File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 72773ms, 87.19% of 83465ms total Dropped 1093 nodes (cum <= 417.32ms) flat flat% sum% cum cum% 0 0% 0% 83181ms 99.66% __libc_start_call_main 0 0% 0% 83181ms 99.66% __libc_start_main_impl 0 0% 0% 83181ms 99.66% _start 0 0% 0% 83165ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 83165ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 83165ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 83165ms 99.64% main 0 0% 0% 83125ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 83125ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 83125ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0036% 0.0036% 83119ms 99.59% AbstractCellBasedSimulation::Solve 13ms 0.016% 0.019% 43527ms 52.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 7ms 0.0084% 0.028% 40881ms 48.98% ForwardEulerNumericalMethod::UpdateAllNodePositions 97ms 0.12% 0.14% 39675ms 47.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 217ms 0.26% 0.4% 30588ms 36.65% NagaiHondaForce::AddForceContribution 0 0% 0.4% 29600ms 35.46% AbstractCellBasedSimulation::UpdateCellPopulation 11467ms 13.74% 14.14% 18260ms 21.88% Cylindrical2dVertexMesh::GetVectorFromAtoB 2ms 0.0024% 14.14% 18193ms 21.80% VertexBasedCellPopulation::Update 1ms 0.0012% 14.15% 18073ms 21.65% MutableVertexMesh::ReMesh 62ms 0.074% 14.22% 13420ms 16.08% Cell::ReadyToDivide 43ms 0.052% 14.27% 12487ms 14.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 266ms 0.32% 14.59% 11357ms 13.61% NagaiHondaForce::GetAdhesionParameter 347ms 0.42% 15.01% 10897ms 13.06% boost::numeric::ublas::c_vector::c_vector (partial-inline) 123ms 0.15% 15.15% 10837ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 82ms 0.098% 15.25% 10412ms 12.47% CellPropertyCollection::GetPropertiesType (inline) 211ms 0.25% 15.50% 9752ms 11.68% boost::numeric::ublas::vector_assign (inline) 106ms 0.13% 15.63% 9291ms 11.13% MutableVertexMesh::CheckForIntersections 2304ms 2.76% 18.39% 8909ms 10.67% __dynamic_cast 82ms 0.098% 18.49% 8878ms 10.64% AbstractCellProperty::IsSubType (inline) 70ms 0.084% 18.57% 8668ms 10.39% VertexBasedCellPopulation::GetDampingConstant 46ms 0.055% 18.63% 8034ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 24ms 0.029% 18.66% 7966ms 9.54% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 862ms 1.03% 19.69% 7836ms 9.39% std::__new_allocator::allocate (inline) 34ms 0.041% 19.73% 7816ms 9.36% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.73% 7408ms 8.88% std::_Rb_tree::_M_create_node (inline) 2245ms 2.69% 22.42% 7404ms 8.87% boost::numeric::ublas::indexing_vector_assign 272ms 0.33% 22.75% 7378ms 8.84% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.75% 7287ms 8.73% std::allocator_traits::allocate (inline) 610ms 0.73% 23.48% 7019ms 8.41% operator new 905ms 1.08% 24.56% 6951ms 8.33% std::_Rb_tree::_M_erase 639ms 0.77% 25.33% 6855ms 8.21% VertexMesh::ElementIncludesPoint 64ms 0.077% 25.40% 6801ms 8.15% Cell::GetMutationState 0 0% 25.40% 6738ms 8.07% std::_Rb_tree::_M_get_node (inline) 21ms 0.025% 25.43% 6602ms 7.91% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.43% 6581ms 7.88% std::_Rb_tree::_Alloc_node::operator() (inline) 151ms 0.18% 25.61% 6381ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 362ms 0.43% 26.04% 6366ms 7.63% VertexMesh::GetCentroidOfElement 0 0% 26.04% 6276ms 7.52% std::_Rb_tree::_M_drop_node (inline) 2557ms 3.06% 29.11% 6231ms 7.47% __GI___libc_malloc 183ms 0.22% 29.33% 6088ms 7.29% std::__new_allocator::deallocate (inline) 0 0% 29.33% 6069ms 7.27% std::allocator_traits::deallocate (inline) 0 0% 29.33% 6050ms 7.25% std::set::~set (inline) 0 0% 29.33% 6016ms 7.21% std::_Rb_tree::_M_put_node (inline) 1103ms 1.32% 30.65% 5776ms 6.92% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 1647ms 1.97% 32.62% 5726ms 6.86% __GI___libc_free 10ms 0.012% 32.63% 5619ms 6.73% MutableVertexMesh::RemoveDeletedNodesAndElements 179ms 0.21% 32.85% 5553ms 6.65% std::_Rb_tree::_Rb_tree (partial-inline) 339ms 0.41% 33.25% 5460ms 6.54% std::map::operator[] (partial-inline) 5284ms 6.33% 39.59% 5284ms 6.33% __strcmp_evex 12ms 0.014% 39.60% 5188ms 6.22% std::set::set (inline) 569ms 0.68% 40.28% 5187ms 6.21% std::_Rb_tree::_M_copy (inline) 103ms 0.12% 40.40% 4818ms 5.77% SimpleWntCellCycleModel::GetWntLevel 4768ms 5.71% 46.12% 4768ms 5.71% boost::numeric::ublas::c_vector::operator() 139ms 0.17% 46.28% 4638ms 5.56% WntConcentration::GetWntLevel 2296ms 2.75% 49.03% 4473ms 5.36% __cxxabiv1::__si_class_type_info::__do_dyncast 539ms 0.65% 49.68% 4423ms 5.30% std::_Rb_tree::_M_clone_node (inline) 1857ms 2.22% 51.91% 4218ms 5.05% std::_Rb_tree::_M_lower_bound (inline) 0 0% 51.91% 4129ms 4.95% std::set::insert (inline) 3733ms 4.47% 56.38% 4071ms 4.88% _int_free 1472ms 1.76% 58.14% 4047ms 4.85% boost::numeric::ublas::c_vector::operator[] (inline) 14ms 0.017% 58.16% 3784ms 4.53% MutableVertexMesh::RemoveDeletedNodes 23ms 0.028% 58.19% 3651ms 4.37% EdgeHelper::RemoveDeletedEdges 0 0% 58.19% 3578ms 4.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 138ms 0.17% 58.35% 3494ms 4.19% MutableElement::ResetIndex 0 0% 58.35% 3486ms 4.18% std::_Rb_tree::lower_bound (inline) 0 0% 58.35% 3486ms 4.18% std::map::lower_bound (inline) 361ms 0.43% 58.78% 3448ms 4.13% std::_Rb_tree::_M_insert_ (inline) 36ms 0.043% 58.83% 3405ms 4.08% EdgeHelper::UpdateEdgesMapKey 96ms 0.12% 58.94% 3294ms 3.95% std::set_intersection (inline) 208ms 0.25% 59.19% 3198ms 3.83% std::__set_intersection 91ms 0.11% 59.30% 3189ms 3.82% AbstractCellPopulation::GetCellUsingLocationIndex 3021ms 3.62% 62.92% 3021ms 3.62% boost::numeric::ublas::same_impl_ex 50ms 0.06% 62.98% 2939ms 3.52% AbstractCellProperty::IsType (inline) 29ms 0.035% 63.01% 2870ms 3.44% Cell::GetCellProliferativeType 8ms 0.0096% 63.02% 2679ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 57ms 0.068% 63.09% 2432ms 2.91% Cell::SetCellProliferativeType 0 0% 63.09% 2432ms 2.91% std::insert_iterator::operator= (inline) 1618ms 1.94% 65.03% 2393ms 2.87% _int_malloc 645ms 0.77% 65.80% 2334ms 2.80% AbstractElement::GetNodeLocation 46ms 0.055% 65.86% 2202ms 2.64% std::_Rb_tree::erase 8ms 0.0096% 65.87% 2142ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 474ms 0.57% 66.44% 2126ms 2.55% AbstractCellProperty::IsSame 471ms 0.56% 67.00% 2049ms 2.45% boost::numeric::ublas::vector_binary::size (inline) 16ms 0.019% 67.02% 2015ms 2.41% CellPropertyCollection::HasProperty 172ms 0.21% 67.23% 2004ms 2.40% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.0012% 67.23% 1987ms 2.38% std::_Rb_tree::_M_insert_unique 0 0% 67.23% 1959ms 2.35% Cell::HasCellProperty (inline) 1954ms 2.34% 69.57% 1954ms 2.34% std::_Rb_tree::_S_right (inline) 0 0% 69.57% 1950ms 2.34% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.57% 1932ms 2.31% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.57% 1930ms 2.31% boost::numeric::ublas::c_vector::operator-= (inline) 21ms 0.025% 69.59% 1791ms 2.15% Cell::GetCellData 173ms 0.21% 69.80% 1777ms 2.13% std::_Rb_tree_const_iterator::operator++ (inline) 72ms 0.086% 69.89% 1739ms 2.08% VertexMesh::GetVolumeOfElement 7ms 0.0084% 69.90% 1670ms 2.00% AbstractCellPopulation::Iterator::operator++ (inline) 143ms 0.17% 70.07% 1657ms 1.99% AbstractCellPopulation::Iterator::IsRealCell (inline) 405ms 0.49% 70.55% 1652ms 1.98% std::type_info::operator== (inline) 0 0% 70.55% 1605ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.55% 1605ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 43ms 0.052% 70.60% 1594ms 1.91% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 26ms 0.031% 70.63% 1593ms 1.91% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.63% 1587ms 1.90% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.63% 1582ms 1.90% VertexBasedCellPopulation::WriteCellVtkResultsToFile 57ms 0.068% 70.70% 1462ms 1.75% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 70.70% 1426ms 1.71% VertexMeshWriter::WriteVtkUsingMesh 1426ms 1.71% 72.41% 1426ms 1.71% std::_Rb_tree_increment 964ms 1.15% 73.57% 1424ms 1.71% std::_Rb_tree::equal_range (inline) 17ms 0.02% 73.59% 1249ms 1.50% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 98ms 0.12% 73.70% 1180ms 1.41% CellPropertyCollection::AddProperty 31ms 0.037% 73.74% 1176ms 1.41% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.74% 1142ms 1.37% tcache_get (inline) 1142ms 1.37% 75.11% 1142ms 1.37% tcache_get_n (inline) 22ms 0.026% 75.14% 1106ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 75.14% 1099ms 1.32% OffLatticeSimulation::ApplyBoundaries 37ms 0.044% 75.18% 1089ms 1.30% Node::RemoveElement 31ms 0.037% 75.22% 1074ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 80ms 0.096% 75.31% 1072ms 1.28% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 75.31% 1059ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 10ms 0.012% 75.32% 1055ms 1.26% std::set::erase (inline) 1020ms 1.22% 76.55% 1020ms 1.22% [libchaste_cell_based.so] 0 0% 76.55% 977ms 1.17% boost::numeric::ublas::norm_2 (inline) 464ms 0.56% 77.10% 970ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 89ms 0.11% 77.21% 948ms 1.14% std::less::operator() (inline) 21ms 0.025% 77.23% 940ms 1.13% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 28ms 0.034% 77.27% 904ms 1.08% CellPropertyRegistry::Get 2ms 0.0024% 77.27% 873ms 1.05% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 67ms 0.08% 77.35% 868ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 697ms 0.84% 78.19% 859ms 1.03% std::operator< (inline) 0 0% 78.19% 827ms 0.99% std::_Rb_tree::_Auto_node::_Auto_node (inline) 805ms 0.96% 79.15% 805ms 0.96% std::_Rb_tree_insert_and_rebalance 102ms 0.12% 79.27% 790ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 79.27% 790ms 0.95% boost::shared_ptr::~shared_ptr (inline) 3ms 0.0036% 79.28% 782ms 0.94% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.28% 771ms 0.92% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0048% 79.28% 771ms 0.92% boost::numeric::ublas::c_vector::swap (inline) 101ms 0.12% 79.40% 767ms 0.92% boost::numeric::ublas::detail::equals 48ms 0.058% 79.46% 767ms 0.92% std::swap_ranges (inline) 79ms 0.095% 79.55% 756ms 0.91% std::_Rb_tree::find (inline) 729ms 0.87% 80.43% 729ms 0.87% Node::rGetLocation 0 0% 80.43% 727ms 0.87% std::_Rb_tree::clear (inline) 0 0% 80.43% 719ms 0.86% std::iter_swap (inline) 719ms 0.86% 81.29% 719ms 0.86% std::swap (inline) 238ms 0.29% 81.57% 717ms 0.86% std::__new_allocator::construct (inline) 0 0% 81.57% 717ms 0.86% std::allocator_traits::construct (inline) 0 0% 81.57% 712ms 0.85% std::map::clear (inline) 0 0% 81.57% 670ms 0.8% std::_Rb_tree::_M_construct_node (inline) 0 0% 81.57% 669ms 0.8% VertexMeshWriter::MakeVtkMesh 635ms 0.76% 82.34% 655ms 0.78% boost::detail::sp_counted_base::release 144ms 0.17% 82.51% 646ms 0.77% boost::shared_ptr::shared_ptr (inline) 2ms 0.0024% 82.51% 646ms 0.77% std::map::find (inline) 0 0% 82.51% 628ms 0.75% boost::numeric::ublas::norm_inf (inline) 275ms 0.33% 82.84% 628ms 0.75% boost::numeric::ublas::vector_norm_inf::apply (inline) 83ms 0.099% 82.94% 614ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 611ms 0.73% 83.67% 611ms 0.73% [libstdc++.so.6.0.33] 339ms 0.41% 84.08% 610ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 17ms 0.02% 84.10% 602ms 0.72% AbstractNumericalMethod::DetectStepSizeExceptions 15ms 0.018% 84.12% 596ms 0.71% MutableElement::RegisterWithEdges (inline) 12ms 0.014% 84.13% 583ms 0.7% Edge::AddElement 581ms 0.7% 84.83% 581ms 0.7% std::vector::size (inline) 577ms 0.69% 85.52% 577ms 0.69% [libchaste_mesh.so] 15ms 0.018% 85.54% 564ms 0.68% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.54% 564ms 0.68% boost::numeric::ublas::vector::vector (inline) 0 0% 85.54% 548ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.54% 546ms 0.65% std::_Vector_base::_M_allocate (inline) 138ms 0.17% 85.70% 539ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 296ms 0.35% 86.06% 516ms 0.62% Edge::GetMapIndex 475ms 0.57% 86.62% 502ms 0.6% boost::detail::shared_count::shared_count (inline) 0 0% 86.62% 496ms 0.59% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.62% 482ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.02% 86.64% 482ms 0.58% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.64% 470ms 0.56% vtkPolygon::New 0 0% 86.64% 470ms 0.56% vtkPolygon::vtkPolygon 3ms 0.0036% 86.65% 455ms 0.55% std::vector::_M_default_append (inline) 100ms 0.12% 86.77% 454ms 0.54% MutableElement::GetNodeLocalIndex 33ms 0.04% 86.81% 448ms 0.54% MutableElement::RegisterWithNodes (inline) 305ms 0.37% 87.17% 421ms 0.5% malloc_consolidate 14ms 0.017% 87.19% 418ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate