File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98178ms, 88.63% of 110774ms total Dropped 1109 nodes (cum <= 553.87ms) flat flat% sum% cum cum% 0 0% 0% 110317ms 99.59% __libc_start_call_main 0 0% 0% 110317ms 99.59% __libc_start_main_impl 0 0% 0% 110317ms 99.59% _start 0 0% 0% 110295ms 99.57% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110295ms 99.57% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110295ms 99.57% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110295ms 99.57% main 0 0% 0% 110259ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110259ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110259ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 110252ms 99.53% AbstractCellBasedSimulation::Solve 26ms 0.023% 0.025% 57777ms 52.16% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.015% 0.041% 54561ms 49.25% ForwardEulerNumericalMethod::UpdateAllNodePositions 105ms 0.095% 0.14% 53579ms 48.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 448ms 0.4% 0.54% 41258ms 37.25% NagaiHondaForce::AddForceContribution 0 0% 0.54% 39407ms 35.57% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.54% 24404ms 22.03% VertexBasedCellPopulation::Update 0 0% 0.54% 24261ms 21.90% MutableVertexMesh::ReMesh 14328ms 12.93% 13.47% 23020ms 20.78% Cylindrical2dVertexMesh::GetVectorFromAtoB 92ms 0.083% 13.56% 17589ms 15.88% Cell::ReadyToDivide 69ms 0.062% 13.62% 16396ms 14.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 346ms 0.31% 13.93% 15420ms 13.92% NagaiHondaForce::GetAdhesionParameter 439ms 0.4% 14.33% 14895ms 13.45% boost::numeric::ublas::c_vector::c_vector (partial-inline) 144ms 0.13% 14.46% 14182ms 12.80% CellPropertyCollection::GetPropertiesType (inline) 120ms 0.11% 14.57% 13983ms 12.62% SimpleWntCellCycleModel::UpdateCellCyclePhase 390ms 0.35% 14.92% 13051ms 11.78% boost::numeric::ublas::vector_assign (inline) 130ms 0.12% 15.04% 12081ms 10.91% MutableVertexMesh::CheckForIntersections 82ms 0.074% 15.11% 11865ms 10.71% VertexBasedCellPopulation::GetDampingConstant 3360ms 3.03% 18.14% 11602ms 10.47% __dynamic_cast 87ms 0.079% 18.22% 11471ms 10.36% AbstractCellProperty::IsSubType (inline) 80ms 0.072% 18.29% 10592ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 76ms 0.069% 18.36% 10485ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1324ms 1.20% 19.56% 10432ms 9.42% std::__new_allocator::allocate (inline) 30ms 0.027% 19.58% 10355ms 9.35% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.58% 9902ms 8.94% std::_Rb_tree::_M_create_node (inline) 0 0% 19.58% 9887ms 8.93% std::allocator_traits::allocate (inline) 2805ms 2.53% 22.12% 9749ms 8.80% boost::numeric::ublas::indexing_vector_assign 1549ms 1.40% 23.52% 9743ms 8.80% std::_Rb_tree::_M_erase 0 0% 23.52% 9211ms 8.32% std::_Rb_tree::_M_get_node (inline) 790ms 0.71% 24.23% 9201ms 8.31% operator new 74ms 0.067% 24.30% 9157ms 8.27% Cell::GetMutationState 378ms 0.34% 24.64% 9135ms 8.25% VertexMesh::GetNextEdgeGradientOfElementAtNode 780ms 0.7% 25.34% 8949ms 8.08% VertexMesh::ElementIncludesPoint 197ms 0.18% 25.52% 8914ms 8.05% std::_Rb_tree::~_Rb_tree (inline) 28ms 0.025% 25.54% 8801ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.54% 8677ms 7.83% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.54% 8539ms 7.71% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.54% 8464ms 7.64% std::set::~set (inline) 475ms 0.43% 25.97% 8311ms 7.50% VertexMesh::GetCentroidOfElement 262ms 0.24% 26.21% 8273ms 7.47% std::__new_allocator::deallocate (inline) 0 0% 26.21% 8232ms 7.43% std::allocator_traits::deallocate (inline) 3202ms 2.89% 29.10% 8231ms 7.43% __GI___libc_malloc 0 0% 29.10% 8168ms 7.37% std::_Rb_tree::_M_put_node (inline) 3211ms 2.90% 32.00% 8046ms 7.26% __GI___libc_free 481ms 0.43% 32.43% 7775ms 7.02% std::map::operator[] (partial-inline) 33ms 0.03% 32.46% 7739ms 6.99% MutableVertexMesh::RemoveDeletedNodesAndElements 1431ms 1.29% 33.75% 7413ms 6.69% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 149ms 0.13% 33.89% 7116ms 6.42% std::_Rb_tree::_Rb_tree (partial-inline) 635ms 0.57% 34.46% 6705ms 6.05% std::_Rb_tree::_M_copy (inline) 8ms 0.0072% 34.47% 6647ms 6.00% std::set::set (inline) 6373ms 5.75% 40.22% 6373ms 5.75% __strcmp_avx2 103ms 0.093% 40.32% 6359ms 5.74% SimpleWntCellCycleModel::GetWntLevel 156ms 0.14% 40.46% 6160ms 5.56% WntConcentration::GetWntLevel 2511ms 2.27% 42.72% 6082ms 5.49% std::_Rb_tree::_M_lower_bound (inline) 6074ms 5.48% 48.21% 6074ms 5.48% boost::numeric::ublas::c_vector::operator() 802ms 0.72% 48.93% 5784ms 5.22% std::_Rb_tree::_M_clone_node (inline) 2849ms 2.57% 51.50% 5754ms 5.19% __cxxabiv1::__si_class_type_info::__do_dyncast 23ms 0.021% 51.52% 5544ms 5.00% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.52% 5524ms 4.99% std::set::insert (inline) 38ms 0.034% 51.56% 5372ms 4.85% EdgeHelper::RemoveDeletedEdges 33ms 0.03% 51.59% 5097ms 4.60% EdgeHelper::UpdateEdgesMapKey 0 0% 51.59% 4988ms 4.50% std::_Rb_tree::lower_bound (inline) 0 0% 51.59% 4988ms 4.50% std::map::lower_bound (inline) 4453ms 4.02% 55.61% 4826ms 4.36% _int_free 1472ms 1.33% 56.94% 4769ms 4.31% boost::numeric::ublas::c_vector::operator[] (inline) 200ms 0.18% 57.12% 4749ms 4.29% MutableElement::ResetIndex 499ms 0.45% 57.57% 4702ms 4.24% std::_Rb_tree::_M_insert_ (inline) 3ms 0.0027% 57.57% 4634ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 65ms 0.059% 57.63% 4562ms 4.12% std::set_intersection (inline) 199ms 0.18% 57.81% 4497ms 4.06% std::__set_intersection 95ms 0.086% 57.89% 4227ms 3.82% AbstractCellPopulation::GetCellUsingLocationIndex 4188ms 3.78% 61.67% 4188ms 3.78% boost::numeric::ublas::same_impl_ex 30ms 0.027% 61.70% 3878ms 3.50% Cell::GetCellProliferativeType 72ms 0.065% 61.77% 3710ms 3.35% AbstractCellProperty::IsType (inline) 5ms 0.0045% 61.77% 3565ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 855ms 0.77% 62.54% 3313ms 2.99% AbstractElement::GetNodeLocation 2383ms 2.15% 64.69% 3258ms 2.94% _int_malloc 0 0% 64.69% 3255ms 2.94% std::insert_iterator::operator= (inline) 812ms 0.73% 65.43% 3186ms 2.88% boost::numeric::ublas::vector_binary::size (inline) 45ms 0.041% 65.47% 3139ms 2.83% Cell::SetCellProliferativeType 48ms 0.043% 65.51% 3047ms 2.75% std::_Rb_tree::erase 440ms 0.4% 65.91% 3038ms 2.74% std::_Rb_tree_const_iterator::operator++ (inline) 2979ms 2.69% 68.60% 2979ms 2.69% std::_Rb_tree::_S_right (inline) 4ms 0.0036% 68.60% 2826ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 4ms 0.0036% 68.60% 2698ms 2.44% std::_Rb_tree::_M_insert_unique (inline) 754ms 0.68% 69.29% 2603ms 2.35% AbstractCellProperty::IsSame 38ms 0.034% 69.32% 2576ms 2.33% CellPropertyCollection::HasProperty 239ms 0.22% 69.54% 2535ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.54% 2473ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.54% 2454ms 2.22% Cell::HasCellProperty (inline) 0 0% 69.54% 2451ms 2.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.54% 2448ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 2409ms 2.17% 71.71% 2409ms 2.17% std::_Rb_tree_increment 28ms 0.025% 71.74% 2405ms 2.17% Cell::GetCellData 124ms 0.11% 71.85% 2329ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 71.85% 2293ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 224ms 0.2% 72.05% 2284ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 31ms 0.028% 72.08% 2238ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 84ms 0.076% 72.16% 2226ms 2.01% VertexMesh::GetVolumeOfElement 1410ms 1.27% 73.43% 2059ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 73.43% 2032ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.43% 2020ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 4ms 0.0036% 73.43% 1941ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.43% 1941ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 499ms 0.45% 73.88% 1849ms 1.67% std::type_info::operator== (inline) 80ms 0.072% 73.95% 1824ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 34ms 0.031% 73.98% 1810ms 1.63% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.98% 1796ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 175ms 0.16% 74.14% 1689ms 1.52% CellPropertyCollection::AddProperty 19ms 0.017% 74.16% 1617ms 1.46% VertexMesh::GetSurfaceAreaOfElement 42ms 0.038% 74.20% 1597ms 1.44% Node::RemoveElement 0 0% 74.20% 1577ms 1.42% tcache_get (inline) 1577ms 1.42% 75.62% 1577ms 1.42% tcache_get_n (inline) 19ms 0.017% 75.64% 1568ms 1.42% std::set::erase (inline) 85ms 0.077% 75.72% 1565ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 40ms 0.036% 75.75% 1538ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 96ms 0.087% 75.84% 1496ms 1.35% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.84% 1487ms 1.34% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0009% 75.84% 1280ms 1.16% OffLatticeSimulation::ApplyBoundaries 80ms 0.072% 75.91% 1269ms 1.15% std::less::operator() (inline) 0 0% 75.91% 1260ms 1.14% boost::numeric::ublas::norm_2 (inline) 566ms 0.51% 76.42% 1249ms 1.13% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.42% 1225ms 1.11% std::_Rb_tree::_Auto_node::_Auto_node (inline) 974ms 0.88% 77.30% 1189ms 1.07% std::operator< (inline) 1168ms 1.05% 78.36% 1168ms 1.05% Node::rGetLocation 62ms 0.056% 78.41% 1155ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 29ms 0.026% 78.44% 1133ms 1.02% CellPropertyRegistry::Get 1114ms 1.01% 79.44% 1114ms 1.01% std::_Rb_tree_insert_and_rebalance 25ms 0.023% 79.47% 1095ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 96ms 0.087% 79.55% 1084ms 0.98% std::_Rb_tree::find (inline) 1081ms 0.98% 80.53% 1081ms 0.98% [libchaste_cell_based.so] 1ms 0.0009% 80.53% 1030ms 0.93% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.53% 1030ms 0.93% std::_Rb_tree::clear (inline) 197ms 0.18% 80.71% 1029ms 0.93% boost::detail::shared_count::~shared_count (inline) 1028ms 0.93% 81.64% 1028ms 0.93% std::vector::size (inline) 8ms 0.0072% 81.64% 1020ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.64% 1013ms 0.91% std::map::clear (inline) 961ms 0.87% 82.51% 961ms 0.87% [libchaste_mesh.so] 413ms 0.37% 82.88% 959ms 0.87% Edge::GetMapIndex 23ms 0.021% 82.90% 924ms 0.83% boost::numeric::ublas::detail::expression_type_check (inline) 159ms 0.14% 83.05% 892ms 0.81% boost::numeric::ublas::detail::equals 0 0% 83.05% 881ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0072% 83.05% 881ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 105ms 0.095% 83.15% 874ms 0.79% MutableElement::GetNodeLocalIndex 68ms 0.061% 83.21% 873ms 0.79% std::swap_ranges (inline) 0 0% 83.21% 863ms 0.78% std::map::find (inline) 1ms 0.0009% 83.21% 850ms 0.77% VertexMeshWriter::MakeVtkMesh 806ms 0.73% 83.94% 809ms 0.73% boost::detail::sp_counted_base::release 806ms 0.73% 84.67% 806ms 0.73% std::swap (inline) 0 0% 84.67% 805ms 0.73% std::iter_swap (inline) 102ms 0.092% 84.76% 773ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 137ms 0.12% 84.88% 749ms 0.68% boost::shared_ptr::shared_ptr (inline) 30ms 0.027% 84.91% 747ms 0.67% Edge::AddElement 100ms 0.09% 85.00% 742ms 0.67% std::__new_allocator::construct (inline) 0 0% 85.00% 742ms 0.67% std::allocator_traits::construct (inline) 15ms 0.014% 85.01% 739ms 0.67% MutableElement::RegisterWithEdges (inline) 734ms 0.66% 85.68% 734ms 0.66% Node::GetIndex 428ms 0.39% 86.06% 716ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.06% 697ms 0.63% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.06% 691ms 0.62% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.06% 681ms 0.61% boost::numeric::ublas::norm_inf (inline) 334ms 0.3% 86.36% 681ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.36% 675ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.38% 675ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.38% 670ms 0.6% std::_Vector_base::_M_allocate (inline) 625ms 0.56% 86.95% 625ms 0.56% operator delete 615ms 0.56% 87.50% 615ms 0.56% boost::shared_ptr::operator-> (inline) 29ms 0.026% 87.53% 614ms 0.55% MutableElement::RegisterWithNodes (inline) 585ms 0.53% 88.06% 612ms 0.55% boost::detail::shared_count::shared_count (inline) 0 0% 88.06% 602ms 0.54% vtkPolygon::New 1ms 0.0009% 88.06% 601ms 0.54% vtkPolygon::vtkPolygon 25ms 0.023% 88.08% 579ms 0.52% Node::AddElement 576ms 0.52% 88.60% 576ms 0.52% [libstdc++.so.6.0.33] 0 0% 88.60% 573ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 6ms 0.0054% 88.61% 571ms 0.52% std::vector::_M_default_append (inline) 25ms 0.023% 88.63% 570ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.63% 570ms 0.51% boost::numeric::ublas::vector::vector (inline)