File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 100417ms, 88.34% of 113677ms total Dropped 1126 nodes (cum <= 568.38ms) flat flat% sum% cum cum% 0 0% 0% 113231ms 99.61% __libc_start_call_main 0 0% 0% 113231ms 99.61% __libc_start_main_impl 0 0% 0% 113231ms 99.61% _start 0 0% 0% 113213ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 113213ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 113213ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 113213ms 99.59% main 0 0% 0% 113172ms 99.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 113172ms 99.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 113172ms 99.56% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0035% 0.0035% 113165ms 99.55% AbstractCellBasedSimulation::Solve 15ms 0.013% 0.017% 58380ms 51.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.019% 0.036% 54734ms 48.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 162ms 0.14% 0.18% 53706ms 47.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.00088% 0.18% 41253ms 36.29% AbstractCellBasedSimulation::UpdateCellPopulation 432ms 0.38% 0.56% 40302ms 35.45% NagaiHondaForce::AddForceContribution 3ms 0.0026% 0.56% 26032ms 22.90% VertexBasedCellPopulation::Update 1ms 0.00088% 0.56% 25889ms 22.77% MutableVertexMesh::ReMesh 14644ms 12.88% 13.45% 23094ms 20.32% Cylindrical2dVertexMesh::GetVectorFromAtoB 102ms 0.09% 13.53% 17913ms 15.76% Cell::ReadyToDivide 48ms 0.042% 13.58% 16651ms 14.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 136ms 0.12% 13.70% 15093ms 13.28% CellPropertyCollection::GetPropertiesType (inline) 405ms 0.36% 14.05% 15043ms 13.23% NagaiHondaForce::GetAdhesionParameter 149ms 0.13% 14.18% 14099ms 12.40% SimpleWntCellCycleModel::UpdateCellCyclePhase 413ms 0.36% 14.55% 14043ms 12.35% boost::numeric::ublas::c_vector::c_vector (partial-inline) 68ms 0.06% 14.61% 12800ms 11.26% VertexBasedCellPopulation::GetDampingConstant 444ms 0.39% 15.00% 12523ms 11.02% boost::numeric::ublas::vector_assign (inline) 3829ms 3.37% 18.37% 12212ms 10.74% __dynamic_cast 125ms 0.11% 18.48% 12211ms 10.74% MutableVertexMesh::CheckForIntersections 78ms 0.069% 18.54% 12094ms 10.64% AbstractCellProperty::IsSubType (inline) 1543ms 1.36% 19.90% 10969ms 9.65% std::__new_allocator::allocate (inline) 84ms 0.074% 19.98% 10872ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 61ms 0.054% 20.03% 10768ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.027% 20.06% 10462ms 9.20% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.06% 10423ms 9.17% std::allocator_traits::allocate (inline) 0 0% 20.06% 10364ms 9.12% std::_Rb_tree::_M_create_node (inline) 92ms 0.081% 20.14% 10279ms 9.04% Cell::GetMutationState 1536ms 1.35% 21.49% 10134ms 8.91% std::_Rb_tree::_M_erase 0 0% 21.49% 9670ms 8.51% std::_Rb_tree::_M_get_node (inline) 791ms 0.7% 22.18% 9555ms 8.41% operator new 2766ms 2.43% 24.62% 9329ms 8.21% boost::numeric::ublas::indexing_vector_assign 830ms 0.73% 25.35% 9169ms 8.07% VertexMesh::ElementIncludesPoint 24ms 0.021% 25.37% 9151ms 8.05% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 25.37% 9088ms 7.99% std::_Rb_tree::_Alloc_node::operator() (inline) 223ms 0.2% 25.57% 9083ms 7.99% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.57% 9060ms 7.97% std::_Rb_tree::_M_drop_node (inline) 272ms 0.24% 25.80% 8832ms 7.77% std::__new_allocator::deallocate (inline) 0 0% 25.80% 8815ms 7.75% std::allocator_traits::deallocate (inline) 350ms 0.31% 26.11% 8812ms 7.75% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 26.11% 8746ms 7.69% std::_Rb_tree::_M_put_node (inline) 38ms 0.033% 26.15% 8738ms 7.69% VertexBasedCellPopulation::GetLocationOfCellCentre 3276ms 2.88% 29.03% 8620ms 7.58% __GI___libc_free 3438ms 3.02% 32.05% 8596ms 7.56% __GI___libc_malloc 0 0% 32.05% 8557ms 7.53% std::set::~set (inline) 532ms 0.47% 32.52% 8254ms 7.26% VertexMesh::GetCentroidOfElement 486ms 0.43% 32.95% 7665ms 6.74% std::map::operator[] (partial-inline) 129ms 0.11% 33.06% 7363ms 6.48% std::_Rb_tree::_Rb_tree (partial-inline) 1314ms 1.16% 34.22% 7091ms 6.24% AbstractMesh::GetDistanceBetweenNodes 688ms 0.61% 34.82% 7006ms 6.16% std::_Rb_tree::_M_copy (inline) 14ms 0.012% 34.83% 6762ms 5.95% std::set::set (inline) 6682ms 5.88% 40.71% 6682ms 5.88% __strcmp_avx2 111ms 0.098% 40.81% 6343ms 5.58% SimpleWntCellCycleModel::GetWntLevel 2341ms 2.06% 42.87% 6220ms 5.47% std::_Rb_tree::_M_lower_bound (inline) 150ms 0.13% 43.00% 6169ms 5.43% WntConcentration::GetWntLevel 6078ms 5.35% 48.35% 6078ms 5.35% boost::numeric::ublas::c_vector::operator() 919ms 0.81% 49.16% 6055ms 5.33% std::_Rb_tree::_M_clone_node (inline) 38ms 0.033% 49.19% 5917ms 5.21% MutableVertexMesh::RemoveDeletedNodes 0 0% 49.19% 5888ms 5.18% std::set::insert (inline) 318ms 0.28% 49.47% 5768ms 5.07% MutableElement::ResetIndex 39ms 0.034% 49.50% 5718ms 5.03% EdgeHelper::RemoveDeletedEdges 2739ms 2.41% 51.91% 5572ms 4.90% __cxxabiv1::__si_class_type_info::__do_dyncast 40ms 0.035% 51.95% 5378ms 4.73% EdgeHelper::UpdateEdgesMapKey 5015ms 4.41% 56.36% 5327ms 4.69% _int_free 527ms 0.46% 56.82% 4987ms 4.39% std::_Rb_tree::_M_insert_ (inline) 0 0% 56.82% 4940ms 4.35% std::_Rb_tree::lower_bound (inline) 0 0% 56.82% 4940ms 4.35% std::map::lower_bound (inline) 1557ms 1.37% 58.19% 4908ms 4.32% boost::numeric::ublas::c_vector::operator[] (inline) 1ms 0.00088% 58.19% 4752ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 83ms 0.073% 58.27% 4555ms 4.01% std::set_intersection (inline) 278ms 0.24% 58.51% 4472ms 3.93% std::__set_intersection 96ms 0.084% 58.60% 4426ms 3.89% AbstractCellPopulation::GetCellUsingLocationIndex 66ms 0.058% 58.65% 4232ms 3.72% Cell::GetCellProliferativeType 44ms 0.039% 58.69% 3925ms 3.45% std::_Rb_tree::erase 3905ms 3.44% 62.13% 3905ms 3.44% boost::numeric::ublas::same_impl_ex 10ms 0.0088% 62.14% 3553ms 3.13% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 79ms 0.069% 62.21% 3544ms 3.12% AbstractCellProperty::IsType (inline) 3490ms 3.07% 65.28% 3490ms 3.07% std::_Rb_tree::_S_right (inline) 2394ms 2.11% 67.38% 3439ms 3.03% _int_malloc 0 0% 67.38% 3300ms 2.90% std::insert_iterator::operator= (inline) 51ms 0.045% 67.43% 3277ms 2.88% Cell::SetCellProliferativeType 818ms 0.72% 68.15% 3230ms 2.84% AbstractElement::GetNodeLocation 3ms 0.0026% 68.15% 2957ms 2.60% std::_Rb_tree::_M_insert_unique (inline) 2ms 0.0018% 68.15% 2931ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 606ms 0.53% 68.68% 2887ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 1902ms 1.67% 70.36% 2846ms 2.50% std::_Rb_tree::equal_range (inline) 448ms 0.39% 70.75% 2811ms 2.47% std::_Rb_tree_const_iterator::operator++ (inline) 48ms 0.042% 70.79% 2633ms 2.32% CellPropertyCollection::HasProperty 26ms 0.023% 70.82% 2620ms 2.30% Cell::GetCellData 0 0% 70.82% 2619ms 2.30% AbstractCellPopulation::WriteResultsToFiles 678ms 0.6% 71.41% 2571ms 2.26% AbstractCellProperty::IsSame 0 0% 71.41% 2546ms 2.24% Cell::HasCellProperty (inline) 264ms 0.23% 71.65% 2504ms 2.20% VertexMesh::GetAreaGradientOfElementAtNode 119ms 0.1% 71.75% 2487ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 71.75% 2484ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 4ms 0.0035% 71.75% 2440ms 2.15% AbstractCellPopulation::Iterator::operator++ (inline) 265ms 0.23% 71.99% 2419ms 2.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 99ms 0.087% 72.07% 2299ms 2.02% VertexMesh::GetVolumeOfElement 29ms 0.026% 72.10% 2198ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 2191ms 1.93% 74.03% 2191ms 1.93% std::_Rb_tree_increment 0 0% 74.03% 2187ms 1.92% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 74.03% 2181ms 1.92% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00088% 74.03% 2170ms 1.91% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00088% 74.03% 1943ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 78ms 0.069% 74.10% 1895ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 486ms 0.43% 74.53% 1893ms 1.67% std::type_info::operator== (inline) 166ms 0.15% 74.67% 1880ms 1.65% CellPropertyCollection::AddProperty 19ms 0.017% 74.69% 1867ms 1.64% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.0044% 74.69% 1786ms 1.57% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.69% 1786ms 1.57% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 47ms 0.041% 74.73% 1749ms 1.54% Node::RemoveElement 17ms 0.015% 74.75% 1712ms 1.51% std::set::erase (inline) 21ms 0.018% 74.77% 1681ms 1.48% VertexMesh::GetSurfaceAreaOfElement 98ms 0.086% 74.85% 1668ms 1.47% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 36ms 0.032% 74.88% 1653ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 1ms 0.00088% 74.89% 1542ms 1.36% tcache_get (inline) 1541ms 1.36% 76.24% 1541ms 1.36% tcache_get_n (inline) 94ms 0.083% 76.32% 1531ms 1.35% boost::numeric::ublas::vector_reference::operator() (inline) 5ms 0.0044% 76.33% 1458ms 1.28% OffLatticeSimulation::ApplyBoundaries 0 0% 76.33% 1330ms 1.17% CellPropertyCollection::~CellPropertyCollection (inline) 93ms 0.082% 76.41% 1295ms 1.14% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 76.41% 1293ms 1.14% boost::numeric::ublas::vector_binary::operator() (inline) 61ms 0.054% 76.46% 1289ms 1.13% std::less::operator() (inline) 0 0% 76.46% 1282ms 1.13% std::_Rb_tree::clear (inline) 0 0% 76.46% 1276ms 1.12% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.46% 1253ms 1.10% std::map::clear (inline) 94ms 0.083% 76.55% 1249ms 1.10% std::_Rb_tree::find (inline) 991ms 0.87% 77.42% 1228ms 1.08% std::operator< (inline) 17ms 0.015% 77.43% 1211ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1153ms 1.01% 78.45% 1153ms 1.01% Node::rGetLocation 0 0% 78.45% 1142ms 1.00% boost::numeric::ublas::norm_2 (inline) 548ms 0.48% 78.93% 1141ms 1.00% Edge::GetMapIndex 15ms 0.013% 78.94% 1137ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 494ms 0.43% 79.38% 1129ms 0.99% boost::numeric::ublas::vector_norm_2::apply 1090ms 0.96% 80.34% 1090ms 0.96% std::_Rb_tree_insert_and_rebalance 38ms 0.033% 80.37% 1069ms 0.94% CellPropertyRegistry::Get 0 0% 80.37% 1060ms 0.93% std::map::find (inline) 1033ms 0.91% 81.28% 1033ms 0.91% [libchaste_cell_based.so] 970ms 0.85% 82.13% 970ms 0.85% std::vector::size (inline) 142ms 0.12% 82.26% 964ms 0.85% boost::detail::shared_count::~shared_count (inline) 0 0% 82.26% 964ms 0.85% boost::shared_ptr::~shared_ptr (inline) 953ms 0.84% 83.10% 953ms 0.84% [libchaste_mesh.so] 2ms 0.0018% 83.10% 915ms 0.8% VertexMeshWriter::MakeVtkMesh 0 0% 83.10% 900ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0079% 83.10% 900ms 0.79% boost::numeric::ublas::c_vector::swap (inline) 85ms 0.075% 83.18% 891ms 0.78% std::swap_ranges (inline) 18ms 0.016% 83.20% 867ms 0.76% boost::numeric::ublas::detail::expression_type_check (inline) 93ms 0.082% 83.28% 853ms 0.75% MutableElement::GetNodeLocalIndex 160ms 0.14% 83.42% 841ms 0.74% boost::numeric::ublas::detail::equals 809ms 0.71% 84.13% 809ms 0.71% std::swap (inline) 806ms 0.71% 84.84% 806ms 0.71% Node::GetIndex 0 0% 84.84% 806ms 0.71% std::iter_swap (inline) 794ms 0.7% 85.54% 799ms 0.7% boost::detail::sp_counted_base::release 105ms 0.092% 85.63% 793ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 122ms 0.11% 85.74% 773ms 0.68% std::__new_allocator::construct (inline) 0 0% 85.74% 773ms 0.68% std::allocator_traits::construct (inline) 0 0% 85.74% 749ms 0.66% std::_Vector_base::_M_allocate (inline) 21ms 0.018% 85.76% 746ms 0.66% MutableElement::RegisterWithEdges (inline) 24ms 0.021% 85.78% 745ms 0.66% Edge::AddElement 461ms 0.41% 86.18% 736ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 93ms 0.082% 86.26% 714ms 0.63% std::_Rb_tree::_M_upper_bound (inline) 0 0% 86.26% 694ms 0.61% std::_Rb_tree::_M_construct_node (inline) 145ms 0.13% 86.39% 683ms 0.6% boost::shared_ptr::shared_ptr (inline) 1ms 0.00088% 86.39% 665ms 0.58% vtkPolygon::New 0 0% 86.39% 663ms 0.58% vtkPolygon::vtkPolygon 30ms 0.026% 86.42% 657ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 86.42% 644ms 0.57% boost::numeric::ublas::norm_inf (inline) 322ms 0.28% 86.70% 644ms 0.57% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.70% 641ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.017% 86.72% 641ms 0.56% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.72% 628ms 0.55% std::map::map (inline) 30ms 0.026% 86.74% 627ms 0.55% Node::AddElement 10ms 0.0088% 86.75% 619ms 0.54% std::vector::_M_default_append (inline) 593ms 0.52% 87.28% 593ms 0.52% [libstdc++.so.6.0.33] 593ms 0.52% 87.80% 593ms 0.52% operator delete 33ms 0.029% 87.83% 579ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.83% 579ms 0.51% boost::numeric::ublas::vector::vector (inline) 579ms 0.51% 88.34% 579ms 0.51% boost::shared_ptr::operator-> (inline)