ms 0.53% Node::IsDeleted 0 0% 85.25% 43ms 0.53% _dl_init 0 0% 85.25% 43ms 0.53% call_init (inline) 0 0% 85.25% 42ms 0.52% BoundaryNodeWriter::Visit 2ms 0.025% 85.28% 42ms 0.52% NodeAttributes::NodeAttributes