File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 73502ms, 87.32% of 84174ms total Dropped 1013 nodes (cum <= 420.87ms) flat flat% sum% cum cum% 0 0% 0% 83895ms 99.67% __libc_start_call_main 0 0% 0% 83895ms 99.67% __libc_start_main_impl 0 0% 0% 83895ms 99.67% _start 0 0% 0% 83880ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 83880ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 83880ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 83880ms 99.65% main 0 0% 0% 83838ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 83838ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 83838ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0048% 0.0048% 83832ms 99.59% AbstractCellBasedSimulation::Solve 17ms 0.02% 0.025% 43545ms 51.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.02% 0.045% 41026ms 48.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 107ms 0.13% 0.17% 40113ms 47.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 239ms 0.28% 0.46% 30905ms 36.72% NagaiHondaForce::AddForceContribution 3ms 0.0036% 0.46% 30060ms 35.71% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0012% 0.46% 18519ms 22.00% VertexBasedCellPopulation::Update 1ms 0.0012% 0.46% 18411ms 21.87% MutableVertexMesh::ReMesh 11433ms 13.58% 14.04% 18208ms 21.63% Cylindrical2dVertexMesh::GetVectorFromAtoB 82ms 0.097% 14.14% 13845ms 16.45% Cell::ReadyToDivide 61ms 0.072% 14.21% 12930ms 15.36% AbstractPhaseBasedCellCycleModel::ReadyToDivide 315ms 0.37% 14.59% 11299ms 13.42% NagaiHondaForce::GetAdhesionParameter 117ms 0.14% 14.73% 11129ms 13.22% SimpleWntCellCycleModel::UpdateCellCyclePhase 345ms 0.41% 15.14% 11003ms 13.07% boost::numeric::ublas::c_vector::c_vector (partial-inline) 78ms 0.093% 15.23% 10300ms 12.24% CellPropertyCollection::GetPropertiesType (inline) 288ms 0.34% 15.57% 9807ms 11.65% boost::numeric::ublas::vector_assign (inline) 106ms 0.13% 15.70% 9321ms 11.07% MutableVertexMesh::CheckForIntersections 2505ms 2.98% 18.67% 8855ms 10.52% __dynamic_cast 60ms 0.071% 18.75% 8791ms 10.44% AbstractCellProperty::IsSubType (inline) 76ms 0.09% 18.84% 8751ms 10.40% VertexBasedCellPopulation::GetDampingConstant 54ms 0.064% 18.90% 8255ms 9.81% AbstractTargetAreaModifier::UpdateTargetAreas 22ms 0.026% 18.93% 8186ms 9.73% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.036% 18.96% 8001ms 9.51% AbstractCellBasedSimulation::DoCellBirth 1000ms 1.19% 20.15% 7514ms 8.93% std::__new_allocator::allocate (inline) 2190ms 2.60% 22.75% 7289ms 8.66% boost::numeric::ublas::indexing_vector_assign 0 0% 22.75% 7162ms 8.51% std::_Rb_tree::_M_create_node (inline) 276ms 0.33% 23.08% 7124ms 8.46% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.08% 7100ms 8.43% std::allocator_traits::allocate (inline) 22ms 0.026% 23.11% 6953ms 8.26% VertexBasedCellPopulation::GetLocationOfCellCentre 953ms 1.13% 24.24% 6864ms 8.15% std::_Rb_tree::_M_erase 710ms 0.84% 25.08% 6815ms 8.10% VertexMesh::ElementIncludesPoint 366ms 0.43% 25.52% 6653ms 7.90% VertexMesh::GetCentroidOfElement 0 0% 25.52% 6594ms 7.83% std::_Rb_tree::_M_get_node (inline) 628ms 0.75% 26.26% 6549ms 7.78% operator new 68ms 0.081% 26.34% 6525ms 7.75% Cell::GetMutationState 0 0% 26.34% 6333ms 7.52% std::_Rb_tree::_Alloc_node::operator() (inline) 188ms 0.22% 26.57% 6285ms 7.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.57% 6198ms 7.36% std::_Rb_tree::_M_drop_node (inline) 166ms 0.2% 26.76% 5999ms 7.13% std::__new_allocator::deallocate (inline) 0 0% 26.76% 5989ms 7.12% std::set::~set (inline) 0 0% 26.76% 5985ms 7.11% std::allocator_traits::deallocate (inline) 0 0% 26.76% 5936ms 7.05% std::_Rb_tree::_M_put_node (inline) 13ms 0.015% 26.78% 5819ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 1119ms 1.33% 28.11% 5815ms 6.91% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 347ms 0.41% 28.52% 5773ms 6.86% std::map::operator[] (partial-inline) 2142ms 2.54% 31.07% 5763ms 6.85% __GI___libc_malloc 1880ms 2.23% 33.30% 5654ms 6.72% __GI___libc_free 175ms 0.21% 33.51% 5597ms 6.65% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.025% 33.53% 5224ms 6.21% std::set::set (inline) 597ms 0.71% 34.24% 5212ms 6.19% std::_Rb_tree::_M_copy (inline) 107ms 0.13% 34.37% 5115ms 6.08% SimpleWntCellCycleModel::GetWntLevel 5115ms 6.08% 40.44% 5115ms 6.08% __strcmp_evex 124ms 0.15% 40.59% 4949ms 5.88% WntConcentration::GetWntLevel 4731ms 5.62% 46.21% 4731ms 5.62% boost::numeric::ublas::c_vector::operator() 1943ms 2.31% 48.52% 4598ms 5.46% std::_Rb_tree::_M_lower_bound (inline) 662ms 0.79% 49.31% 4400ms 5.23% std::_Rb_tree::_M_clone_node (inline) 1611ms 1.91% 51.22% 4249ms 5.05% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 51.22% 4004ms 4.76% std::set::insert (inline) 12ms 0.014% 51.24% 3979ms 4.73% MutableVertexMesh::RemoveDeletedNodes 2148ms 2.55% 53.79% 3877ms 4.61% __cxxabiv1::__si_class_type_info::__do_dyncast 24ms 0.029% 53.82% 3834ms 4.55% EdgeHelper::RemoveDeletedEdges 0 0% 53.82% 3769ms 4.48% std::_Rb_tree::lower_bound (inline) 0 0% 53.82% 3769ms 4.48% std::map::lower_bound (inline) 3429ms 4.07% 57.89% 3764ms 4.47% _int_free 33ms 0.039% 57.93% 3621ms 4.30% EdgeHelper::UpdateEdgesMapKey 169ms 0.2% 58.13% 3578ms 4.25% MutableElement::ResetIndex 0 0% 58.13% 3532ms 4.20% AbstractCellBasedSimulation::DoCellRemoval (inline) 103ms 0.12% 58.25% 3470ms 4.12% AbstractCellPopulation::GetCellUsingLocationIndex 93ms 0.11% 58.36% 3349ms 3.98% std::set_intersection (inline) 377ms 0.45% 58.81% 3348ms 3.98% std::_Rb_tree::_M_insert_ (inline) 178ms 0.21% 59.02% 3256ms 3.87% std::__set_intersection 21ms 0.025% 59.05% 3085ms 3.67% Cell::GetCellProliferativeType 44ms 0.052% 59.10% 2927ms 3.48% AbstractCellProperty::IsType (inline) 2901ms 3.45% 62.55% 2901ms 3.45% boost::numeric::ublas::same_impl_ex 10ms 0.012% 62.56% 2683ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 61ms 0.072% 62.63% 2484ms 2.95% Cell::SetCellProliferativeType 0 0% 62.63% 2468ms 2.93% std::insert_iterator::operator= (inline) 1737ms 2.06% 64.69% 2444ms 2.90% _int_malloc 641ms 0.76% 65.45% 2289ms 2.72% AbstractElement::GetNodeLocation 2204ms 2.62% 68.07% 2204ms 2.62% std::_Rb_tree::_S_right (inline) 44ms 0.052% 68.13% 2187ms 2.60% std::_Rb_tree::erase 6ms 0.0071% 68.13% 2154ms 2.56% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.13% 2124ms 2.52% boost::numeric::ublas::c_vector::operator-= (inline) 539ms 0.64% 68.77% 2088ms 2.48% AbstractCellProperty::IsSame 490ms 0.58% 69.36% 2066ms 2.45% boost::numeric::ublas::vector_binary::size (inline) 191ms 0.23% 69.58% 1985ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 36ms 0.043% 69.62% 1963ms 2.33% CellPropertyCollection::HasProperty 0 0% 69.62% 1952ms 2.32% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.0012% 69.63% 1936ms 2.30% AbstractCellPopulation::WriteResultsToFiles 209ms 0.25% 69.87% 1900ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.87% 1888ms 2.24% Cell::HasCellProperty (inline) 56ms 0.067% 69.94% 1851ms 2.20% VertexMesh::GetVolumeOfElement 1ms 0.0012% 69.94% 1850ms 2.20% std::_Rb_tree::_M_insert_unique 19ms 0.023% 69.96% 1764ms 2.10% Cell::GetCellData 46ms 0.055% 70.02% 1731ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0036% 70.02% 1652ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 117ms 0.14% 70.16% 1632ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 27ms 0.032% 70.19% 1622ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 0 0% 70.19% 1588ms 1.89% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.19% 1582ms 1.88% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.0012% 70.20% 1567ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.20% 1567ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 383ms 0.46% 70.65% 1549ms 1.84% std::type_info::operator== (inline) 1497ms 1.78% 72.43% 1497ms 1.78% std::_Rb_tree_increment 55ms 0.065% 72.49% 1461ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.0012% 72.50% 1446ms 1.72% VertexMeshWriter::WriteVtkUsingMesh 907ms 1.08% 73.57% 1383ms 1.64% std::_Rb_tree::equal_range (inline) 22ms 0.026% 73.60% 1288ms 1.53% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.029% 73.63% 1272ms 1.51% VertexMesh::GetSurfaceAreaOfElement 21ms 0.025% 73.65% 1157ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 43ms 0.051% 73.70% 1151ms 1.37% Node::RemoveElement 57ms 0.068% 73.77% 1132ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 7ms 0.0083% 73.78% 1112ms 1.32% std::set::erase (inline) 1056ms 1.25% 75.03% 1056ms 1.25% [libchaste_cell_based.so] 1ms 0.0012% 75.04% 1054ms 1.25% OffLatticeSimulation::ApplyBoundaries 107ms 0.13% 75.16% 1049ms 1.25% CellPropertyCollection::AddProperty 0 0% 75.16% 1045ms 1.24% tcache_get (inline) 1045ms 1.24% 76.40% 1045ms 1.24% tcache_get_n (inline) 0 0% 76.40% 1020ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 64ms 0.076% 76.48% 992ms 1.18% boost::numeric::ublas::vector_reference::operator() (inline) 29ms 0.034% 76.51% 985ms 1.17% CellPropertyRegistry::Get 0 0% 76.51% 984ms 1.17% boost::numeric::ublas::norm_2 (inline) 455ms 0.54% 77.05% 975ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 57ms 0.068% 77.12% 937ms 1.11% std::less::operator() (inline) 119ms 0.14% 77.26% 897ms 1.07% boost::numeric::ublas::detail::expression_type_check (inline) 19ms 0.023% 77.29% 888ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 72ms 0.086% 77.37% 886ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 727ms 0.86% 78.24% 880ms 1.05% std::operator< (inline) 0 0% 78.24% 864ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0059% 78.24% 864ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 82ms 0.097% 78.34% 859ms 1.02% std::swap_ranges (inline) 0 0% 78.34% 829ms 0.98% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1ms 0.0012% 78.34% 825ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 807ms 0.96% 79.30% 807ms 0.96% std::_Rb_tree_insert_and_rebalance 68ms 0.081% 79.38% 805ms 0.96% std::_Rb_tree::find (inline) 102ms 0.12% 79.50% 802ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 79.50% 802ms 0.95% boost::shared_ptr::~shared_ptr (inline) 781ms 0.93% 80.43% 781ms 0.93% Node::rGetLocation 778ms 0.92% 81.35% 778ms 0.92% std::swap (inline) 0 0% 81.35% 777ms 0.92% std::iter_swap (inline) 0 0% 81.35% 773ms 0.92% std::_Rb_tree::clear (inline) 146ms 0.17% 81.53% 766ms 0.91% boost::numeric::ublas::detail::equals 0 0% 81.53% 762ms 0.91% std::map::clear (inline) 0 0% 81.53% 693ms 0.82% VertexMeshWriter::MakeVtkMesh 0 0% 81.53% 674ms 0.8% std::map::find (inline) 642ms 0.76% 82.29% 666ms 0.79% boost::detail::sp_counted_base::release 646ms 0.77% 83.06% 646ms 0.77% std::vector::size (inline) 186ms 0.22% 83.28% 626ms 0.74% std::__new_allocator::construct (inline) 0 0% 83.28% 626ms 0.74% std::allocator_traits::construct (inline) 622ms 0.74% 84.02% 622ms 0.74% [libchaste_mesh.so] 54ms 0.064% 84.08% 612ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 129ms 0.15% 84.23% 594ms 0.71% boost::shared_ptr::shared_ptr (inline) 335ms 0.4% 84.63% 594ms 0.71% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 11ms 0.013% 84.64% 584ms 0.69% MutableElement::RegisterWithEdges (inline) 0 0% 84.64% 584ms 0.69% boost::numeric::ublas::norm_inf (inline) 287ms 0.34% 84.99% 584ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 13ms 0.015% 85.00% 583ms 0.69% Edge::AddElement 575ms 0.68% 85.68% 575ms 0.68% [libstdc++.so.6.0.33] 304ms 0.36% 86.05% 569ms 0.68% Edge::GetMapIndex 0 0% 86.05% 568ms 0.67% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.05% 566ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.05% 525ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 1ms 0.0012% 86.05% 515ms 0.61% vtkPolygon::New 1ms 0.0012% 86.05% 511ms 0.61% vtkPolygon::vtkPolygon 2ms 0.0024% 86.05% 506ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.05% 504ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.019% 86.07% 504ms 0.6% std::_Rb_tree::_M_insert_node (inline) 97ms 0.12% 86.18% 499ms 0.59% MutableElement::GetNodeLocalIndex 30ms 0.036% 86.22% 488ms 0.58% MutableElement::RegisterWithNodes (inline) 432ms 0.51% 86.73% 465ms 0.55% boost::detail::shared_count::shared_count (inline) 29ms 0.034% 86.77% 452ms 0.54% Node::AddElement 443ms 0.53% 87.29% 443ms 0.53% Node::GetIndex 21ms 0.025% 87.32% 435ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.32% 435ms 0.52% boost::numeric::ublas::vector::vector (inline) 2ms 0.0024% 87.32% 427ms 0.51% std::vector::_M_default_append (inline)