File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97578ms, 88.39% of 110390ms total Dropped 1156 nodes (cum <= 551.95ms) flat flat% sum% cum cum% 0 0% 0% 110007ms 99.65% __libc_start_call_main 0 0% 0% 110007ms 99.65% __libc_start_main_impl 0 0% 0% 110007ms 99.65% _start 0 0% 0% 109987ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109987ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109987ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109987ms 99.63% main 0 0% 0% 109941ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109941ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109941ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109932ms 99.59% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.018% 56712ms 51.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.03% 53207ms 48.20% ForwardEulerNumericalMethod::UpdateAllNodePositions 138ms 0.13% 0.15% 52087ms 47.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 291ms 0.26% 0.42% 40240ms 36.45% NagaiHondaForce::AddForceContribution 4ms 0.0036% 0.42% 40008ms 36.24% AbstractCellBasedSimulation::UpdateCellPopulation 7ms 0.0063% 0.43% 25008ms 22.65% VertexBasedCellPopulation::Update 0 0% 0.43% 24845ms 22.51% MutableVertexMesh::ReMesh 14912ms 13.51% 13.94% 23581ms 21.36% Cylindrical2dVertexMesh::GetVectorFromAtoB 114ms 0.1% 14.04% 17515ms 15.87% Cell::ReadyToDivide 70ms 0.063% 14.10% 16205ms 14.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 306ms 0.28% 14.38% 14651ms 13.27% NagaiHondaForce::GetAdhesionParameter 516ms 0.47% 14.85% 14132ms 12.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 168ms 0.15% 15.00% 13852ms 12.55% SimpleWntCellCycleModel::UpdateCellCyclePhase 128ms 0.12% 15.12% 13446ms 12.18% CellPropertyCollection::GetPropertiesType (inline) 283ms 0.26% 15.37% 12586ms 11.40% boost::numeric::ublas::vector_assign (inline) 153ms 0.14% 15.51% 11936ms 10.81% MutableVertexMesh::CheckForIntersections 3314ms 3.00% 18.51% 11355ms 10.29% __dynamic_cast 102ms 0.092% 18.61% 11274ms 10.21% AbstractCellProperty::IsSubType (inline) 97ms 0.088% 18.69% 11244ms 10.19% VertexBasedCellPopulation::GetDampingConstant 75ms 0.068% 18.76% 10619ms 9.62% AbstractTargetAreaModifier::UpdateTargetAreas 35ms 0.032% 18.79% 10531ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 32ms 0.029% 18.82% 10202ms 9.24% AbstractCellBasedSimulation::DoCellBirth 1390ms 1.26% 20.08% 10201ms 9.24% std::__new_allocator::allocate (inline) 0 0% 20.08% 9622ms 8.72% std::_Rb_tree::_M_create_node (inline) 0 0% 20.08% 9622ms 8.72% std::allocator_traits::allocate (inline) 2884ms 2.61% 22.69% 9601ms 8.70% boost::numeric::ublas::indexing_vector_assign 370ms 0.34% 23.03% 9460ms 8.57% VertexMesh::GetNextEdgeGradientOfElementAtNode 1443ms 1.31% 24.34% 9361ms 8.48% std::_Rb_tree::_M_erase 804ms 0.73% 25.06% 8825ms 7.99% operator new 0 0% 25.06% 8820ms 7.99% std::_Rb_tree::_M_get_node (inline) 42ms 0.038% 25.10% 8688ms 7.87% VertexBasedCellPopulation::GetLocationOfCellCentre 808ms 0.73% 25.83% 8685ms 7.87% VertexMesh::ElementIncludesPoint 14ms 0.013% 25.85% 8643ms 7.83% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 25.85% 8523ms 7.72% std::_Rb_tree::_Alloc_node::operator() (inline) 82ms 0.074% 25.92% 8418ms 7.63% Cell::GetMutationState 0 0% 25.92% 8372ms 7.58% std::_Rb_tree::_M_drop_node (inline) 224ms 0.2% 26.12% 8330ms 7.55% std::_Rb_tree::~_Rb_tree (inline) 465ms 0.42% 26.55% 8291ms 7.51% VertexMesh::GetCentroidOfElement 241ms 0.22% 26.76% 8128ms 7.36% std::__new_allocator::deallocate (inline) 0 0% 26.76% 8124ms 7.36% std::allocator_traits::deallocate (inline) 0 0% 26.76% 8055ms 7.30% std::_Rb_tree::_M_put_node (inline) 0 0% 26.76% 7896ms 7.15% std::set::~set (inline) 2869ms 2.60% 29.36% 7792ms 7.06% __GI___libc_malloc 2436ms 2.21% 31.57% 7584ms 6.87% __GI___libc_free 1346ms 1.22% 32.79% 7532ms 6.82% AbstractMesh::GetDistanceBetweenNodes 170ms 0.15% 32.94% 7421ms 6.72% std::_Rb_tree::_Rb_tree (partial-inline) 504ms 0.46% 33.40% 7385ms 6.69% std::map::operator[] (partial-inline) 771ms 0.7% 34.10% 7014ms 6.35% std::_Rb_tree::_M_copy (inline) 29ms 0.026% 34.12% 6799ms 6.16% std::set::set (inline) 165ms 0.15% 34.27% 6320ms 5.73% SimpleWntCellCycleModel::GetWntLevel 6265ms 5.68% 39.95% 6265ms 5.68% __strcmp_avx2 6098ms 5.52% 45.47% 6098ms 5.52% boost::numeric::ublas::c_vector::operator() 181ms 0.16% 45.64% 6081ms 5.51% WntConcentration::GetWntLevel 835ms 0.76% 46.39% 5987ms 5.42% std::_Rb_tree::_M_clone_node (inline) 2409ms 2.18% 48.58% 5739ms 5.20% std::_Rb_tree::_M_lower_bound (inline) 2867ms 2.60% 51.17% 5636ms 5.11% __cxxabiv1::__si_class_type_info::__do_dyncast 13ms 0.012% 51.18% 5526ms 5.01% MutableVertexMesh::RemoveDeletedNodes 252ms 0.23% 51.41% 5457ms 4.94% MutableElement::ResetIndex 43ms 0.039% 51.45% 5315ms 4.81% EdgeHelper::RemoveDeletedEdges 1914ms 1.73% 53.19% 5286ms 4.79% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.19% 5244ms 4.75% std::set::insert (inline) 4616ms 4.18% 57.37% 5125ms 4.64% _int_free 53ms 0.048% 57.42% 4987ms 4.52% EdgeHelper::UpdateEdgesMapKey 0 0% 57.42% 4780ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 57.42% 4671ms 4.23% std::_Rb_tree::lower_bound (inline) 0 0% 57.42% 4671ms 4.23% std::map::lower_bound (inline) 515ms 0.47% 57.88% 4403ms 3.99% std::_Rb_tree::_M_insert_ (inline) 144ms 0.13% 58.01% 4390ms 3.98% AbstractCellPopulation::GetCellUsingLocationIndex 156ms 0.14% 58.15% 4241ms 3.84% std::set_intersection (inline) 252ms 0.23% 58.38% 4085ms 3.70% std::__set_intersection 47ms 0.043% 58.42% 3940ms 3.57% Cell::GetCellProliferativeType 3838ms 3.48% 61.90% 3838ms 3.48% boost::numeric::ublas::same_impl_ex 61ms 0.055% 61.96% 3715ms 3.37% AbstractCellProperty::IsType (inline) 67ms 0.061% 62.02% 3619ms 3.28% std::_Rb_tree::erase 16ms 0.014% 62.03% 3532ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2128ms 1.93% 63.96% 3246ms 2.94% _int_malloc 1ms 0.00091% 63.96% 3110ms 2.82% std::insert_iterator::operator= (inline) 899ms 0.81% 64.77% 3096ms 2.80% AbstractElement::GetNodeLocation 60ms 0.054% 64.83% 3088ms 2.80% Cell::SetCellProliferativeType 2901ms 2.63% 67.46% 2901ms 2.63% std::_Rb_tree::_S_right (inline) 10ms 0.0091% 67.47% 2711ms 2.46% std::_Rb_tree::_M_insert_unique_ (inline) 228ms 0.21% 67.67% 2659ms 2.41% VertexMesh::GetAreaGradientOfElementAtNode 30ms 0.027% 67.70% 2645ms 2.40% CellPropertyCollection::HasProperty 621ms 0.56% 68.26% 2645ms 2.40% boost::numeric::ublas::vector_binary::size (inline) 0 0% 68.26% 2611ms 2.37% boost::numeric::ublas::c_vector::assign (inline) 0 0% 68.26% 2592ms 2.35% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 68.26% 2563ms 2.32% Cell::HasCellProperty (inline) 777ms 0.7% 68.97% 2562ms 2.32% AbstractCellProperty::IsSame 0 0% 68.97% 2553ms 2.31% AbstractCellPopulation::WriteResultsToFiles 0 0% 68.97% 2533ms 2.29% std::_Rb_tree::_M_insert_unique 283ms 0.26% 69.22% 2498ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 27ms 0.024% 69.25% 2483ms 2.25% Cell::GetCellData 1576ms 1.43% 70.67% 2403ms 2.18% std::_Rb_tree::equal_range (inline) 79ms 0.072% 70.75% 2353ms 2.13% VertexMesh::GetVolumeOfElement 59ms 0.053% 70.80% 2259ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.0045% 70.80% 2193ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 180ms 0.16% 70.97% 2180ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 34ms 0.031% 71.00% 2171ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.00% 2095ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 71.00% 2078ms 1.88% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 71.00% 2033ms 1.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.00% 2033ms 1.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1935ms 1.75% 72.75% 1935ms 1.75% std::_Rb_tree_increment 0 0% 72.75% 1876ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 68ms 0.062% 72.81% 1846ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 439ms 0.4% 73.21% 1785ms 1.62% std::type_info::operator== (inline) 28ms 0.025% 73.24% 1651ms 1.50% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 44ms 0.04% 73.28% 1632ms 1.48% Node::RemoveElement 9ms 0.0082% 73.28% 1596ms 1.45% std::set::erase (inline) 48ms 0.043% 73.33% 1590ms 1.44% VertexMesh::GetSurfaceAreaOfElement 41ms 0.037% 73.37% 1490ms 1.35% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.37% 1471ms 1.33% tcache_get (inline) 1471ms 1.33% 74.70% 1471ms 1.33% tcache_get_n (inline) 65ms 0.059% 74.76% 1454ms 1.32% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1442ms 1.31% 76.06% 1442ms 1.31% [libchaste_cell_based.so] 0 0% 76.06% 1386ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 76.06% 1382ms 1.25% OffLatticeSimulation::ApplyBoundaries 126ms 0.11% 76.18% 1363ms 1.23% CellPropertyCollection::AddProperty 57ms 0.052% 76.23% 1361ms 1.23% boost::numeric::ublas::vector_reference::operator() (inline) 85ms 0.077% 76.31% 1331ms 1.21% std::_Rb_tree::_M_erase_aux (partial-inline) 85ms 0.077% 76.38% 1266ms 1.15% std::less::operator() (inline) 0 0% 76.38% 1261ms 1.14% boost::numeric::ublas::norm_2 (inline) 0 0% 76.38% 1259ms 1.14% std::_Rb_tree::clear (inline) 569ms 0.52% 76.90% 1249ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.90% 1237ms 1.12% std::map::clear (inline) 9ms 0.0082% 76.91% 1209ms 1.10% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 938ms 0.85% 77.76% 1181ms 1.07% std::operator< (inline) 25ms 0.023% 77.78% 1168ms 1.06% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1118ms 1.01% 78.79% 1118ms 1.01% std::_Rb_tree_insert_and_rebalance 29ms 0.026% 78.82% 1102ms 1% CellPropertyRegistry::Get 0 0% 78.82% 1099ms 1% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.82% 1087ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 17ms 0.015% 78.84% 1087ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 78ms 0.071% 78.91% 1070ms 0.97% std::swap_ranges (inline) 12ms 0.011% 78.92% 1068ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 88ms 0.08% 79.00% 1064ms 0.96% std::_Rb_tree::find (inline) 218ms 0.2% 79.19% 1045ms 0.95% boost::numeric::ublas::detail::equals 91ms 0.082% 79.28% 1011ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 79.28% 1011ms 0.92% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.28% 992ms 0.9% std::iter_swap (inline) 992ms 0.9% 80.17% 992ms 0.9% std::swap (inline) 963ms 0.87% 81.05% 963ms 0.87% Node::rGetLocation 3ms 0.0027% 81.05% 917ms 0.83% std::map::find (inline) 851ms 0.77% 81.82% 886ms 0.8% boost::detail::sp_counted_base::release 276ms 0.25% 82.07% 883ms 0.8% std::__new_allocator::construct (inline) 0 0% 82.07% 883ms 0.8% std::allocator_traits::construct (inline) 1ms 0.00091% 82.07% 871ms 0.79% VertexMeshWriter::MakeVtkMesh 453ms 0.41% 82.48% 813ms 0.74% Edge::GetMapIndex 83ms 0.075% 82.56% 809ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 82.56% 802ms 0.73% std::_Rb_tree::_M_construct_node (inline) 800ms 0.72% 83.28% 800ms 0.72% std::vector::size (inline) 0 0% 83.28% 796ms 0.72% std::_Vector_base::_M_allocate (inline) 794ms 0.72% 84.00% 794ms 0.72% [libchaste_mesh.so] 0 0% 84.00% 784ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 15ms 0.014% 84.01% 777ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.01% 772ms 0.7% boost::numeric::ublas::norm_inf (inline) 416ms 0.38% 84.39% 772ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 423ms 0.38% 84.77% 772ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 17ms 0.015% 84.79% 769ms 0.7% Edge::AddElement 197ms 0.18% 84.97% 759ms 0.69% boost::shared_ptr::shared_ptr (inline) 28ms 0.025% 84.99% 698ms 0.63% MutableElement::RegisterWithNodes (inline) 0 0% 84.99% 687ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 35ms 0.032% 85.03% 687ms 0.62% std::_Rb_tree::_M_insert_node (inline) 681ms 0.62% 85.64% 681ms 0.62% [libstdc++.so.6.0.33] 28ms 0.025% 85.67% 666ms 0.6% Node::AddElement 11ms 0.01% 85.68% 666ms 0.6% std::vector::_M_default_append (inline) 127ms 0.12% 85.79% 663ms 0.6% MutableElement::GetNodeLocalIndex 0 0% 85.79% 657ms 0.6% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.79% 657ms 0.6% std::map::map (inline) 88ms 0.08% 85.87% 650ms 0.59% std::_Rb_tree::_M_upper_bound (inline) 459ms 0.42% 86.29% 613ms 0.56% malloc_consolidate 30ms 0.027% 86.32% 609ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.32% 609ms 0.55% boost::numeric::ublas::vector::vector (inline) 606ms 0.55% 86.86% 606ms 0.55% Node::GetIndex 1ms 0.00091% 86.87% 601ms 0.54% vtkPolygon::New 2ms 0.0018% 86.87% 599ms 0.54% vtkPolygon::vtkPolygon 595ms 0.54% 87.41% 595ms 0.54% boost::shared_ptr::operator-> (inline) 2ms 0.0018% 87.41% 578ms 0.52% VertexElementMap::VertexElementMap 0 0% 87.41% 575ms 0.52% std::vector::resize (inline) 533ms 0.48% 87.89% 562ms 0.51% boost::detail::shared_count::shared_count (inline) 555ms 0.5% 88.39% 555ms 0.5% tcache_put (inline)