File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96998ms, 88.51% of 109595ms total Dropped 1122 nodes (cum <= 547.98ms) flat flat% sum% cum cum% 0 0% 0% 109125ms 99.57% __libc_start_call_main 0 0% 0% 109125ms 99.57% __libc_start_main_impl 0 0% 0% 109125ms 99.57% _start 0 0% 0% 109104ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109104ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109104ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109104ms 99.55% main 0 0% 0% 109061ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109061ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109061ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 109054ms 99.51% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.019% 56509ms 51.56% OffLatticeSimulation::UpdateCellLocationsAndTopology 23ms 0.021% 0.04% 53239ms 48.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 127ms 0.12% 0.16% 51711ms 47.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 352ms 0.32% 0.48% 39781ms 36.30% NagaiHondaForce::AddForceContribution 0 0% 0.48% 39463ms 36.01% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0036% 0.48% 24517ms 22.37% VertexBasedCellPopulation::Update 1ms 0.00091% 0.48% 24389ms 22.25% MutableVertexMesh::ReMesh 14419ms 13.16% 13.64% 22619ms 20.64% Cylindrical2dVertexMesh::GetVectorFromAtoB 113ms 0.1% 13.74% 17459ms 15.93% Cell::ReadyToDivide 144ms 0.13% 13.87% 16227ms 14.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 352ms 0.32% 14.19% 14989ms 13.68% NagaiHondaForce::GetAdhesionParameter 427ms 0.39% 14.58% 14002ms 12.78% boost::numeric::ublas::c_vector::c_vector (partial-inline) 137ms 0.13% 14.71% 13754ms 12.55% SimpleWntCellCycleModel::UpdateCellCyclePhase 123ms 0.11% 14.82% 13589ms 12.40% CellPropertyCollection::GetPropertiesType (inline) 347ms 0.32% 15.14% 12398ms 11.31% boost::numeric::ublas::vector_assign (inline) 142ms 0.13% 15.27% 12043ms 10.99% MutableVertexMesh::CheckForIntersections 70ms 0.064% 15.33% 11414ms 10.41% VertexBasedCellPopulation::GetDampingConstant 3197ms 2.92% 18.25% 11239ms 10.26% __dynamic_cast 74ms 0.068% 18.32% 11129ms 10.15% AbstractCellProperty::IsSubType (inline) 1970ms 1.80% 20.11% 10960ms 10.00% std::__new_allocator::allocate (inline) 84ms 0.077% 20.19% 10542ms 9.62% AbstractTargetAreaModifier::UpdateTargetAreas 71ms 0.065% 20.25% 10438ms 9.52% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 20.25% 10418ms 9.51% std::allocator_traits::allocate (inline) 29ms 0.026% 20.28% 10278ms 9.38% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.28% 10267ms 9.37% std::_Rb_tree::_M_create_node (inline) 0 0% 20.28% 9659ms 8.81% std::_Rb_tree::_M_get_node (inline) 1420ms 1.30% 21.58% 9399ms 8.58% std::_Rb_tree::_M_erase 1328ms 1.21% 22.79% 9150ms 8.35% operator new 0 0% 22.79% 9086ms 8.29% std::_Rb_tree::_Alloc_node::operator() (inline) 2609ms 2.38% 25.17% 9043ms 8.25% boost::numeric::ublas::indexing_vector_assign 801ms 0.73% 25.90% 8947ms 8.16% VertexMesh::ElementIncludesPoint 23ms 0.021% 25.92% 8663ms 7.90% VertexBasedCellPopulation::GetLocationOfCellCentre 75ms 0.068% 25.99% 8642ms 7.89% Cell::GetMutationState 363ms 0.33% 26.32% 8635ms 7.88% VertexMesh::GetNextEdgeGradientOfElementAtNode 221ms 0.2% 26.52% 8488ms 7.74% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.52% 8483ms 7.74% std::_Rb_tree::_M_drop_node (inline) 262ms 0.24% 26.76% 8292ms 7.57% std::__new_allocator::deallocate (inline) 0 0% 26.76% 8255ms 7.53% std::allocator_traits::deallocate (inline) 3184ms 2.91% 29.67% 8193ms 7.48% __GI___libc_free 481ms 0.44% 30.11% 8190ms 7.47% VertexMesh::GetCentroidOfElement 0 0% 30.11% 8163ms 7.45% std::_Rb_tree::_M_put_node (inline) 0 0% 30.11% 7974ms 7.28% std::set::~set (inline) 13ms 0.012% 30.12% 7908ms 7.22% MutableVertexMesh::RemoveDeletedNodesAndElements 2980ms 2.72% 32.84% 7621ms 6.95% __GI___libc_malloc 153ms 0.14% 32.98% 7471ms 6.82% std::_Rb_tree::_Rb_tree (partial-inline) 444ms 0.41% 33.38% 7161ms 6.53% std::map::operator[] (partial-inline) 567ms 0.52% 33.90% 7067ms 6.45% std::_Rb_tree::_M_copy (inline) 1388ms 1.27% 35.16% 7060ms 6.44% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 12ms 0.011% 35.18% 7008ms 6.39% std::set::set (inline) 6436ms 5.87% 41.05% 6436ms 5.87% __strcmp_avx2 107ms 0.098% 41.15% 6257ms 5.71% SimpleWntCellCycleModel::GetWntLevel 847ms 0.77% 41.92% 6243ms 5.70% std::_Rb_tree::_M_clone_node (inline) 146ms 0.13% 42.05% 6066ms 5.53% WntConcentration::GetWntLevel 5976ms 5.45% 47.50% 5976ms 5.45% boost::numeric::ublas::c_vector::operator() 2395ms 2.19% 49.69% 5626ms 5.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 49.69% 5557ms 5.07% std::set::insert (inline) 2699ms 2.46% 52.15% 5522ms 5.04% __cxxabiv1::__si_class_type_info::__do_dyncast 32ms 0.029% 52.18% 5447ms 4.97% MutableVertexMesh::RemoveDeletedNodes 39ms 0.036% 52.22% 5265ms 4.80% EdgeHelper::RemoveDeletedEdges 4644ms 4.24% 56.46% 5001ms 4.56% _int_free 209ms 0.19% 56.65% 4977ms 4.54% MutableElement::ResetIndex 36ms 0.033% 56.68% 4953ms 4.52% EdgeHelper::UpdateEdgesMapKey 1486ms 1.36% 58.03% 4873ms 4.45% boost::numeric::ublas::c_vector::operator[] (inline) 482ms 0.44% 58.47% 4724ms 4.31% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.47% 4659ms 4.25% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.47% 4526ms 4.13% std::_Rb_tree::lower_bound (inline) 0 0% 58.47% 4526ms 4.13% std::map::lower_bound (inline) 64ms 0.058% 58.53% 4492ms 4.10% std::set_intersection (inline) 307ms 0.28% 58.81% 4428ms 4.04% std::__set_intersection 112ms 0.1% 58.92% 4199ms 3.83% AbstractCellPopulation::GetCellUsingLocationIndex 3975ms 3.63% 62.54% 3975ms 3.63% boost::numeric::ublas::same_impl_ex 31ms 0.028% 62.57% 3933ms 3.59% Cell::GetCellProliferativeType 52ms 0.047% 62.62% 3776ms 3.45% AbstractCellProperty::IsType (inline) 10ms 0.0091% 62.63% 3498ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 879ms 0.8% 63.43% 3400ms 3.10% AbstractElement::GetNodeLocation 2189ms 2.00% 65.43% 3191ms 2.91% _int_malloc 33ms 0.03% 65.46% 3184ms 2.91% std::_Rb_tree::erase 0 0% 65.46% 3171ms 2.89% std::insert_iterator::operator= (inline) 46ms 0.042% 65.50% 3099ms 2.83% Cell::SetCellProliferativeType 625ms 0.57% 66.07% 2892ms 2.64% boost::numeric::ublas::vector_binary::size (inline) 2857ms 2.61% 68.68% 2857ms 2.61% std::_Rb_tree::_S_right (inline) 2ms 0.0018% 68.68% 2839ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 443ms 0.4% 69.08% 2782ms 2.54% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00091% 69.08% 2718ms 2.48% std::_Rb_tree::_M_insert_unique 750ms 0.68% 69.77% 2694ms 2.46% AbstractCellProperty::IsSame 43ms 0.039% 69.81% 2662ms 2.43% CellPropertyCollection::HasProperty 258ms 0.24% 70.04% 2581ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.04% 2555ms 2.33% Cell::HasCellProperty (inline) 0 0% 70.04% 2511ms 2.29% AbstractCellPopulation::WriteResultsToFiles 21ms 0.019% 70.06% 2418ms 2.21% Cell::GetCellData 0 0% 70.06% 2406ms 2.20% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.06% 2358ms 2.15% boost::numeric::ublas::c_vector::operator-= (inline) 105ms 0.096% 70.16% 2312ms 2.11% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 109ms 0.099% 70.26% 2260ms 2.06% VertexMesh::GetVolumeOfElement 2ms 0.0018% 70.26% 2230ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 247ms 0.23% 70.48% 2221ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 2152ms 1.96% 72.45% 2152ms 1.96% std::_Rb_tree_increment 28ms 0.026% 72.47% 2138ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 1381ms 1.26% 73.73% 2096ms 1.91% std::_Rb_tree::equal_range (inline) 0 0% 73.73% 2051ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 73.73% 2028ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 4ms 0.0036% 73.74% 1958ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.74% 1958ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 466ms 0.43% 74.16% 1944ms 1.77% std::type_info::operator== (inline) 83ms 0.076% 74.24% 1859ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.24% 1821ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 16ms 0.015% 74.25% 1707ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 22ms 0.02% 74.27% 1645ms 1.50% VertexMesh::GetSurfaceAreaOfElement 38ms 0.035% 74.31% 1579ms 1.44% Node::RemoveElement 135ms 0.12% 74.43% 1556ms 1.42% CellPropertyCollection::AddProperty 19ms 0.017% 74.45% 1552ms 1.42% std::set::erase (inline) 22ms 0.02% 74.47% 1522ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 80ms 0.073% 74.54% 1504ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 128ms 0.12% 74.66% 1466ms 1.34% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.66% 1306ms 1.19% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00091% 74.66% 1300ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 74.66% 1276ms 1.16% tcache_get (inline) 1276ms 1.16% 75.82% 1276ms 1.16% tcache_get_n (inline) 84ms 0.077% 75.90% 1252ms 1.14% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.90% 1232ms 1.12% boost::numeric::ublas::norm_2 (inline) 527ms 0.48% 76.38% 1217ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1206ms 1.10% 77.48% 1206ms 1.10% Node::rGetLocation 0 0% 77.48% 1181ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.48% 1136ms 1.04% std::_Rb_tree::clear (inline) 1134ms 1.03% 78.52% 1134ms 1.03% std::_Rb_tree_insert_and_rebalance 1126ms 1.03% 79.54% 1126ms 1.03% [libchaste_cell_based.so] 0 0% 79.54% 1120ms 1.02% std::map::clear (inline) 63ms 0.057% 79.60% 1119ms 1.02% std::less::operator() (inline) 5ms 0.0046% 79.60% 1109ms 1.01% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 20ms 0.018% 79.62% 1107ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 101ms 0.092% 79.72% 1107ms 1.01% std::_Rb_tree::find (inline) 30ms 0.027% 79.74% 1073ms 0.98% CellPropertyRegistry::Get 849ms 0.77% 80.52% 1056ms 0.96% std::operator< (inline) 155ms 0.14% 80.66% 1041ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.66% 1041ms 0.95% boost::shared_ptr::~shared_ptr (inline) 22ms 0.02% 80.68% 968ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 422ms 0.39% 81.06% 939ms 0.86% Edge::GetMapIndex 939ms 0.86% 81.92% 939ms 0.86% std::vector::size (inline) 176ms 0.16% 82.08% 938ms 0.86% boost::numeric::ublas::detail::equals 914ms 0.83% 82.92% 914ms 0.83% [libchaste_mesh.so] 0 0% 82.92% 905ms 0.83% std::map::find (inline) 0 0% 82.92% 876ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 82.92% 876ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 98ms 0.089% 83.01% 871ms 0.79% std::swap_ranges (inline) 1ms 0.00091% 83.01% 867ms 0.79% VertexMeshWriter::MakeVtkMesh 852ms 0.78% 83.79% 859ms 0.78% boost::detail::sp_counted_base::release 14ms 0.013% 83.80% 805ms 0.73% MutableElement::RegisterWithEdges (inline) 33ms 0.03% 83.83% 799ms 0.73% Edge::AddElement 0 0% 83.83% 773ms 0.71% std::iter_swap (inline) 773ms 0.71% 84.54% 773ms 0.71% std::swap (inline) 0 0% 84.54% 765ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 97ms 0.089% 84.62% 760ms 0.69% MutableElement::GetNodeLocalIndex 2ms 0.0018% 84.63% 755ms 0.69% std::_Vector_base::_M_allocate (inline) 10ms 0.0091% 84.64% 736ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 110ms 0.1% 84.74% 736ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 97ms 0.089% 84.82% 726ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 84.82% 726ms 0.66% boost::numeric::ublas::norm_inf (inline) 348ms 0.32% 85.14% 726ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 443ms 0.4% 85.55% 724ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 92ms 0.084% 85.63% 713ms 0.65% boost::shared_ptr::shared_ptr (inline) 691ms 0.63% 86.26% 691ms 0.63% Node::GetIndex 20ms 0.018% 86.28% 670ms 0.61% MutableElement::RegisterWithNodes (inline) 125ms 0.11% 86.39% 666ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.39% 666ms 0.61% std::allocator_traits::construct (inline) 32ms 0.029% 86.42% 655ms 0.6% Node::AddElement 0 0% 86.42% 647ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.44% 647ms 0.59% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.44% 632ms 0.58% vtkPolygon::New 0 0% 86.44% 632ms 0.58% vtkPolygon::vtkPolygon 8ms 0.0073% 86.45% 629ms 0.57% std::vector::_M_default_append (inline) 627ms 0.57% 87.02% 627ms 0.57% [libstdc++.so.6.0.33] 590ms 0.54% 87.56% 621ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 87.56% 608ms 0.55% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.56% 597ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 589ms 0.54% 88.10% 589ms 0.54% operator delete 20ms 0.018% 88.11% 562ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.11% 562ms 0.51% boost::numeric::ublas::vector::vector (inline) 429ms 0.39% 88.51% 556ms 0.51% malloc_consolidate