File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95419ms, 87.61% of 108917ms total Dropped 1140 nodes (cum <= 544.59ms) flat flat% sum% cum cum% 0 0% 0% 108541ms 99.65% __libc_start_call_main 0 0% 0% 108541ms 99.65% __libc_start_main_impl 0 0% 0% 108541ms 99.65% _start 0 0% 0% 108517ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108517ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108517ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108517ms 99.63% main 0 0% 0% 108471ms 99.59% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108471ms 99.59% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108471ms 99.59% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108463ms 99.58% AbstractCellBasedSimulation::Solve 19ms 0.017% 0.022% 56439ms 51.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.033% 53032ms 48.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 146ms 0.13% 0.17% 51507ms 47.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 294ms 0.27% 0.44% 39913ms 36.65% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.44% 38807ms 35.63% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.44% 23879ms 21.92% VertexBasedCellPopulation::Update 0 0% 0.44% 23738ms 21.79% MutableVertexMesh::ReMesh 14763ms 13.55% 14.00% 23464ms 21.54% Cylindrical2dVertexMesh::GetVectorFromAtoB 95ms 0.087% 14.08% 17570ms 16.13% Cell::ReadyToDivide 75ms 0.069% 14.15% 16188ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 360ms 0.33% 14.48% 14140ms 12.98% NagaiHondaForce::GetAdhesionParameter 418ms 0.38% 14.87% 13937ms 12.80% boost::numeric::ublas::c_vector::c_vector (partial-inline) 131ms 0.12% 14.99% 13873ms 12.74% SimpleWntCellCycleModel::UpdateCellCyclePhase 94ms 0.086% 15.07% 13718ms 12.59% CellPropertyCollection::GetPropertiesType (inline) 238ms 0.22% 15.29% 12508ms 11.48% boost::numeric::ublas::vector_assign (inline) 141ms 0.13% 15.42% 11934ms 10.96% MutableVertexMesh::CheckForIntersections 3375ms 3.10% 18.52% 11695ms 10.74% __dynamic_cast 49ms 0.045% 18.57% 11580ms 10.63% AbstractCellProperty::IsSubType (inline) 102ms 0.094% 18.66% 11050ms 10.15% VertexBasedCellPopulation::GetDampingConstant 61ms 0.056% 18.72% 10736ms 9.86% AbstractTargetAreaModifier::UpdateTargetAreas 48ms 0.044% 18.76% 10638ms 9.77% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 34ms 0.031% 18.79% 10214ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1295ms 1.19% 19.98% 9646ms 8.86% std::__new_allocator::allocate (inline) 2865ms 2.63% 22.61% 9533ms 8.75% boost::numeric::ublas::indexing_vector_assign 400ms 0.37% 22.98% 9526ms 8.75% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.98% 9179ms 8.43% std::_Rb_tree::_M_create_node (inline) 0 0% 22.98% 9096ms 8.35% std::allocator_traits::allocate (inline) 1189ms 1.09% 24.07% 8860ms 8.13% std::_Rb_tree::_M_erase 845ms 0.78% 24.84% 8706ms 7.99% VertexMesh::ElementIncludesPoint 29ms 0.027% 24.87% 8680ms 7.97% VertexBasedCellPopulation::GetLocationOfCellCentre 813ms 0.75% 25.62% 8437ms 7.75% operator new 0 0% 25.62% 8419ms 7.73% std::_Rb_tree::_M_get_node (inline) 64ms 0.059% 25.68% 8415ms 7.73% Cell::GetMutationState 477ms 0.44% 26.11% 8272ms 7.59% VertexMesh::GetCentroidOfElement 0 0% 26.11% 8117ms 7.45% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.11% 8037ms 7.38% std::_Rb_tree::_M_drop_node (inline) 252ms 0.23% 26.35% 8036ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 205ms 0.19% 26.53% 7778ms 7.14% std::__new_allocator::deallocate (inline) 0 0% 26.53% 7771ms 7.13% std::allocator_traits::deallocate (inline) 0 0% 26.53% 7696ms 7.07% std::_Rb_tree::_M_put_node (inline) 14ms 0.013% 26.55% 7645ms 7.02% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.55% 7612ms 6.99% std::set::~set (inline) 1537ms 1.41% 27.96% 7551ms 6.93% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 496ms 0.46% 28.41% 7415ms 6.81% std::map::operator[] (partial-inline) 2795ms 2.57% 30.98% 7400ms 6.79% __GI___libc_malloc 2467ms 2.27% 33.24% 7284ms 6.69% __GI___libc_free 173ms 0.16% 33.40% 6919ms 6.35% std::_Rb_tree::_Rb_tree (partial-inline) 6628ms 6.09% 39.49% 6628ms 6.09% __strcmp_avx2 761ms 0.7% 40.19% 6502ms 5.97% std::_Rb_tree::_M_copy (inline) 26ms 0.024% 40.21% 6440ms 5.91% std::set::set (inline) 131ms 0.12% 40.33% 6163ms 5.66% SimpleWntCellCycleModel::GetWntLevel 6076ms 5.58% 45.91% 6076ms 5.58% boost::numeric::ublas::c_vector::operator() 166ms 0.15% 46.06% 5957ms 5.47% WntConcentration::GetWntLevel 2549ms 2.34% 48.40% 5894ms 5.41% std::_Rb_tree::_M_lower_bound (inline) 2931ms 2.69% 51.09% 5720ms 5.25% __cxxabiv1::__si_class_type_info::__do_dyncast 776ms 0.71% 51.81% 5513ms 5.06% std::_Rb_tree::_M_clone_node (inline) 2000ms 1.84% 53.64% 5284ms 4.85% boost::numeric::ublas::c_vector::operator[] (inline) 11ms 0.01% 53.65% 5243ms 4.81% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.65% 5207ms 4.78% std::set::insert (inline) 49ms 0.045% 53.70% 5064ms 4.65% EdgeHelper::RemoveDeletedEdges 0 0% 53.70% 4821ms 4.43% std::_Rb_tree::lower_bound (inline) 0 0% 53.70% 4821ms 4.43% std::map::lower_bound (inline) 4355ms 4.00% 57.70% 4796ms 4.40% _int_free 41ms 0.038% 57.73% 4721ms 4.33% EdgeHelper::UpdateEdgesMapKey 0 0% 57.73% 4700ms 4.32% AbstractCellBasedSimulation::DoCellRemoval (inline) 207ms 0.19% 57.92% 4677ms 4.29% MutableElement::ResetIndex 472ms 0.43% 58.36% 4403ms 4.04% std::_Rb_tree::_M_insert_ (inline) 116ms 0.11% 58.46% 4296ms 3.94% AbstractCellPopulation::GetCellUsingLocationIndex 130ms 0.12% 58.58% 4192ms 3.85% std::set_intersection (inline) 37ms 0.034% 58.62% 4093ms 3.76% Cell::GetCellProliferativeType 237ms 0.22% 58.83% 4062ms 3.73% std::__set_intersection 43ms 0.039% 58.87% 3906ms 3.59% AbstractCellProperty::IsType (inline) 3812ms 3.50% 62.37% 3812ms 3.50% boost::numeric::ublas::same_impl_ex 16ms 0.015% 62.39% 3579ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 42ms 0.039% 62.43% 3158ms 2.90% Cell::SetCellProliferativeType 0 0% 62.43% 3127ms 2.87% std::insert_iterator::operator= (inline) 2126ms 1.95% 64.38% 3092ms 2.84% _int_malloc 0 0% 64.38% 3057ms 2.81% boost::numeric::ublas::c_vector::operator-= (inline) 893ms 0.82% 65.20% 2982ms 2.74% AbstractElement::GetNodeLocation 50ms 0.046% 65.25% 2973ms 2.73% std::_Rb_tree::erase 42ms 0.039% 65.28% 2868ms 2.63% CellPropertyCollection::HasProperty 767ms 0.7% 65.99% 2835ms 2.60% AbstractCellProperty::IsSame 0 0% 65.99% 2778ms 2.55% Cell::HasCellProperty (inline) 2777ms 2.55% 68.54% 2777ms 2.55% std::_Rb_tree::_S_right (inline) 6ms 0.0055% 68.54% 2695ms 2.47% std::_Rb_tree::_M_insert_unique_ (inline) 668ms 0.61% 69.16% 2607ms 2.39% boost::numeric::ublas::vector_binary::size (inline) 26ms 0.024% 69.18% 2597ms 2.38% Cell::GetCellData 194ms 0.18% 69.36% 2589ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.36% 2554ms 2.34% boost::numeric::ublas::c_vector::assign (inline) 247ms 0.23% 69.59% 2531ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00092% 69.59% 2512ms 2.31% std::_Rb_tree::_M_insert_unique (inline) 0 0% 69.59% 2431ms 2.23% AbstractCellPopulation::WriteResultsToFiles 47ms 0.043% 69.63% 2231ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 76ms 0.07% 69.70% 2206ms 2.03% VertexMesh::GetVolumeOfElement 4ms 0.0037% 69.70% 2188ms 2.01% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.70% 2188ms 2.01% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 8ms 0.0073% 69.71% 2168ms 1.99% AbstractCellPopulation::Iterator::operator++ (inline) 173ms 0.16% 69.87% 2160ms 1.98% AbstractCellPopulation::Iterator::IsRealCell (inline) 506ms 0.46% 70.33% 2068ms 1.90% std::type_info::operator== (inline) 36ms 0.033% 70.37% 2057ms 1.89% std::_Rb_tree::_M_emplace_hint_unique 2052ms 1.88% 72.25% 2052ms 1.88% std::_Rb_tree_increment 0 0% 72.25% 1973ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.25% 1967ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1233ms 1.13% 73.38% 1891ms 1.74% std::_Rb_tree::equal_range (inline) 59ms 0.054% 73.44% 1817ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.44% 1775ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.018% 73.46% 1700ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.027% 73.48% 1562ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 43ms 0.039% 73.52% 1559ms 1.43% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.52% 1538ms 1.41% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0073% 73.53% 1538ms 1.41% boost::numeric::ublas::c_vector::swap (inline) 507ms 0.47% 73.99% 1530ms 1.40% std::swap_ranges (inline) 81ms 0.074% 74.07% 1513ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 39ms 0.036% 74.11% 1473ms 1.35% Node::RemoveElement 130ms 0.12% 74.22% 1468ms 1.35% CellPropertyCollection::AddProperty 14ms 0.013% 74.24% 1440ms 1.32% std::set::erase (inline) 1ms 0.00092% 74.24% 1417ms 1.30% OffLatticeSimulation::ApplyBoundaries 0 0% 74.24% 1397ms 1.28% boost::numeric::ublas::norm_2 (inline) 58ms 0.053% 74.29% 1392ms 1.28% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.29% 1377ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 582ms 0.53% 74.83% 1377ms 1.26% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.00092% 74.83% 1361ms 1.25% tcache_get (inline) 1360ms 1.25% 76.08% 1360ms 1.25% tcache_get_n (inline) 1317ms 1.21% 77.28% 1317ms 1.21% [libchaste_cell_based.so] 55ms 0.05% 77.34% 1265ms 1.16% std::less::operator() (inline) 972ms 0.89% 78.23% 1210ms 1.11% std::operator< (inline) 22ms 0.02% 78.25% 1209ms 1.11% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 71ms 0.065% 78.31% 1203ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 32ms 0.029% 78.34% 1188ms 1.09% CellPropertyRegistry::Get 103ms 0.095% 78.44% 1114ms 1.02% std::_Rb_tree::find (inline) 1109ms 1.02% 79.45% 1109ms 1.02% std::_Rb_tree_insert_and_rebalance 5ms 0.0046% 79.46% 1094ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.46% 1084ms 1% std::_Rb_tree::clear (inline) 11ms 0.01% 79.47% 1070ms 0.98% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.47% 1069ms 0.98% std::map::clear (inline) 0 0% 79.47% 1062ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 199ms 0.18% 79.65% 1049ms 0.96% boost::numeric::ublas::detail::equals 117ms 0.11% 79.76% 1029ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 79.76% 1029ms 0.94% boost::shared_ptr::~shared_ptr (inline) 1024ms 0.94% 80.70% 1024ms 0.94% std::swap (inline) 0 0% 80.70% 1023ms 0.94% std::iter_swap (inline) 976ms 0.9% 81.60% 976ms 0.9% Node::rGetLocation 0 0% 81.60% 952ms 0.87% std::map::find (inline) 849ms 0.78% 82.38% 872ms 0.8% boost::detail::sp_counted_base::release 1ms 0.00092% 82.38% 857ms 0.79% VertexMeshWriter::MakeVtkMesh 108ms 0.099% 82.48% 843ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 228ms 0.21% 82.68% 825ms 0.76% std::__new_allocator::construct (inline) 0 0% 82.68% 825ms 0.76% std::allocator_traits::construct (inline) 192ms 0.18% 82.86% 820ms 0.75% boost::shared_ptr::shared_ptr (inline) 0 0% 82.86% 791ms 0.73% boost::numeric::ublas::norm_inf (inline) 400ms 0.37% 83.23% 791ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 787ms 0.72% 83.95% 787ms 0.72% [libchaste_mesh.so] 771ms 0.71% 84.66% 771ms 0.71% std::vector::size (inline) 29ms 0.027% 84.69% 766ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.69% 760ms 0.7% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.69% 758ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 26ms 0.024% 84.71% 758ms 0.7% Edge::AddElement 428ms 0.39% 85.10% 756ms 0.69% Edge::GetMapIndex 756ms 0.69% 85.80% 756ms 0.69% [libstdc++.so.6.0.33] 22ms 0.02% 85.82% 752ms 0.69% AbstractNumericalMethod::DetectStepSizeExceptions 140ms 0.13% 85.95% 730ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.95% 728ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 371ms 0.34% 86.29% 691ms 0.63% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.29% 675ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.29% 643ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.31% 643ms 0.59% std::_Rb_tree::_M_insert_node (inline) 597ms 0.55% 86.86% 628ms 0.58% boost::detail::shared_count::shared_count (inline) 42ms 0.039% 86.90% 610ms 0.56% MutableElement::RegisterWithNodes (inline) 1ms 0.00092% 86.90% 607ms 0.56% vtkPolygon::New 4ms 0.0037% 86.90% 605ms 0.56% vtkPolygon::vtkPolygon 13ms 0.012% 86.91% 584ms 0.54% std::vector::_M_default_append (inline) 32ms 0.029% 86.94% 582ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.94% 582ms 0.53% boost::numeric::ublas::vector::vector (inline) 571ms 0.52% 87.47% 571ms 0.52% Node::GetIndex 24ms 0.022% 87.49% 563ms 0.52% Node::AddElement 128ms 0.12% 87.61% 553ms 0.51% MutableElement::GetNodeLocalIndex