File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97797ms, 87.32% of 111992ms total Dropped 1157 nodes (cum <= 559.96ms) flat flat% sum% cum cum% 0 0% 0% 111660ms 99.70% __libc_start_call_main 0 0% 0% 111660ms 99.70% __libc_start_main_impl 0 0% 0% 111660ms 99.70% _start 0 0% 0% 111639ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 111639ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 111639ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 111639ms 99.68% main 0 0% 0% 111597ms 99.65% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 111597ms 99.65% CxxTest::TestRunner::runTest (inline) 0 0% 0% 111597ms 99.65% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 111588ms 99.64% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.016% 57578ms 51.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.014% 0.03% 54039ms 48.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 156ms 0.14% 0.17% 52868ms 47.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.00089% 0.17% 40622ms 36.27% AbstractCellBasedSimulation::UpdateCellPopulation 336ms 0.3% 0.47% 40584ms 36.24% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.47% 25319ms 22.61% VertexBasedCellPopulation::Update 3ms 0.0027% 0.48% 25146ms 22.45% MutableVertexMesh::ReMesh 14720ms 13.14% 13.62% 23442ms 20.93% Cylindrical2dVertexMesh::GetVectorFromAtoB 93ms 0.083% 13.70% 17884ms 15.97% Cell::ReadyToDivide 59ms 0.053% 13.75% 16499ms 14.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 362ms 0.32% 14.08% 14704ms 13.13% NagaiHondaForce::GetAdhesionParameter 168ms 0.15% 14.23% 14184ms 12.67% SimpleWntCellCycleModel::UpdateCellCyclePhase 497ms 0.44% 14.67% 14024ms 12.52% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.1% 14.77% 13965ms 12.47% CellPropertyCollection::GetPropertiesType (inline) 323ms 0.29% 15.06% 12513ms 11.17% boost::numeric::ublas::vector_assign (inline) 161ms 0.14% 15.20% 12031ms 10.74% MutableVertexMesh::CheckForIntersections 3574ms 3.19% 18.40% 11843ms 10.57% __dynamic_cast 84ms 0.075% 18.47% 11770ms 10.51% AbstractCellProperty::IsSubType (inline) 90ms 0.08% 18.55% 11605ms 10.36% VertexBasedCellPopulation::GetDampingConstant 63ms 0.056% 18.61% 10783ms 9.63% AbstractTargetAreaModifier::UpdateTargetAreas 44ms 0.039% 18.65% 10703ms 9.56% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.024% 18.67% 10443ms 9.32% AbstractCellBasedSimulation::DoCellBirth 1570ms 1.40% 20.07% 10327ms 9.22% std::__new_allocator::allocate (inline) 0 0% 20.07% 9825ms 8.77% std::_Rb_tree::_M_create_node (inline) 0 0% 20.07% 9775ms 8.73% std::allocator_traits::allocate (inline) 2829ms 2.53% 22.60% 9515ms 8.50% boost::numeric::ublas::indexing_vector_assign 346ms 0.31% 22.91% 9455ms 8.44% VertexMesh::GetNextEdgeGradientOfElementAtNode 1385ms 1.24% 24.14% 9288ms 8.29% std::_Rb_tree::_M_erase 0 0% 24.14% 9003ms 8.04% std::_Rb_tree::_M_get_node (inline) 112ms 0.1% 24.24% 8886ms 7.93% Cell::GetMutationState 776ms 0.69% 24.94% 8849ms 7.90% operator new 34ms 0.03% 24.97% 8825ms 7.88% VertexBasedCellPopulation::GetLocationOfCellCentre 12ms 0.011% 24.98% 8752ms 7.81% MutableVertexMesh::RemoveDeletedNodesAndElements 839ms 0.75% 25.73% 8695ms 7.76% VertexMesh::ElementIncludesPoint 0 0% 25.73% 8604ms 7.68% std::_Rb_tree::_Alloc_node::operator() (inline) 490ms 0.44% 26.17% 8405ms 7.51% VertexMesh::GetCentroidOfElement 0 0% 26.17% 8330ms 7.44% std::_Rb_tree::_M_drop_node (inline) 267ms 0.24% 26.40% 8244ms 7.36% std::_Rb_tree::~_Rb_tree (inline) 237ms 0.21% 26.62% 8122ms 7.25% std::__new_allocator::deallocate (inline) 0 0% 26.62% 8115ms 7.25% std::allocator_traits::deallocate (inline) 0 0% 26.62% 8031ms 7.17% std::_Rb_tree::_M_put_node (inline) 484ms 0.43% 27.05% 7932ms 7.08% std::map::operator[] (partial-inline) 2865ms 2.56% 29.61% 7815ms 6.98% __GI___libc_malloc 0 0% 29.61% 7792ms 6.96% std::set::~set (inline) 2643ms 2.36% 31.97% 7633ms 6.82% __GI___libc_free 139ms 0.12% 32.09% 7544ms 6.74% std::_Rb_tree::_Rb_tree (partial-inline) 1407ms 1.26% 33.35% 7384ms 6.59% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 714ms 0.64% 33.98% 7129ms 6.37% std::_Rb_tree::_M_copy (inline) 30ms 0.027% 34.01% 6937ms 6.19% std::set::set (inline) 6557ms 5.85% 39.87% 6557ms 5.85% __strcmp_avx2 142ms 0.13% 39.99% 6395ms 5.71% SimpleWntCellCycleModel::GetWntLevel 6329ms 5.65% 45.64% 6329ms 5.65% boost::numeric::ublas::c_vector::operator() 2530ms 2.26% 47.90% 6276ms 5.60% std::_Rb_tree::_M_lower_bound (inline) 194ms 0.17% 48.08% 6186ms 5.52% WntConcentration::GetWntLevel 868ms 0.78% 48.85% 6167ms 5.51% std::_Rb_tree::_M_clone_node (inline) 21ms 0.019% 48.87% 5888ms 5.26% MutableVertexMesh::RemoveDeletedNodes 30ms 0.027% 48.90% 5707ms 5.10% EdgeHelper::RemoveDeletedEdges 2003ms 1.79% 50.68% 5504ms 4.91% boost::numeric::ublas::c_vector::operator[] (inline) 2855ms 2.55% 53.23% 5444ms 4.86% __cxxabiv1::__si_class_type_info::__do_dyncast 252ms 0.23% 53.46% 5392ms 4.81% MutableElement::ResetIndex 45ms 0.04% 53.50% 5350ms 4.78% EdgeHelper::UpdateEdgesMapKey 0 0% 53.50% 5206ms 4.65% std::set::insert (inline) 0 0% 53.50% 5143ms 4.59% std::_Rb_tree::lower_bound (inline) 0 0% 53.50% 5143ms 4.59% std::map::lower_bound (inline) 4582ms 4.09% 57.59% 4980ms 4.45% _int_free 3ms 0.0027% 57.59% 4844ms 4.33% AbstractCellBasedSimulation::DoCellRemoval (inline) 138ms 0.12% 57.72% 4636ms 4.14% AbstractCellPopulation::GetCellUsingLocationIndex 485ms 0.43% 58.15% 4316ms 3.85% std::_Rb_tree::_M_insert_ (inline) 138ms 0.12% 58.27% 4275ms 3.82% std::set_intersection (inline) 232ms 0.21% 58.48% 4137ms 3.69% std::__set_intersection 37ms 0.033% 58.51% 3912ms 3.49% Cell::GetCellProliferativeType 3864ms 3.45% 61.96% 3864ms 3.45% boost::numeric::ublas::same_impl_ex 47ms 0.042% 62.01% 3755ms 3.35% AbstractCellProperty::IsType (inline) 66ms 0.059% 62.06% 3613ms 3.23% std::_Rb_tree::erase 19ms 0.017% 62.08% 3592ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2213ms 1.98% 64.06% 3355ms 3.00% _int_malloc 3201ms 2.86% 66.92% 3201ms 2.86% std::_Rb_tree::_S_right (inline) 86ms 0.077% 66.99% 3177ms 2.84% Cell::SetCellProliferativeType 0 0% 66.99% 3144ms 2.81% std::insert_iterator::operator= (inline) 867ms 0.77% 67.77% 3028ms 2.70% AbstractElement::GetNodeLocation 35ms 0.031% 67.80% 2825ms 2.52% CellPropertyCollection::HasProperty 8ms 0.0071% 67.80% 2759ms 2.46% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 67.80% 2713ms 2.42% Cell::HasCellProperty (inline) 256ms 0.23% 68.03% 2712ms 2.42% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 68.03% 2696ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 829ms 0.74% 68.77% 2659ms 2.37% AbstractCellProperty::IsSame 211ms 0.19% 68.96% 2659ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.96% 2625ms 2.34% boost::numeric::ublas::c_vector::assign (inline) 623ms 0.56% 69.52% 2602ms 2.32% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.52% 2558ms 2.28% AbstractCellPopulation::WriteResultsToFiles 29ms 0.026% 69.54% 2518ms 2.25% Cell::GetCellData 3ms 0.0027% 69.55% 2447ms 2.18% std::_Rb_tree::_M_insert_unique 1601ms 1.43% 70.98% 2381ms 2.13% std::_Rb_tree::equal_range (inline) 3ms 0.0027% 70.98% 2289ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 185ms 0.17% 71.14% 2288ms 2.04% AbstractCellPopulation::Iterator::IsRealCell (inline) 79ms 0.071% 71.21% 2262ms 2.02% VertexMesh::GetVolumeOfElement 46ms 0.041% 71.26% 2257ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 47ms 0.042% 71.30% 2235ms 2.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.0036% 71.30% 2158ms 1.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.30% 2158ms 1.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2158ms 1.93% 73.23% 2158ms 1.93% std::_Rb_tree_increment 0 0% 73.23% 2096ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00089% 73.23% 2073ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 73.23% 1870ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 423ms 0.38% 73.61% 1830ms 1.63% std::type_info::operator== (inline) 19ms 0.017% 73.62% 1771ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 71ms 0.063% 73.69% 1764ms 1.58% MutableVertexMesh::CheckForSwapsFromShortEdges 60ms 0.054% 73.74% 1685ms 1.50% Node::RemoveElement 7ms 0.0063% 73.75% 1629ms 1.45% std::set::erase (inline) 45ms 0.04% 73.79% 1577ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 70ms 0.063% 73.85% 1566ms 1.40% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 40ms 0.036% 73.89% 1562ms 1.39% VertexMesh::GetSurfaceAreaOfElement 0 0% 73.89% 1413ms 1.26% tcache_get (inline) 1413ms 1.26% 75.15% 1413ms 1.26% tcache_get_n (inline) 146ms 0.13% 75.28% 1411ms 1.26% CellPropertyCollection::AddProperty 0 0% 75.28% 1391ms 1.24% boost::numeric::ublas::norm_2 (inline) 58ms 0.052% 75.33% 1390ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.33% 1383ms 1.23% OffLatticeSimulation::ApplyBoundaries 608ms 0.54% 75.87% 1370ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 50ms 0.045% 75.92% 1363ms 1.22% std::less::operator() (inline) 1357ms 1.21% 77.13% 1357ms 1.21% [libchaste_cell_based.so] 122ms 0.11% 77.24% 1351ms 1.21% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.24% 1317ms 1.18% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 77.24% 1313ms 1.17% std::_Rb_tree::clear (inline) 1082ms 0.97% 78.20% 1313ms 1.17% std::operator< (inline) 0 0% 78.20% 1298ms 1.16% std::map::clear (inline) 0 0% 78.20% 1221ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 5ms 0.0045% 78.21% 1204ms 1.08% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 117ms 0.1% 78.31% 1192ms 1.06% std::_Rb_tree::find (inline) 18ms 0.016% 78.33% 1178ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 19ms 0.017% 78.35% 1120ms 1.00% CellPropertyRegistry::Get 0 0% 78.35% 1105ms 0.99% boost::numeric::ublas::c_vector::assign_temporary (inline) 16ms 0.014% 78.36% 1105ms 0.99% boost::numeric::ublas::c_vector::swap (inline) 1089ms 0.97% 79.33% 1089ms 0.97% std::_Rb_tree_insert_and_rebalance 66ms 0.059% 79.39% 1089ms 0.97% std::swap_ranges (inline) 5ms 0.0045% 79.40% 1061ms 0.95% boost::numeric::ublas::detail::expression_type_check (inline) 198ms 0.18% 79.57% 1046ms 0.93% boost::numeric::ublas::detail::equals 1026ms 0.92% 80.49% 1026ms 0.92% std::swap (inline) 0 0% 80.49% 1023ms 0.91% std::iter_swap (inline) 1011ms 0.9% 81.39% 1011ms 0.9% Node::rGetLocation 102ms 0.091% 81.48% 1004ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 81.48% 1004ms 0.9% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.48% 983ms 0.88% std::map::find (inline) 246ms 0.22% 81.70% 919ms 0.82% std::__new_allocator::construct (inline) 0 0% 81.70% 919ms 0.82% std::allocator_traits::construct (inline) 501ms 0.45% 82.15% 892ms 0.8% Edge::GetMapIndex 1ms 0.00089% 82.15% 866ms 0.77% VertexMeshWriter::MakeVtkMesh 836ms 0.75% 82.90% 858ms 0.77% boost::detail::sp_counted_base::release 839ms 0.75% 83.65% 839ms 0.75% std::vector::size (inline) 102ms 0.091% 83.74% 828ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.74% 822ms 0.73% std::_Rb_tree::_M_construct_node (inline) 811ms 0.72% 84.46% 811ms 0.72% [libchaste_mesh.so] 458ms 0.41% 84.87% 806ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.87% 768ms 0.69% boost::numeric::ublas::norm_inf (inline) 398ms 0.36% 85.23% 768ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00089% 85.23% 764ms 0.68% std::_Vector_base::_M_allocate (inline) 21ms 0.019% 85.25% 756ms 0.68% MutableElement::RegisterWithEdges (inline) 22ms 0.02% 85.27% 751ms 0.67% Edge::AddElement 0 0% 85.27% 741ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 153ms 0.14% 85.40% 720ms 0.64% MutableElement::GetNodeLocalIndex 175ms 0.16% 85.56% 714ms 0.64% boost::shared_ptr::shared_ptr (inline) 0 0% 85.56% 694ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 683ms 0.61% 86.17% 683ms 0.61% [libstdc++.so.6.0.33] 0 0% 86.17% 658ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.026% 86.19% 658ms 0.59% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.19% 643ms 0.57% std::map::map (inline) 38ms 0.034% 86.23% 642ms 0.57% MutableElement::RegisterWithNodes (inline) 633ms 0.57% 86.79% 633ms 0.57% Node::GetIndex 4ms 0.0036% 86.80% 624ms 0.56% std::vector::_M_default_append (inline) 0 0% 86.80% 612ms 0.55% vtkPolygon::New 0 0% 86.80% 611ms 0.55% vtkPolygon::vtkPolygon 41ms 0.037% 86.83% 609ms 0.54% Node::AddElement 90ms 0.08% 86.91% 608ms 0.54% std::_Rb_tree::_M_upper_bound (inline) 435ms 0.39% 87.30% 583ms 0.52% malloc_consolidate 24ms 0.021% 87.32% 576ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.32% 576ms 0.51% boost::numeric::ublas::vector::vector (inline) 2ms 0.0018% 87.32% 562ms 0.5% VertexElementMap::VertexElementMap 0 0% 87.32% 560ms 0.5% std::vector::resize (inline)