File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95240ms, 88.17% of 108013ms total Dropped 1095 nodes (cum <= 540.07ms) flat flat% sum% cum cum% 0 0% 0% 107550ms 99.57% __libc_start_call_main 0 0% 0% 107550ms 99.57% __libc_start_main_impl 0 0% 0% 107550ms 99.57% _start 0 0% 0% 107531ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107531ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107531ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107531ms 99.55% main 0 0% 0% 107491ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107491ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107491ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 107483ms 99.51% AbstractCellBasedSimulation::Solve 19ms 0.018% 0.02% 55921ms 51.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.018% 0.038% 52584ms 48.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 148ms 0.14% 0.17% 51461ms 47.64% AbstractNumericalMethod::ComputeForcesIncludingDamping 380ms 0.35% 0.53% 40095ms 37.12% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.53% 38946ms 36.06% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.53% 24115ms 22.33% VertexBasedCellPopulation::Update 0 0% 0.53% 24000ms 22.22% MutableVertexMesh::ReMesh 14634ms 13.55% 14.08% 23119ms 21.40% Cylindrical2dVertexMesh::GetVectorFromAtoB 89ms 0.082% 14.16% 17293ms 16.01% Cell::ReadyToDivide 67ms 0.062% 14.22% 16095ms 14.90% AbstractPhaseBasedCellCycleModel::ReadyToDivide 333ms 0.31% 14.53% 14856ms 13.75% NagaiHondaForce::GetAdhesionParameter 388ms 0.36% 14.89% 14661ms 13.57% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.1% 14.99% 13609ms 12.60% SimpleWntCellCycleModel::UpdateCellCyclePhase 120ms 0.11% 15.10% 13313ms 12.33% CellPropertyCollection::GetPropertiesType (inline) 325ms 0.3% 15.41% 13160ms 12.18% boost::numeric::ublas::vector_assign (inline) 122ms 0.11% 15.52% 12041ms 11.15% MutableVertexMesh::CheckForIntersections 3100ms 2.87% 18.39% 10937ms 10.13% __dynamic_cast 96ms 0.089% 18.48% 10873ms 10.07% AbstractCellProperty::IsSubType (inline) 68ms 0.063% 18.54% 10869ms 10.06% VertexBasedCellPopulation::GetDampingConstant 77ms 0.071% 18.61% 10240ms 9.48% AbstractTargetAreaModifier::UpdateTargetAreas 19ms 0.018% 18.63% 10195ms 9.44% AbstractCellBasedSimulation::DoCellBirth 64ms 0.059% 18.69% 10143ms 9.39% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1344ms 1.24% 19.93% 9924ms 9.19% std::__new_allocator::allocate (inline) 2739ms 2.54% 22.47% 9780ms 9.05% boost::numeric::ublas::indexing_vector_assign 0 0% 22.47% 9427ms 8.73% std::allocator_traits::allocate (inline) 0 0% 22.47% 9409ms 8.71% std::_Rb_tree::_M_create_node (inline) 1381ms 1.28% 23.75% 9213ms 8.53% std::_Rb_tree::_M_erase 334ms 0.31% 24.06% 8881ms 8.22% VertexMesh::GetNextEdgeGradientOfElementAtNode 788ms 0.73% 24.79% 8876ms 8.22% VertexMesh::ElementIncludesPoint 0 0% 24.79% 8773ms 8.12% std::_Rb_tree::_M_get_node (inline) 24ms 0.022% 24.81% 8669ms 8.03% VertexBasedCellPopulation::GetLocationOfCellCentre 739ms 0.68% 25.49% 8619ms 7.98% operator new 192ms 0.18% 25.67% 8321ms 7.70% std::_Rb_tree::~_Rb_tree (inline) 56ms 0.052% 25.72% 8297ms 7.68% Cell::GetMutationState 0 0% 25.72% 8253ms 7.64% std::_Rb_tree::_Alloc_node::operator() (inline) 445ms 0.41% 26.13% 8241ms 7.63% VertexMesh::GetCentroidOfElement 0 0% 26.13% 8210ms 7.60% std::_Rb_tree::_M_drop_node (inline) 232ms 0.21% 26.35% 8008ms 7.41% std::__new_allocator::deallocate (inline) 0 0% 26.35% 7977ms 7.39% std::allocator_traits::deallocate (inline) 3320ms 3.07% 29.42% 7969ms 7.38% __GI___libc_free 0 0% 29.42% 7930ms 7.34% std::_Rb_tree::_M_put_node (inline) 0 0% 29.42% 7861ms 7.28% std::set::~set (inline) 2995ms 2.77% 32.20% 7681ms 7.11% __GI___libc_malloc 16ms 0.015% 32.21% 7462ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 1448ms 1.34% 33.55% 7349ms 6.80% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 452ms 0.42% 33.97% 7234ms 6.70% std::map::operator[] (partial-inline) 160ms 0.15% 34.12% 6710ms 6.21% std::_Rb_tree::_Rb_tree (partial-inline) 666ms 0.62% 34.73% 6334ms 5.86% std::_Rb_tree::_M_copy (inline) 10ms 0.0093% 34.74% 6297ms 5.83% std::set::set (inline) 129ms 0.12% 34.86% 6248ms 5.78% SimpleWntCellCycleModel::GetWntLevel 6236ms 5.77% 40.64% 6236ms 5.77% __strcmp_avx2 6191ms 5.73% 46.37% 6191ms 5.73% boost::numeric::ublas::c_vector::operator() 147ms 0.14% 46.50% 6034ms 5.59% WntConcentration::GetWntLevel 2441ms 2.26% 48.76% 5768ms 5.34% std::_Rb_tree::_M_lower_bound (inline) 0 0% 48.76% 5599ms 5.18% std::set::insert (inline) 2653ms 2.46% 51.22% 5485ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 704ms 0.65% 51.87% 5393ms 4.99% std::_Rb_tree::_M_clone_node (inline) 23ms 0.021% 51.89% 5278ms 4.89% MutableVertexMesh::RemoveDeletedNodes 31ms 0.029% 51.92% 5132ms 4.75% EdgeHelper::RemoveDeletedEdges 34ms 0.031% 51.95% 4872ms 4.51% EdgeHelper::UpdateEdgesMapKey 1472ms 1.36% 53.32% 4752ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 606ms 0.56% 53.88% 4700ms 4.35% std::_Rb_tree::_M_insert_ (inline) 201ms 0.19% 54.06% 4681ms 4.33% MutableElement::ResetIndex 55ms 0.051% 54.11% 4676ms 4.33% std::set_intersection (inline) 4327ms 4.01% 58.12% 4646ms 4.30% _int_free 0 0% 58.12% 4645ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 58.12% 4645ms 4.30% std::map::lower_bound (inline) 0 0% 58.12% 4628ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 266ms 0.25% 58.37% 4621ms 4.28% std::__set_intersection 35ms 0.032% 58.40% 4079ms 3.78% Cell::GetCellProliferativeType 4071ms 3.77% 62.17% 4071ms 3.77% boost::numeric::ublas::same_impl_ex 103ms 0.095% 62.26% 3980ms 3.68% AbstractCellPopulation::GetCellUsingLocationIndex 58ms 0.054% 62.32% 3615ms 3.35% AbstractCellProperty::IsType (inline) 16ms 0.015% 62.33% 3546ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.33% 3386ms 3.13% std::insert_iterator::operator= (inline) 53ms 0.049% 62.38% 3195ms 2.96% Cell::SetCellProliferativeType 2255ms 2.09% 64.47% 3118ms 2.89% _int_malloc 714ms 0.66% 65.13% 3093ms 2.86% AbstractElement::GetNodeLocation 5ms 0.0046% 65.13% 3006ms 2.78% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.035% 65.17% 2987ms 2.77% std::_Rb_tree::erase 584ms 0.54% 65.71% 2767ms 2.56% boost::numeric::ublas::vector_binary::size (inline) 2767ms 2.56% 68.27% 2767ms 2.56% std::_Rb_tree::_S_right (inline) 408ms 0.38% 68.65% 2756ms 2.55% std::_Rb_tree_const_iterator::operator++ (inline) 249ms 0.23% 68.88% 2600ms 2.41% VertexMesh::GetAreaGradientOfElementAtNode 1ms 0.00093% 68.88% 2593ms 2.40% std::_Rb_tree::_M_insert_unique 738ms 0.68% 69.56% 2590ms 2.40% AbstractCellProperty::IsSame 0 0% 69.56% 2564ms 2.37% boost::numeric::ublas::c_vector::operator-= (inline) 47ms 0.044% 69.61% 2500ms 2.31% CellPropertyCollection::HasProperty 0 0% 69.61% 2449ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 98ms 0.091% 69.70% 2400ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.70% 2382ms 2.21% Cell::HasCellProperty (inline) 0 0% 69.70% 2355ms 2.18% AbstractCellPopulation::WriteResultsToFiles 24ms 0.022% 69.72% 2275ms 2.11% Cell::GetCellData 118ms 0.11% 69.83% 2260ms 2.09% VertexMesh::GetVolumeOfElement 7ms 0.0065% 69.84% 2182ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 2172ms 2.01% 71.85% 2172ms 2.01% std::_Rb_tree_increment 184ms 0.17% 72.02% 2145ms 1.99% AbstractCellPopulation::Iterator::IsRealCell 34ms 0.031% 72.05% 2088ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 1384ms 1.28% 73.33% 2024ms 1.87% std::_Rb_tree::equal_range (inline) 1ms 0.00093% 73.33% 2009ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.33% 2009ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 73.33% 1944ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 85ms 0.079% 73.41% 1940ms 1.80% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00093% 73.41% 1927ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 432ms 0.4% 73.81% 1852ms 1.71% std::type_info::operator== (inline) 0 0% 73.81% 1725ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 35ms 0.032% 73.84% 1680ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 22ms 0.02% 73.86% 1636ms 1.51% VertexMesh::GetSurfaceAreaOfElement 172ms 0.16% 74.02% 1566ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 150ms 0.14% 74.16% 1558ms 1.44% CellPropertyCollection::AddProperty 34ms 0.031% 74.19% 1545ms 1.43% Node::RemoveElement 19ms 0.018% 74.21% 1525ms 1.41% std::set::erase (inline) 0 0% 74.21% 1498ms 1.39% boost::numeric::ublas::vector_binary::operator() (inline) 76ms 0.07% 74.28% 1480ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 30ms 0.028% 74.31% 1479ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.31% 1446ms 1.34% OffLatticeSimulation::ApplyBoundaries 0 0% 74.31% 1405ms 1.30% tcache_get (inline) 1405ms 1.30% 75.61% 1405ms 1.30% tcache_get_n (inline) 0 0% 75.61% 1216ms 1.13% boost::numeric::ublas::norm_2 (inline) 533ms 0.49% 76.10% 1207ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 104ms 0.096% 76.20% 1193ms 1.10% std::less::operator() (inline) 1177ms 1.09% 77.29% 1177ms 1.09% Node::rGetLocation 0 0% 77.29% 1156ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1145ms 1.06% 78.35% 1145ms 1.06% [libchaste_cell_based.so] 97ms 0.09% 78.44% 1128ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 96ms 0.089% 78.53% 1099ms 1.02% std::_Rb_tree::find (inline) 1093ms 1.01% 79.54% 1093ms 1.01% std::_Rb_tree_insert_and_rebalance 881ms 0.82% 80.36% 1089ms 1.01% std::operator< (inline) 0 0% 80.36% 1084ms 1.00% std::_Rb_tree::clear (inline) 21ms 0.019% 80.37% 1078ms 1% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.37% 1076ms 1% std::map::clear (inline) 23ms 0.021% 80.40% 1060ms 0.98% boost::numeric::ublas::detail::expression_type_check (inline) 195ms 0.18% 80.58% 1032ms 0.96% boost::numeric::ublas::detail::equals 30ms 0.028% 80.60% 1024ms 0.95% CellPropertyRegistry::Get 8ms 0.0074% 80.61% 1019ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 998ms 0.92% 81.54% 998ms 0.92% [libchaste_mesh.so] 947ms 0.88% 82.41% 947ms 0.88% std::vector::size (inline) 148ms 0.14% 82.55% 938ms 0.87% boost::detail::shared_count::~shared_count (inline) 0 0% 82.55% 938ms 0.87% boost::shared_ptr::~shared_ptr (inline) 390ms 0.36% 82.91% 919ms 0.85% Edge::GetMapIndex 0 0% 82.91% 917ms 0.85% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0065% 82.92% 917ms 0.85% boost::numeric::ublas::c_vector::swap (inline) 90ms 0.083% 83.00% 910ms 0.84% std::swap_ranges (inline) 0 0% 83.00% 885ms 0.82% std::map::find (inline) 98ms 0.091% 83.09% 855ms 0.79% MutableElement::GetNodeLocalIndex 178ms 0.16% 83.26% 824ms 0.76% boost::shared_ptr::shared_ptr (inline) 0 0% 83.26% 820ms 0.76% std::iter_swap (inline) 820ms 0.76% 84.01% 820ms 0.76% std::swap (inline) 1ms 0.00093% 84.02% 819ms 0.76% VertexMeshWriter::MakeVtkMesh 0 0% 84.02% 793ms 0.73% boost::numeric::ublas::norm_inf (inline) 418ms 0.39% 84.40% 793ms 0.73% boost::numeric::ublas::vector_norm_inf::apply (inline) 17ms 0.016% 84.42% 780ms 0.72% MutableElement::RegisterWithEdges (inline) 24ms 0.022% 84.44% 775ms 0.72% Edge::AddElement 763ms 0.71% 85.15% 767ms 0.71% boost::detail::sp_counted_base::release 111ms 0.1% 85.25% 753ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 746ms 0.69% 85.94% 746ms 0.69% Node::GetIndex 482ms 0.45% 86.39% 737ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.39% 699ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 82ms 0.076% 86.46% 683ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.46% 683ms 0.63% std::allocator_traits::construct (inline) 0 0% 86.46% 650ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 25ms 0.023% 86.49% 650ms 0.6% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.49% 650ms 0.6% std::_Vector_base::_M_allocate (inline) 621ms 0.57% 87.06% 646ms 0.6% boost::detail::shared_count::shared_count (inline) 0 0% 87.06% 636ms 0.59% std::_Rb_tree::_M_construct_node (inline) 38ms 0.035% 87.10% 597ms 0.55% MutableElement::RegisterWithNodes (inline) 0 0% 87.10% 589ms 0.55% vtkPolygon::New 0 0% 87.10% 589ms 0.55% vtkPolygon::vtkPolygon 0 0% 87.10% 587ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 568ms 0.53% 87.62% 568ms 0.53% [libstdc++.so.6.0.33] 8ms 0.0074% 87.63% 565ms 0.52% std::vector::_M_default_append (inline) 560ms 0.52% 88.15% 560ms 0.52% boost::shared_ptr::operator-> (inline) 29ms 0.027% 88.17% 555ms 0.51% Node::AddElement