File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98908ms, 88.48% of 111790ms total Dropped 1112 nodes (cum <= 558.95ms) flat flat% sum% cum cum% 0 0% 0% 111319ms 99.58% __libc_start_call_main 0 0% 0% 111319ms 99.58% __libc_start_main_impl 0 0% 0% 111319ms 99.58% _start 0 0% 0% 111300ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 111300ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 111300ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 111300ms 99.56% main 0 0% 0% 111256ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 111256ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 111256ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00089% 0.00089% 111249ms 99.52% AbstractCellBasedSimulation::Solve 25ms 0.022% 0.023% 57430ms 51.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.017% 0.04% 54019ms 48.32% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.16% 52898ms 47.32% AbstractNumericalMethod::ComputeForcesIncludingDamping 362ms 0.32% 0.48% 40648ms 36.36% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.48% 40550ms 36.27% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0036% 0.48% 25539ms 22.85% VertexBasedCellPopulation::Update 3ms 0.0027% 0.49% 25399ms 22.72% MutableVertexMesh::ReMesh 14713ms 13.16% 13.65% 23172ms 20.73% Cylindrical2dVertexMesh::GetVectorFromAtoB 107ms 0.096% 13.74% 17567ms 15.71% Cell::ReadyToDivide 63ms 0.056% 13.80% 16311ms 14.59% AbstractPhaseBasedCellCycleModel::ReadyToDivide 392ms 0.35% 14.15% 15107ms 13.51% NagaiHondaForce::GetAdhesionParameter 444ms 0.4% 14.55% 14841ms 13.28% boost::numeric::ublas::c_vector::c_vector (partial-inline) 138ms 0.12% 14.67% 13987ms 12.51% CellPropertyCollection::GetPropertiesType (inline) 144ms 0.13% 14.80% 13954ms 12.48% SimpleWntCellCycleModel::UpdateCellCyclePhase 377ms 0.34% 15.14% 13320ms 11.92% boost::numeric::ublas::vector_assign (inline) 130ms 0.12% 15.25% 12212ms 10.92% MutableVertexMesh::CheckForIntersections 101ms 0.09% 15.34% 11740ms 10.50% VertexBasedCellPopulation::GetDampingConstant 3491ms 3.12% 18.47% 11532ms 10.32% __dynamic_cast 72ms 0.064% 18.53% 11381ms 10.18% AbstractCellProperty::IsSubType (inline) 93ms 0.083% 18.62% 10706ms 9.58% AbstractTargetAreaModifier::UpdateTargetAreas 1432ms 1.28% 19.90% 10610ms 9.49% std::__new_allocator::allocate (inline) 79ms 0.071% 19.97% 10587ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 19.99% 10263ms 9.18% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.99% 10070ms 9.01% std::_Rb_tree::_M_create_node (inline) 0 0% 19.99% 10009ms 8.95% std::allocator_traits::allocate (inline) 2637ms 2.36% 22.35% 9751ms 8.72% boost::numeric::ublas::indexing_vector_assign 1537ms 1.37% 23.72% 9395ms 8.40% std::_Rb_tree::_M_erase 0 0% 23.72% 9294ms 8.31% std::_Rb_tree::_M_get_node (inline) 867ms 0.78% 24.50% 9270ms 8.29% operator new 832ms 0.74% 25.24% 9152ms 8.19% VertexMesh::ElementIncludesPoint 40ms 0.036% 25.28% 8910ms 7.97% VertexBasedCellPopulation::GetLocationOfCellCentre 91ms 0.081% 25.36% 8902ms 7.96% Cell::GetMutationState 354ms 0.32% 25.67% 8900ms 7.96% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.67% 8825ms 7.89% std::_Rb_tree::_Alloc_node::operator() (inline) 12ms 0.011% 25.68% 8613ms 7.70% MutableVertexMesh::RemoveDeletedNodesAndElements 455ms 0.41% 26.09% 8419ms 7.53% VertexMesh::GetCentroidOfElement 226ms 0.2% 26.29% 8364ms 7.48% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.29% 8239ms 7.37% std::_Rb_tree::_M_drop_node (inline) 3260ms 2.92% 29.21% 8189ms 7.33% __GI___libc_malloc 262ms 0.23% 29.44% 8002ms 7.16% std::__new_allocator::deallocate (inline) 0 0% 29.44% 7957ms 7.12% std::allocator_traits::deallocate (inline) 3102ms 2.77% 32.22% 7910ms 7.08% __GI___libc_free 0 0% 32.22% 7900ms 7.07% std::set::~set (inline) 0 0% 32.22% 7896ms 7.06% std::_Rb_tree::_M_put_node (inline) 459ms 0.41% 32.63% 7439ms 6.65% std::map::operator[] (partial-inline) 195ms 0.17% 32.80% 7415ms 6.63% std::_Rb_tree::_Rb_tree (partial-inline) 1349ms 1.21% 34.01% 7156ms 6.40% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 663ms 0.59% 34.60% 6942ms 6.21% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 34.61% 6817ms 6.10% std::set::set (inline) 118ms 0.11% 34.72% 6428ms 5.75% SimpleWntCellCycleModel::GetWntLevel 6291ms 5.63% 40.35% 6291ms 5.63% boost::numeric::ublas::c_vector::operator() 6284ms 5.62% 45.97% 6284ms 5.62% __strcmp_avx2 134ms 0.12% 46.09% 6210ms 5.56% WntConcentration::GetWntLevel 846ms 0.76% 46.85% 5983ms 5.35% std::_Rb_tree::_M_clone_node (inline) 2290ms 2.05% 48.89% 5867ms 5.25% std::_Rb_tree::_M_lower_bound (inline) 32ms 0.029% 48.92% 5787ms 5.18% MutableVertexMesh::RemoveDeletedNodes 2785ms 2.49% 51.41% 5667ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 47ms 0.042% 51.46% 5610ms 5.02% EdgeHelper::RemoveDeletedEdges 0 0% 51.46% 5579ms 4.99% std::set::insert (inline) 294ms 0.26% 51.72% 5485ms 4.91% MutableElement::ResetIndex 40ms 0.036% 51.76% 5282ms 4.72% EdgeHelper::UpdateEdgesMapKey 1441ms 1.29% 53.04% 4809ms 4.30% boost::numeric::ublas::c_vector::operator[] (inline) 592ms 0.53% 53.57% 4801ms 4.29% std::_Rb_tree::_M_insert_ (inline) 4481ms 4.01% 57.58% 4795ms 4.29% _int_free 1ms 0.00089% 57.58% 4736ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 57.58% 4676ms 4.18% std::_Rb_tree::lower_bound (inline) 0 0% 57.58% 4676ms 4.18% std::map::lower_bound (inline) 59ms 0.053% 57.64% 4611ms 4.12% std::set_intersection (inline) 282ms 0.25% 57.89% 4552ms 4.07% std::__set_intersection 125ms 0.11% 58.00% 4187ms 3.75% AbstractCellPopulation::GetCellUsingLocationIndex 3978ms 3.56% 61.56% 3978ms 3.56% boost::numeric::ublas::same_impl_ex 48ms 0.043% 61.60% 3964ms 3.55% Cell::GetCellProliferativeType 64ms 0.057% 61.66% 3793ms 3.39% AbstractCellProperty::IsType (inline) 49ms 0.044% 61.70% 3658ms 3.27% std::_Rb_tree::erase 7ms 0.0063% 61.71% 3593ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 61.71% 3436ms 3.07% std::insert_iterator::operator= (inline) 2291ms 2.05% 63.76% 3311ms 2.96% _int_malloc 35ms 0.031% 63.79% 3216ms 2.88% Cell::SetCellProliferativeType 3176ms 2.84% 66.63% 3176ms 2.84% std::_Rb_tree::_S_right (inline) 791ms 0.71% 67.34% 3152ms 2.82% AbstractElement::GetNodeLocation 7ms 0.0063% 67.34% 2979ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 381ms 0.34% 67.68% 2859ms 2.56% std::_Rb_tree_const_iterator::operator++ (inline) 708ms 0.63% 68.32% 2837ms 2.54% boost::numeric::ublas::vector_binary::size (inline) 769ms 0.69% 69.01% 2717ms 2.43% AbstractCellProperty::IsSame 53ms 0.047% 69.05% 2643ms 2.36% CellPropertyCollection::HasProperty 1ms 0.00089% 69.05% 2600ms 2.33% std::_Rb_tree::_M_insert_unique (inline) 1717ms 1.54% 70.59% 2564ms 2.29% std::_Rb_tree::equal_range (inline) 276ms 0.25% 70.84% 2554ms 2.28% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.84% 2524ms 2.26% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.84% 2518ms 2.25% Cell::HasCellProperty (inline) 29ms 0.026% 70.86% 2507ms 2.24% Cell::GetCellData 0 0% 70.86% 2494ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.86% 2413ms 2.16% boost::numeric::ublas::c_vector::operator-= (inline) 109ms 0.098% 70.96% 2360ms 2.11% VertexMesh::GetVolumeOfElement 4ms 0.0036% 70.96% 2279ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 2278ms 2.04% 73.00% 2278ms 2.04% std::_Rb_tree_increment 111ms 0.099% 73.10% 2274ms 2.03% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 243ms 0.22% 73.32% 2265ms 2.03% AbstractCellPopulation::Iterator::IsRealCell 52ms 0.047% 73.37% 2242ms 2.01% std::_Rb_tree::_M_emplace_hint_unique 0 0% 73.37% 2080ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.37% 2079ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 492ms 0.44% 73.81% 1948ms 1.74% std::type_info::operator== (inline) 0 0% 73.81% 1894ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.81% 1894ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.81% 1849ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 69ms 0.062% 73.87% 1844ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 36ms 0.032% 73.90% 1729ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.046% 73.94% 1691ms 1.51% Node::RemoveElement 20ms 0.018% 73.96% 1652ms 1.48% std::set::erase (inline) 16ms 0.014% 73.98% 1595ms 1.43% VertexMesh::GetSurfaceAreaOfElement 174ms 0.16% 74.13% 1587ms 1.42% CellPropertyCollection::AddProperty 128ms 0.11% 74.25% 1562ms 1.40% boost::numeric::ublas::vector_reference::operator() (inline) 24ms 0.021% 74.27% 1550ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 72ms 0.064% 74.33% 1520ms 1.36% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.33% 1432ms 1.28% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.33% 1416ms 1.27% tcache_get (inline) 1416ms 1.27% 75.60% 1416ms 1.27% tcache_get_n (inline) 0 0% 75.60% 1314ms 1.18% OffLatticeSimulation::ApplyBoundaries 90ms 0.081% 75.68% 1266ms 1.13% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.68% 1263ms 1.13% std::_Rb_tree::clear (inline) 0 0% 75.68% 1253ms 1.12% std::map::clear (inline) 70ms 0.063% 75.74% 1250ms 1.12% std::less::operator() (inline) 0 0% 75.74% 1245ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 109ms 0.098% 75.84% 1197ms 1.07% std::_Rb_tree::find (inline) 1191ms 1.07% 76.91% 1191ms 1.07% [libchaste_cell_based.so] 945ms 0.85% 77.75% 1180ms 1.06% std::operator< (inline) 0 0% 77.75% 1154ms 1.03% boost::numeric::ublas::norm_2 (inline) 511ms 0.46% 78.21% 1149ms 1.03% boost::numeric::ublas::vector_norm_2::apply 19ms 0.017% 78.23% 1129ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1106ms 0.99% 79.21% 1106ms 0.99% Node::rGetLocation 1090ms 0.98% 80.19% 1090ms 0.98% std::_Rb_tree_insert_and_rebalance 6ms 0.0054% 80.20% 1088ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 29ms 0.026% 80.22% 1083ms 0.97% CellPropertyRegistry::Get 492ms 0.44% 80.66% 1044ms 0.93% Edge::GetMapIndex 14ms 0.013% 80.67% 1032ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 196ms 0.18% 80.85% 1005ms 0.9% boost::numeric::ublas::detail::equals 989ms 0.88% 81.73% 989ms 0.88% std::vector::size (inline) 130ms 0.12% 81.85% 981ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.85% 981ms 0.88% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.85% 963ms 0.86% std::map::find (inline) 928ms 0.83% 82.68% 928ms 0.83% [libchaste_mesh.so] 0 0% 82.68% 920ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.0098% 82.69% 920ms 0.82% boost::numeric::ublas::c_vector::swap 86ms 0.077% 82.77% 909ms 0.81% std::swap_ranges (inline) 0 0% 82.77% 859ms 0.77% VertexMeshWriter::MakeVtkMesh 182ms 0.16% 82.93% 828ms 0.74% boost::shared_ptr::shared_ptr (inline) 143ms 0.13% 83.06% 828ms 0.74% std::__new_allocator::construct (inline) 0 0% 83.06% 828ms 0.74% std::allocator_traits::construct (inline) 824ms 0.74% 83.79% 824ms 0.74% std::swap (inline) 0 0% 83.79% 823ms 0.74% std::iter_swap (inline) 816ms 0.73% 84.52% 818ms 0.73% boost::detail::sp_counted_base::release 23ms 0.021% 84.55% 813ms 0.73% MutableElement::RegisterWithEdges (inline) 33ms 0.03% 84.57% 810ms 0.72% Edge::AddElement 102ms 0.091% 84.67% 782ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 103ms 0.092% 84.76% 781ms 0.7% MutableElement::GetNodeLocalIndex 0 0% 84.76% 776ms 0.69% std::_Rb_tree::_M_construct_node (inline) 0 0% 84.76% 741ms 0.66% boost::numeric::ublas::norm_inf (inline) 401ms 0.36% 85.12% 741ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.12% 717ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.12% 715ms 0.64% std::_Vector_base::_M_allocate (inline) 712ms 0.64% 85.75% 712ms 0.64% Node::GetIndex 427ms 0.38% 86.14% 710ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 611ms 0.55% 86.68% 646ms 0.58% boost::detail::shared_count::shared_count (inline) 81ms 0.072% 86.75% 644ms 0.58% std::_Rb_tree::_M_upper_bound (inline) 0 0% 86.75% 637ms 0.57% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.017% 86.77% 637ms 0.57% std::_Rb_tree::_M_insert_node (inline) 630ms 0.56% 87.34% 630ms 0.56% operator delete 628ms 0.56% 87.90% 628ms 0.56% [libstdc++.so.6.0.33] 0 0% 87.90% 619ms 0.55% std::map::map (inline) 17ms 0.015% 87.91% 618ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.91% 618ms 0.55% boost::numeric::ublas::vector::vector (inline) 0 0% 87.91% 602ms 0.54% vtkPolygon::New 3ms 0.0027% 87.91% 602ms 0.54% vtkPolygon::vtkPolygon 586ms 0.52% 88.44% 586ms 0.52% boost::shared_ptr::operator-> (inline) 13ms 0.012% 88.45% 582ms 0.52% std::vector::_M_default_append (inline) 29ms 0.026% 88.48% 571ms 0.51% MutableElement::RegisterWithNodes (inline)