File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6789ms, 85.08% of 7980ms total Dropped 633 nodes (cum <= 39.90ms) flat flat% sum% cum cum% 0 0% 0% 7942ms 99.52% __libc_start_call_main 0 0% 0% 7942ms 99.52% __libc_start_main_impl 0 0% 0% 7942ms 99.52% _start 0 0% 0% 7926ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7926ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7926ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7926ms 99.32% main 0 0% 0% 7884ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7884ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7884ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 2ms 0.025% 0.025% 7881ms 98.76% AbstractCellBasedSimulation::Solve 0 0% 0.025% 3437ms 43.07% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.063% 2928ms 36.69% MeshBasedCellPopulation::Update 0 0% 0.063% 2830ms 35.46% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.075% 1602ms 20.08% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.075% 1450ms 18.17% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.088% 1445ms 18.11% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.1% 1430ms 17.92% MutableMesh::ReMesh 5ms 0.063% 0.16% 1406ms 17.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.21% 0.38% 1255ms 15.73% MeshBasedCellPopulation::SpringIterator::operator++ 119ms 1.49% 1.87% 1036ms 12.98% TetrahedralMesh::EdgeIterator::operator++ 465ms 5.83% 7.69% 986ms 12.36% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.075% 7.77% 970ms 12.16% AbstractTwoBodyInteractionForce::AddForceContribution 21ms 0.26% 8.03% 909ms 11.39% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.05% 8.08% 908ms 11.38% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.063% 8.15% 877ms 10.99% CellPopulationElementWriter::Visit 54ms 0.68% 8.82% 870ms 10.90% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 271ms 3.40% 12.22% 868ms 10.88% __dynamic_cast 32ms 0.4% 12.62% 779ms 9.76% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 12.62% 753ms 9.44% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.13% 12.74% 743ms 9.31% TetrahedralMesh::ImportFromMesher 5ms 0.063% 12.81% 685ms 8.58% AbstractCellProperty::IsSubType (inline) 48ms 0.6% 13.41% 617ms 7.73% std::map::operator[] (partial-inline) 0 0% 13.41% 575ms 7.21% std::ostream::operator<< (inline) 93ms 1.17% 14.57% 573ms 7.18% std::ostream::_M_insert 34ms 0.43% 15.00% 563ms 7.06% operator new 12ms 0.15% 15.15% 546ms 6.84% std::set::insert (inline) 20ms 0.25% 15.40% 534ms 6.69% std::_Rb_tree::_M_insert_unique 5ms 0.063% 15.46% 530ms 6.64% Cell::GetCellProliferativeType 177ms 2.22% 17.68% 529ms 6.63% __GI___libc_malloc 0 0% 17.68% 523ms 6.55% std::_Rb_tree::lower_bound (inline) 0 0% 17.68% 523ms 6.55% std::map::lower_bound (inline) 28ms 0.35% 18.03% 522ms 6.54% std::_Rb_tree::find (inline) 39ms 0.49% 18.52% 516ms 6.47% std::__new_allocator::allocate (inline) 0 0% 18.52% 511ms 6.40% std::allocator_traits::allocate (inline) 0 0% 18.52% 508ms 6.37% triangulate 3ms 0.038% 18.56% 492ms 6.17% AbstractCellBasedSimulation::DoCellBirth 0 0% 18.56% 480ms 6.02% std::set::count (inline) 6ms 0.075% 18.63% 449ms 5.63% LegacyCellProliferativeTypesWriter::VisitCell 442ms 5.54% 24.17% 442ms 5.54% __strcmp_avx2 0 0% 24.17% 441ms 5.53% delaunay 0 0% 24.17% 439ms 5.50% divconqdelaunay 225ms 2.82% 26.99% 434ms 5.44% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.99% 425ms 5.33% std::_Rb_tree::_M_create_node (inline) 0 0% 26.99% 405ms 5.08% std::_Rb_tree::_Alloc_node::operator() (inline) 33ms 0.41% 27.41% 395ms 4.95% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.41% 385ms 4.82% std::_Rb_tree::_M_get_node (inline) 3ms 0.038% 27.44% 382ms 4.79% Cell::GetMutationState 0 0% 27.44% 363ms 4.55% std::set::~set (inline) 20ms 0.25% 27.69% 361ms 4.52% std::_Rb_tree::_Rb_tree (partial-inline) 83ms 1.04% 28.73% 359ms 4.50% std::_Rb_tree::_M_erase 0 0% 28.73% 357ms 4.47% NodeLocationWriter::Visit 342ms 4.29% 33.02% 342ms 4.29% std::_Rb_tree::_S_right (inline) 0 0% 33.02% 337ms 4.22% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 33.02% 337ms 4.22% MeshBasedCellPopulation::GetDampingConstant 28ms 0.35% 33.37% 336ms 4.21% std::_Rb_tree::_M_insert_ (inline) 11ms 0.14% 33.51% 333ms 4.17% std::less::operator() (inline) 3ms 0.038% 33.55% 331ms 4.15% std::set::set (inline) 5ms 0.063% 33.61% 326ms 4.09% Cell::ReadyToDivide 322ms 4.04% 37.64% 322ms 4.04% std::operator< (inline) 25ms 0.31% 37.96% 317ms 3.97% std::num_put::_M_insert_float 0 0% 37.96% 316ms 3.96% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.96% 315ms 3.95% AbstractCellBasedWriter::OpenOutputFileForAppend 118ms 1.48% 39.44% 312ms 3.91% __GI___libc_free 0 0% 39.44% 310ms 3.88% OutputFileHandler::OpenOutputFile 30ms 0.38% 39.81% 307ms 3.85% std::_Rb_tree::_M_copy (inline) 5ms 0.063% 39.87% 298ms 3.73% Element::Element 5ms 0.063% 39.94% 290ms 3.63% AbstractCellPopulation::IsCellAttachedToLocationIndex 78ms 0.98% 40.91% 275ms 3.45% std::_Rb_tree::_M_clone_node (inline) 179ms 2.24% 43.16% 274ms 3.43% _int_malloc 2ms 0.025% 43.18% 263ms 3.30% CellProliferativeTypesWriter::VisitCell 7ms 0.088% 43.27% 258ms 3.23% divconqrecurse 4ms 0.05% 43.32% 254ms 3.18% std::__new_allocator::deallocate (inline) 0 0% 43.32% 251ms 3.15% std::_Rb_tree::_M_drop_node (inline) 0 0% 43.32% 248ms 3.11% std::allocator_traits::deallocate (inline) 71ms 0.89% 44.21% 245ms 3.07% mergehulls 5ms 0.063% 44.27% 243ms 3.05% std::__cxx11::collate::do_transform 6ms 0.075% 44.35% 234ms 2.93% CellPropertyCollection::HasProperty 1ms 0.013% 44.36% 233ms 2.92% AbstractCellProperty::IsType (inline) 0 0% 44.36% 232ms 2.91% Cell::HasCellProperty (inline) 1ms 0.013% 44.37% 228ms 2.86% ___vsnprintf 0 0% 44.37% 227ms 2.84% __vsnprintf_internal (inline) 30ms 0.38% 44.75% 221ms 2.77% __printf_buffer 21ms 0.26% 45.01% 210ms 2.63% TetrahedralMesh::Clear 3ms 0.038% 45.05% 209ms 2.62% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.05% 207ms 2.59% std::_Rb_tree::_M_put_node (inline) 14ms 0.18% 45.23% 202ms 2.53% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.088% 45.31% 198ms 2.48% Element::RegisterWithNodes (inline) 162ms 2.03% 47.34% 194ms 2.43% _int_free 3ms 0.038% 47.38% 186ms 2.33% Node::AddElement 4ms 0.05% 47.43% 179ms 2.24% MeshBasedCellPopulation::SpringsEnd (inline) 65ms 0.81% 48.25% 178ms 2.23% std::_Rb_tree::_M_get_insert_unique_pos (inline) 3ms 0.038% 48.28% 173ms 2.17% __printf_fp_l_buffer 0 0% 48.28% 173ms 2.17% __printf_fp_spec (inline) 44ms 0.55% 48.83% 168ms 2.11% TetrahedralMesh::EdgesEnd (partial-inline) 92ms 1.15% 49.99% 163ms 2.04% __printf_fp_buffer_1 49ms 0.61% 50.60% 160ms 2.01% AbstractCellProperty::IsSame 0 0% 50.60% 150ms 1.88% std::basic_ofstream::basic_ofstream (inline) 11ms 0.14% 50.74% 148ms 1.85% AbstractTetrahedralElement::CalculateJacobian 3ms 0.038% 50.78% 148ms 1.85% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.78% 145ms 1.82% std::basic_ofstream::open (inline) 63ms 0.79% 51.57% 144ms 1.80% std::__ostream_insert 1ms 0.013% 51.58% 144ms 1.80% std::basic_filebuf::open 0 0% 51.58% 138ms 1.73% AbstractCellBasedWriter::CloseFile 0 0% 51.58% 138ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 11ms 0.14% 51.72% 138ms 1.73% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 51.74% 138ms 1.73% std::basic_ofstream::close (inline) 1ms 0.013% 51.75% 136ms 1.70% std::basic_filebuf::close 0 0% 51.75% 135ms 1.69% OutputFileHandler::CommonConstructor 0 0% 51.75% 135ms 1.69% OutputFileHandler::OutputFileHandler 3ms 0.038% 51.79% 134ms 1.68% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 51.83% 134ms 1.68% boost::numeric::ublas::vector_assign (inline) 134ms 1.68% 53.51% 134ms 1.68% std::_Rb_tree_increment 6ms 0.075% 53.58% 133ms 1.67% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 53.58% 133ms 1.67% OutputFileHandler::MakeFoldersAndReturnFullPath 19ms 0.24% 53.82% 131ms 1.64% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 53.82% 128ms 1.60% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 53.83% 128ms 1.60% std::filesystem::permissions 0 0% 53.83% 127ms 1.59% AbstractCellPopulation::Iterator::operator++ (inline) 126ms 1.58% 55.41% 126ms 1.58% __GI_fchmodat 0 0% 55.41% 126ms 1.58% std::_Vector_base::_M_allocate (inline) 7ms 0.088% 55.50% 122ms 1.53% Node::~Node 7ms 0.088% 55.59% 118ms 1.48% std::operator<< (inline) 17ms 0.21% 55.80% 116ms 1.45% AbstractTetrahedralElement::RefreshJacobian 18ms 0.23% 56.03% 115ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.025% 56.05% 114ms 1.43% alternateaxes 4ms 0.05% 56.10% 112ms 1.40% std::vector::push_back (inline) 1ms 0.013% 56.12% 111ms 1.39% _IO_new_fopen 0 0% 56.12% 111ms 1.39% std::__basic_file::open 26ms 0.33% 56.44% 111ms 1.39% std::type_info::operator== (inline) 106ms 1.33% 57.77% 111ms 1.39% vertexmedian 0 0% 57.77% 110ms 1.38% __fopen_internal (inline) 108ms 1.35% 59.12% 108ms 1.35% incircle 108ms 1.35% 60.48% 108ms 1.35% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 60.50% 107ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 60.50% 107ms 1.34% _IO_new_file_fopen 0 0% 60.50% 106ms 1.33% __GI__IO_file_open 10ms 0.13% 60.63% 106ms 1.33% std::vector::_M_realloc_insert 104ms 1.30% 61.93% 104ms 1.30% [libchaste_cell_based.so] 44ms 0.55% 62.48% 103ms 1.29% boost::shared_ptr::shared_ptr (inline) 0 0% 62.48% 102ms 1.28% std::basic_filebuf::_M_terminate_output 1ms 0.013% 62.49% 102ms 1.28% std::basic_filebuf::overflow 10ms 0.13% 62.62% 101ms 1.27% boost::detail::shared_count::~shared_count (inline) 0 0% 62.62% 101ms 1.27% boost::shared_ptr::~shared_ptr (inline) 0 0% 62.62% 101ms 1.27% std::__basic_file::xsputn 0 0% 62.62% 101ms 1.27% std::basic_filebuf::_M_convert_to_external 36ms 0.45% 63.07% 101ms 1.27% std::num_put::_M_insert_int 61ms 0.76% 63.83% 100ms 1.25% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 99ms 1.24% 65.08% 100ms 1.25% __GI___libc_write 0 0% 65.08% 99ms 1.24% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 26ms 0.33% 65.40% 95ms 1.19% boost::numeric::ublas::indexing_vector_assign 93ms 1.17% 66.57% 93ms 1.17% __libc_open64 4ms 0.05% 66.62% 91ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 85ms 1.07% 67.68% 86ms 1.08% boost::detail::sp_counted_base::release 37ms 0.46% 68.15% 84ms 1.05% AbstractElement::GetNodeLocation 52ms 0.65% 68.80% 82ms 1.03% std::basic_filebuf::xsputn 80ms 1.00% 69.80% 80ms 1.00% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 77ms 0.96% 70.76% 77ms 0.96% Node::GetIndex 0 0% 70.76% 74ms 0.93% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.76% 73ms 0.91% Cell::GetCellId 6ms 0.075% 70.84% 73ms 0.91% TetrahedralMesh::EdgeIterator::GetNodeB 73ms 0.91% 71.75% 73ms 0.91% std::vector::size (inline) 0 0% 71.75% 72ms 0.9% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 71.75% 72ms 0.9% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.75% 72ms 0.9% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 71.77% 72ms 0.9% std::filesystem::create_directory 48ms 0.6% 72.37% 70ms 0.88% malloc_consolidate 1ms 0.013% 72.38% 70ms 0.88% tcache_get (inline) 69ms 0.86% 73.25% 69ms 0.86% tcache_get_n (inline) 7ms 0.088% 73.33% 66ms 0.83% CellPropertyCollection::AddProperty 63ms 0.79% 74.12% 63ms 0.79% counterclockwise 6ms 0.075% 74.20% 62ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeA 37ms 0.46% 74.66% 61ms 0.76% AbstractTetrahedralMesh::GetElement 57ms 0.71% 75.38% 61ms 0.76% vertexsort 6ms 0.075% 75.45% 60ms 0.75% Node::ConstructNodeAttributes (inline) 0 0% 75.45% 60ms 0.75% std::filesystem::status 45ms 0.56% 76.02% 59ms 0.74% AbstractElement::GetNodeGlobalIndex 59ms 0.74% 76.75% 59ms 0.74% __GI___fstatat64 58ms 0.73% 77.48% 59ms 0.74% boost::detail::shared_count::shared_count (inline) 56ms 0.7% 78.18% 56ms 0.7% [libchaste_mesh.so] 0 0% 78.18% 55ms 0.69% Node::ClearAppliedForce 45ms 0.56% 78.75% 55ms 0.69% std::num_put::do_put 52ms 0.65% 79.40% 52ms 0.65% Node::IsDeleted 30ms 0.38% 79.77% 52ms 0.65% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.77% 52ms 0.65% boost::numeric::ublas::norm_2 (inline) 20ms 0.25% 80.03% 52ms 0.65% boost::numeric::ublas::vector_norm_2::apply (inline) 41ms 0.51% 80.54% 52ms 0.65% std::basic_streambuf::xsputn 26ms 0.33% 80.86% 51ms 0.64% AbstractCellCycleModel::GetAge 50ms 0.63% 81.49% 50ms 0.63% boost::shared_ptr::operator-> (inline) 0 0% 81.49% 50ms 0.63% std::vector::vector (inline) 1ms 0.013% 81.50% 49ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 49ms 0.61% 82.12% 49ms 0.61% boost::numeric::ublas::c_vector::operator() (partial-inline) 25ms 0.31% 82.43% 48ms 0.6% AbstractTetrahedralMesh::GetNumAllElements 48ms 0.6% 83.03% 48ms 0.6% __memcpy_avx_unaligned_erms 0 0% 83.03% 46ms 0.58% std::_Rb_tree::_M_emplace_hint_unique 7ms 0.088% 83.12% 46ms 0.58% std::_Vector_base::_M_deallocate (inline) 0 0% 83.12% 45ms 0.56% BoundaryNodeWriter::Visit 0 0% 83.12% 45ms 0.56% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 83.12% 44ms 0.55% std::_Rb_tree::_M_destroy_node (inline) 0 0% 83.12% 44ms 0.55% std::__new_allocator::destroy (inline) 0 0% 83.12% 44ms 0.55% std::allocator_traits::destroy (inline) 0 0% 83.12% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 43ms 0.54% 83.66% 43ms 0.54% [libstdc++.so.6.0.33] 0 0% 83.66% 43ms 0.54% std::_Vector_base::_Vector_base (inline) 7ms 0.088% 83.75% 42ms 0.53% Inverse 0 0% 83.75% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 83.75% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 42ms 0.53% 84.27% 42ms 0.53% Node::rGetLocation 22ms 0.28% 84.55% 42ms 0.53% hack_digit 2ms 0.025% 84.57% 42ms 0.53% std::__new_allocator::construct (inline) 0 0% 84.57% 42ms 0.53% std::allocator_traits::construct (inline) 0 0% 84.57% 41ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.57% 40ms 0.5% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.57% 40ms 0.5% std::_Vector_base::_M_create_storage (inline) 40ms 0.5% 85.08% 40ms 0.5% std::ostream::sentry::sentry