File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97693ms, 88.89% of 109903ms total Dropped 1020 nodes (cum <= 549.51ms) flat flat% sum% cum cum% 0 0% 0% 109426ms 99.57% __libc_start_call_main 0 0% 0% 109426ms 99.57% __libc_start_main_impl 0 0% 0% 109426ms 99.57% _start 0 0% 0% 109407ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109407ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109407ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109407ms 99.55% main 0 0% 0% 109370ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109370ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109370ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 7ms 0.0064% 0.0064% 109363ms 99.51% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.016% 56996ms 51.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.015% 0.032% 53844ms 48.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 137ms 0.12% 0.16% 52860ms 48.10% AbstractNumericalMethod::ComputeForcesIncludingDamping 386ms 0.35% 0.51% 40679ms 37.01% NagaiHondaForce::AddForceContribution 0 0% 0.51% 39488ms 35.93% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.51% 24393ms 22.20% VertexBasedCellPopulation::Update 0 0% 0.51% 24266ms 22.08% MutableVertexMesh::ReMesh 14399ms 13.10% 13.61% 22949ms 20.88% Cylindrical2dVertexMesh::GetVectorFromAtoB 77ms 0.07% 13.68% 17583ms 16.00% Cell::ReadyToDivide 90ms 0.082% 13.76% 16443ms 14.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 334ms 0.3% 14.07% 15416ms 14.03% NagaiHondaForce::GetAdhesionParameter 418ms 0.38% 14.45% 14228ms 12.95% boost::numeric::ublas::c_vector::c_vector (partial-inline) 131ms 0.12% 14.57% 14014ms 12.75% CellPropertyCollection::GetPropertiesType (inline) 122ms 0.11% 14.68% 13931ms 12.68% SimpleWntCellCycleModel::UpdateCellCyclePhase 418ms 0.38% 15.06% 12671ms 11.53% boost::numeric::ublas::vector_assign (inline) 127ms 0.12% 15.17% 12029ms 10.95% MutableVertexMesh::CheckForIntersections 68ms 0.062% 15.23% 11661ms 10.61% VertexBasedCellPopulation::GetDampingConstant 3591ms 3.27% 18.50% 11633ms 10.58% __dynamic_cast 85ms 0.077% 18.58% 11517ms 10.48% AbstractCellProperty::IsSubType (inline) 124ms 0.11% 18.69% 10554ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 1409ms 1.28% 19.97% 10520ms 9.57% std::__new_allocator::allocate (inline) 36ms 0.033% 20.01% 10427ms 9.49% AbstractCellBasedSimulation::DoCellBirth 32ms 0.029% 20.04% 10410ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 20.04% 9901ms 9.01% std::allocator_traits::allocate (inline) 0 0% 20.04% 9881ms 8.99% std::_Rb_tree::_M_create_node (inline) 2545ms 2.32% 22.35% 9428ms 8.58% boost::numeric::ublas::indexing_vector_assign 1377ms 1.25% 23.60% 9318ms 8.48% std::_Rb_tree::_M_erase 0 0% 23.60% 9231ms 8.40% std::_Rb_tree::_M_get_node (inline) 812ms 0.74% 24.34% 9212ms 8.38% operator new 394ms 0.36% 24.70% 9059ms 8.24% VertexMesh::GetNextEdgeGradientOfElementAtNode 75ms 0.068% 24.77% 8992ms 8.18% Cell::GetMutationState 755ms 0.69% 25.46% 8958ms 8.15% VertexMesh::ElementIncludesPoint 33ms 0.03% 25.49% 8848ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.49% 8700ms 7.92% std::_Rb_tree::_Alloc_node::operator() (inline) 224ms 0.2% 25.69% 8487ms 7.72% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.69% 8301ms 7.55% std::_Rb_tree::_M_drop_node (inline) 505ms 0.46% 26.15% 8223ms 7.48% VertexMesh::GetCentroidOfElement 3134ms 2.85% 29.00% 8214ms 7.47% __GI___libc_malloc 523ms 0.48% 29.48% 8120ms 7.39% std::map::operator[] (partial-inline) 242ms 0.22% 29.70% 8044ms 7.32% std::__new_allocator::deallocate (inline) 0 0% 29.70% 8031ms 7.31% std::set::~set (inline) 0 0% 29.70% 8013ms 7.29% std::allocator_traits::deallocate (inline) 0 0% 29.70% 7962ms 7.24% std::_Rb_tree::_M_put_node (inline) 3077ms 2.80% 32.50% 7783ms 7.08% __GI___libc_free 15ms 0.014% 32.51% 7707ms 7.01% MutableVertexMesh::RemoveDeletedNodesAndElements 132ms 0.12% 32.63% 7215ms 6.56% std::_Rb_tree::_Rb_tree (partial-inline) 1286ms 1.17% 33.80% 7176ms 6.53% AbstractMesh::GetDistanceBetweenNodes 742ms 0.68% 34.48% 6843ms 6.23% std::_Rb_tree::_M_copy (inline) 11ms 0.01% 34.49% 6785ms 6.17% std::set::set (inline) 2493ms 2.27% 36.76% 6509ms 5.92% std::_Rb_tree::_M_lower_bound (inline) 121ms 0.11% 36.87% 6408ms 5.83% SimpleWntCellCycleModel::GetWntLevel 6298ms 5.73% 42.60% 6298ms 5.73% boost::numeric::ublas::c_vector::operator() 6221ms 5.66% 48.26% 6221ms 5.66% __strcmp_avx2 127ms 0.12% 48.37% 6201ms 5.64% WntConcentration::GetWntLevel 825ms 0.75% 49.12% 5847ms 5.32% std::_Rb_tree::_M_clone_node (inline) 2765ms 2.52% 51.64% 5595ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.025% 51.66% 5525ms 5.03% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.66% 5490ms 5.00% std::set::insert (inline) 42ms 0.038% 51.70% 5362ms 4.88% EdgeHelper::RemoveDeletedEdges 0 0% 51.70% 5325ms 4.85% std::_Rb_tree::lower_bound (inline) 0 0% 51.70% 5325ms 4.85% std::map::lower_bound (inline) 22ms 0.02% 51.72% 5095ms 4.64% EdgeHelper::UpdateEdgesMapKey 1471ms 1.34% 53.06% 4862ms 4.42% boost::numeric::ublas::c_vector::operator[] (inline) 208ms 0.19% 53.25% 4789ms 4.36% MutableElement::ResetIndex 4393ms 4.00% 57.25% 4701ms 4.28% _int_free 504ms 0.46% 57.70% 4680ms 4.26% std::_Rb_tree::_M_insert_ (inline) 43ms 0.039% 57.74% 4660ms 4.24% std::set_intersection (inline) 2ms 0.0018% 57.75% 4654ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 251ms 0.23% 57.97% 4617ms 4.20% std::__set_intersection 119ms 0.11% 58.08% 4439ms 4.04% AbstractCellPopulation::GetCellUsingLocationIndex 60ms 0.055% 58.14% 4068ms 3.70% Cell::GetCellProliferativeType 3991ms 3.63% 61.77% 3991ms 3.63% boost::numeric::ublas::same_impl_ex 9ms 0.0082% 61.78% 3558ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 76ms 0.069% 61.85% 3542ms 3.22% AbstractCellProperty::IsType (inline) 0 0% 61.85% 3352ms 3.05% std::insert_iterator::operator= (inline) 3325ms 3.03% 64.87% 3325ms 3.03% std::_Rb_tree::_S_right (inline) 811ms 0.74% 65.61% 3227ms 2.94% AbstractElement::GetNodeLocation 2344ms 2.13% 67.74% 3205ms 2.92% _int_malloc 56ms 0.051% 67.79% 3195ms 2.91% Cell::SetCellProliferativeType 43ms 0.039% 67.83% 3092ms 2.81% std::_Rb_tree::erase 4ms 0.0036% 67.84% 2943ms 2.68% std::_Rb_tree::_M_insert_unique_ (inline) 379ms 0.34% 68.18% 2851ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 618ms 0.56% 68.74% 2808ms 2.55% boost::numeric::ublas::vector_binary::size (inline) 3ms 0.0027% 68.75% 2547ms 2.32% std::_Rb_tree::_M_insert_unique 706ms 0.64% 69.39% 2485ms 2.26% AbstractCellProperty::IsSame 46ms 0.042% 69.43% 2469ms 2.25% CellPropertyCollection::HasProperty 215ms 0.2% 69.63% 2459ms 2.24% VertexMesh::GetAreaGradientOfElementAtNode 118ms 0.11% 69.73% 2402ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.73% 2388ms 2.17% AbstractCellPopulation::Iterator::operator++ (inline) 209ms 0.19% 69.92% 2377ms 2.16% AbstractCellPopulation::Iterator::IsRealCell 0 0% 69.92% 2368ms 2.15% Cell::HasCellProperty (inline) 0 0% 69.92% 2367ms 2.15% boost::numeric::ublas::c_vector::assign (inline) 24ms 0.022% 69.94% 2357ms 2.14% Cell::GetCellData 0 0% 69.94% 2318ms 2.11% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.94% 2293ms 2.09% AbstractCellPopulation::WriteResultsToFiles 2290ms 2.08% 72.03% 2290ms 2.08% std::_Rb_tree_increment 86ms 0.078% 72.11% 2252ms 2.05% VertexMesh::GetVolumeOfElement 37ms 0.034% 72.14% 2218ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 1461ms 1.33% 73.47% 2149ms 1.96% std::_Rb_tree::equal_range (inline) 38ms 0.035% 73.50% 1900ms 1.73% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.50% 1882ms 1.71% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.50% 1871ms 1.70% VertexBasedCellPopulation::WriteCellVtkResultsToFile 59ms 0.054% 73.56% 1866ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.56% 1786ms 1.63% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.56% 1786ms 1.63% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 437ms 0.4% 73.96% 1779ms 1.62% std::type_info::operator== (inline) 0 0% 73.96% 1694ms 1.54% VertexMeshWriter::WriteVtkUsingMesh 0 0% 73.96% 1674ms 1.52% tcache_get (inline) 1674ms 1.52% 75.48% 1674ms 1.52% tcache_get_n (inline) 39ms 0.035% 75.51% 1647ms 1.50% Node::RemoveElement 90ms 0.082% 75.60% 1637ms 1.49% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 17ms 0.015% 75.61% 1632ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 15ms 0.014% 75.62% 1620ms 1.47% std::set::erase (inline) 24ms 0.022% 75.65% 1611ms 1.47% VertexMesh::GetSurfaceAreaOfElement 118ms 0.11% 75.75% 1531ms 1.39% boost::numeric::ublas::vector_reference::operator() (inline) 179ms 0.16% 75.92% 1522ms 1.38% CellPropertyCollection::AddProperty 0 0% 75.92% 1384ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 68ms 0.062% 75.98% 1352ms 1.23% std::less::operator() (inline) 1051ms 0.96% 76.94% 1284ms 1.17% std::operator< (inline) 1ms 0.00091% 76.94% 1271ms 1.16% OffLatticeSimulation::ApplyBoundaries 1221ms 1.11% 78.05% 1221ms 1.11% Node::rGetLocation 0 0% 78.05% 1181ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.05% 1175ms 1.07% boost::numeric::ublas::norm_2 (inline) 522ms 0.47% 78.52% 1172ms 1.07% boost::numeric::ublas::vector_norm_2::apply 114ms 0.1% 78.63% 1162ms 1.06% std::_Rb_tree::find (inline) 70ms 0.064% 78.69% 1117ms 1.02% std::_Rb_tree::_M_erase_aux (partial-inline) 1111ms 1.01% 79.70% 1111ms 1.01% std::_Rb_tree_insert_and_rebalance 18ms 0.016% 79.72% 1095ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1088ms 0.99% 80.71% 1088ms 0.99% [libchaste_cell_based.so] 0 0% 80.71% 1058ms 0.96% std::_Rb_tree::clear (inline) 6ms 0.0055% 80.71% 1043ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.71% 1041ms 0.95% std::map::clear (inline) 992ms 0.9% 81.61% 992ms 0.9% std::vector::size (inline) 150ms 0.14% 81.75% 988ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 81.75% 988ms 0.9% boost::shared_ptr::~shared_ptr (inline) 27ms 0.025% 81.78% 983ms 0.89% CellPropertyRegistry::Get 0 0% 81.78% 980ms 0.89% std::map::find (inline) 955ms 0.87% 82.64% 955ms 0.87% [libchaste_mesh.so] 397ms 0.36% 83.01% 942ms 0.86% Edge::GetMapIndex 0 0% 83.01% 914ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 83.02% 914ms 0.83% boost::numeric::ublas::c_vector::swap (inline) 83ms 0.076% 83.09% 902ms 0.82% std::swap_ranges (inline) 0 0% 83.09% 850ms 0.77% VertexMeshWriter::MakeVtkMesh 25ms 0.023% 83.12% 835ms 0.76% boost::numeric::ublas::detail::expression_type_check (inline) 821ms 0.75% 83.86% 821ms 0.75% std::swap (inline) 0 0% 83.86% 819ms 0.75% std::iter_swap (inline) 127ms 0.12% 83.98% 818ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 804ms 0.73% 84.71% 811ms 0.74% boost::detail::sp_counted_base::release 483ms 0.44% 85.15% 806ms 0.73% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 155ms 0.14% 85.29% 803ms 0.73% boost::numeric::ublas::detail::equals 86ms 0.078% 85.37% 792ms 0.72% MutableElement::GetNodeLocalIndex 766ms 0.7% 86.06% 766ms 0.7% Node::GetIndex 25ms 0.023% 86.09% 755ms 0.69% Edge::AddElement 14ms 0.013% 86.10% 743ms 0.68% MutableElement::RegisterWithEdges (inline) 139ms 0.13% 86.23% 738ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 86.23% 735ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 116ms 0.11% 86.33% 695ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.33% 695ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.33% 680ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 86.35% 680ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.35% 664ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.35% 650ms 0.59% std::_Rb_tree::_M_construct_node (inline) 18ms 0.016% 86.37% 637ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.37% 637ms 0.58% boost::numeric::ublas::vector::vector (inline) 0 0% 86.37% 622ms 0.57% vtkPolygon::New 0 0% 86.37% 621ms 0.57% vtkPolygon::vtkPolygon 25ms 0.023% 86.39% 612ms 0.56% MutableElement::RegisterWithNodes (inline) 612ms 0.56% 86.95% 612ms 0.56% [libstdc++.so.6.0.33] 0 0% 86.95% 611ms 0.56% boost::numeric::ublas::norm_inf (inline) 317ms 0.29% 87.24% 611ms 0.56% boost::numeric::ublas::vector_norm_inf::apply (inline) 601ms 0.55% 87.79% 601ms 0.55% operator delete 600ms 0.55% 88.33% 600ms 0.55% boost::shared_ptr::operator-> (inline) 577ms 0.53% 88.86% 599ms 0.55% boost::detail::shared_count::shared_count (inline) 31ms 0.028% 88.88% 585ms 0.53% Node::AddElement 6ms 0.0055% 88.89% 552ms 0.5% std::vector::_M_default_append (inline)