File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96389ms, 88.49% of 108921ms total Dropped 1143 nodes (cum <= 544.61ms) flat flat% sum% cum cum% 0 0% 0% 108481ms 99.60% __libc_start_call_main 0 0% 0% 108481ms 99.60% __libc_start_main_impl 0 0% 0% 108481ms 99.60% _start 0 0% 0% 108460ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108460ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108460ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108460ms 99.58% main 0 0% 0% 108421ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108421ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108421ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108413ms 99.53% AbstractCellBasedSimulation::Solve 23ms 0.021% 0.025% 56238ms 51.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.039% 53039ms 48.69% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.16% 51454ms 47.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 362ms 0.33% 0.49% 39756ms 36.50% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.49% 39082ms 35.88% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.49% 24182ms 22.20% VertexBasedCellPopulation::Update 2ms 0.0018% 0.49% 24037ms 22.07% MutableVertexMesh::ReMesh 14466ms 13.28% 13.78% 22857ms 20.98% Cylindrical2dVertexMesh::GetVectorFromAtoB 143ms 0.13% 13.91% 17511ms 16.08% Cell::ReadyToDivide 111ms 0.1% 14.01% 16255ms 14.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 360ms 0.33% 14.34% 14635ms 13.44% NagaiHondaForce::GetAdhesionParameter 476ms 0.44% 14.78% 14304ms 13.13% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.1% 14.88% 13733ms 12.61% SimpleWntCellCycleModel::UpdateCellCyclePhase 150ms 0.14% 15.02% 13590ms 12.48% CellPropertyCollection::GetPropertiesType (inline) 411ms 0.38% 15.39% 12768ms 11.72% boost::numeric::ublas::vector_assign (inline) 153ms 0.14% 15.54% 12028ms 11.04% MutableVertexMesh::CheckForIntersections 3176ms 2.92% 18.45% 11207ms 10.29% __dynamic_cast 84ms 0.077% 18.53% 11172ms 10.26% VertexBasedCellPopulation::GetDampingConstant 77ms 0.071% 18.60% 11083ms 10.18% AbstractCellProperty::IsSubType (inline) 98ms 0.09% 18.69% 10569ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 71ms 0.065% 18.75% 10447ms 9.59% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.78% 10333ms 9.49% AbstractCellBasedSimulation::DoCellBirth 1263ms 1.16% 19.93% 10194ms 9.36% std::__new_allocator::allocate (inline) 0 0% 19.93% 9701ms 8.91% std::allocator_traits::allocate (inline) 0 0% 19.93% 9646ms 8.86% std::_Rb_tree::_M_create_node (inline) 2712ms 2.49% 22.42% 9455ms 8.68% boost::numeric::ublas::indexing_vector_assign 845ms 0.78% 23.20% 9120ms 8.37% operator new 1367ms 1.26% 24.46% 9051ms 8.31% std::_Rb_tree::_M_erase 0 0% 24.46% 9028ms 8.29% std::_Rb_tree::_M_get_node (inline) 428ms 0.39% 24.85% 8996ms 8.26% VertexMesh::GetNextEdgeGradientOfElementAtNode 788ms 0.72% 25.57% 8903ms 8.17% VertexMesh::ElementIncludesPoint 19ms 0.017% 25.59% 8711ms 8.00% VertexBasedCellPopulation::GetLocationOfCellCentre 57ms 0.052% 25.64% 8550ms 7.85% Cell::GetMutationState 0 0% 25.64% 8463ms 7.77% std::_Rb_tree::_Alloc_node::operator() (inline) 239ms 0.22% 25.86% 8289ms 7.61% std::_Rb_tree::~_Rb_tree (inline) 492ms 0.45% 26.31% 8209ms 7.54% VertexMesh::GetCentroidOfElement 3227ms 2.96% 29.28% 8098ms 7.43% __GI___libc_malloc 0 0% 29.28% 8090ms 7.43% std::_Rb_tree::_M_drop_node (inline) 244ms 0.22% 29.50% 7920ms 7.27% std::__new_allocator::deallocate (inline) 0 0% 29.50% 7881ms 7.24% std::allocator_traits::deallocate (inline) 3119ms 2.86% 32.36% 7868ms 7.22% __GI___libc_free 0 0% 32.36% 7822ms 7.18% std::set::~set (inline) 0 0% 32.36% 7787ms 7.15% std::_Rb_tree::_M_put_node (inline) 27ms 0.025% 32.39% 7560ms 6.94% MutableVertexMesh::RemoveDeletedNodesAndElements 495ms 0.45% 32.84% 7545ms 6.93% std::map::operator[] (partial-inline) 1390ms 1.28% 34.12% 7117ms 6.53% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 112ms 0.1% 34.22% 6818ms 6.26% std::_Rb_tree::_Rb_tree (partial-inline) 607ms 0.56% 34.78% 6473ms 5.94% std::_Rb_tree::_M_copy (inline) 6445ms 5.92% 40.70% 6445ms 5.92% __strcmp_avx2 15ms 0.014% 40.71% 6398ms 5.87% std::set::set (inline) 118ms 0.11% 40.82% 6326ms 5.81% SimpleWntCellCycleModel::GetWntLevel 137ms 0.13% 40.94% 6128ms 5.63% WntConcentration::GetWntLevel 6048ms 5.55% 46.50% 6048ms 5.55% boost::numeric::ublas::c_vector::operator() 2548ms 2.34% 48.84% 5996ms 5.50% std::_Rb_tree::_M_lower_bound (inline) 2689ms 2.47% 51.30% 5629ms 5.17% __cxxabiv1::__si_class_type_info::__do_dyncast 709ms 0.65% 51.96% 5616ms 5.16% std::_Rb_tree::_M_clone_node (inline) 0 0% 51.96% 5502ms 5.05% std::set::insert (inline) 37ms 0.034% 51.99% 5377ms 4.94% MutableVertexMesh::RemoveDeletedNodes 30ms 0.028% 52.02% 5207ms 4.78% EdgeHelper::RemoveDeletedEdges 27ms 0.025% 52.04% 4945ms 4.54% EdgeHelper::UpdateEdgesMapKey 1542ms 1.42% 53.46% 4849ms 4.45% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.46% 4834ms 4.44% std::_Rb_tree::lower_bound (inline) 0 0% 53.46% 4834ms 4.44% std::map::lower_bound (inline) 4402ms 4.04% 57.50% 4738ms 4.35% _int_free 212ms 0.19% 57.69% 4695ms 4.31% MutableElement::ResetIndex 577ms 0.53% 58.22% 4672ms 4.29% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.22% 4555ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 41ms 0.038% 58.26% 4418ms 4.06% std::set_intersection (inline) 253ms 0.23% 58.49% 4377ms 4.02% std::__set_intersection 106ms 0.097% 58.59% 4088ms 3.75% AbstractCellPopulation::GetCellUsingLocationIndex 3948ms 3.62% 62.21% 3948ms 3.62% boost::numeric::ublas::same_impl_ex 33ms 0.03% 62.25% 3835ms 3.52% Cell::GetCellProliferativeType 83ms 0.076% 62.32% 3782ms 3.47% AbstractCellProperty::IsType (inline) 7ms 0.0064% 62.33% 3495ms 3.21% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.33% 3196ms 2.93% std::insert_iterator::operator= (inline) 803ms 0.74% 63.06% 3188ms 2.93% AbstractElement::GetNodeLocation 2229ms 2.05% 65.11% 3179ms 2.92% _int_malloc 48ms 0.044% 65.16% 3006ms 2.76% Cell::SetCellProliferativeType 42ms 0.039% 65.19% 2956ms 2.71% std::_Rb_tree::erase 2907ms 2.67% 67.86% 2907ms 2.67% std::_Rb_tree::_S_right (inline) 5ms 0.0046% 67.87% 2799ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 616ms 0.57% 68.43% 2792ms 2.56% boost::numeric::ublas::vector_binary::size (inline) 736ms 0.68% 69.11% 2753ms 2.53% AbstractCellProperty::IsSame 403ms 0.37% 69.48% 2751ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.48% 2703ms 2.48% std::_Rb_tree::_M_insert_unique (inline) 35ms 0.032% 69.51% 2567ms 2.36% CellPropertyCollection::HasProperty 232ms 0.21% 69.72% 2516ms 2.31% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.72% 2502ms 2.30% AbstractCellPopulation::WriteResultsToFiles 16ms 0.015% 69.74% 2471ms 2.27% Cell::GetCellData 0 0% 69.74% 2469ms 2.27% Cell::HasCellProperty (inline) 0 0% 69.74% 2430ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.74% 2407ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 121ms 0.11% 69.85% 2384ms 2.19% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 229ms 0.21% 70.06% 2348ms 2.16% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 70.06% 2347ms 2.15% AbstractCellPopulation::Iterator::operator++ (inline) 88ms 0.081% 70.14% 2198ms 2.02% VertexMesh::GetVolumeOfElement 38ms 0.035% 70.18% 2168ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 2146ms 1.97% 72.15% 2146ms 1.97% std::_Rb_tree_increment 0 0% 72.15% 2059ms 1.89% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.15% 2050ms 1.88% VertexBasedCellPopulation::WriteCellVtkResultsToFile 491ms 0.45% 72.60% 2017ms 1.85% std::type_info::operator== (inline) 1312ms 1.20% 73.80% 1985ms 1.82% std::_Rb_tree::equal_range (inline) 2ms 0.0018% 73.80% 1895ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.80% 1895ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 71ms 0.065% 73.87% 1856ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.87% 1838ms 1.69% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.017% 73.89% 1821ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 187ms 0.17% 74.06% 1663ms 1.53% CellPropertyCollection::AddProperty 92ms 0.084% 74.14% 1583ms 1.45% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 24ms 0.022% 74.16% 1582ms 1.45% VertexMesh::GetSurfaceAreaOfElement 21ms 0.019% 74.18% 1570ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 37ms 0.034% 74.22% 1529ms 1.40% Node::RemoveElement 0 0% 74.22% 1525ms 1.40% tcache_get (inline) 1525ms 1.40% 75.62% 1525ms 1.40% tcache_get_n (inline) 17ms 0.016% 75.63% 1501ms 1.38% std::set::erase (inline) 141ms 0.13% 75.76% 1487ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.76% 1393ms 1.28% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.76% 1280ms 1.18% OffLatticeSimulation::ApplyBoundaries 0 0% 75.76% 1219ms 1.12% boost::numeric::ublas::norm_2 (inline) 63ms 0.058% 75.82% 1214ms 1.11% std::less::operator() (inline) 534ms 0.49% 76.31% 1212ms 1.11% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1191ms 1.09% 77.40% 1191ms 1.09% Node::rGetLocation 0 0% 77.40% 1183ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 956ms 0.88% 78.28% 1151ms 1.06% std::operator< (inline) 27ms 0.025% 78.31% 1132ms 1.04% CellPropertyRegistry::Get 1130ms 1.04% 79.34% 1130ms 1.04% std::_Rb_tree_insert_and_rebalance 89ms 0.082% 79.43% 1128ms 1.04% std::_Rb_tree::find (inline) 73ms 0.067% 79.49% 1118ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1087ms 1% 80.49% 1087ms 1% [libchaste_cell_based.so] 14ms 0.013% 80.50% 1080ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 8ms 0.0073% 80.51% 1025ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.51% 1001ms 0.92% std::_Rb_tree::clear (inline) 0 0% 80.51% 993ms 0.91% std::map::clear (inline) 130ms 0.12% 80.63% 962ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 80.63% 962ms 0.88% boost::shared_ptr::~shared_ptr (inline) 946ms 0.87% 81.50% 946ms 0.87% std::vector::size (inline) 920ms 0.84% 82.34% 920ms 0.84% [libchaste_mesh.so] 29ms 0.027% 82.37% 918ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.37% 913ms 0.84% std::map::find (inline) 2ms 0.0018% 82.37% 910ms 0.84% VertexMeshWriter::MakeVtkMesh 367ms 0.34% 82.71% 906ms 0.83% Edge::GetMapIndex 156ms 0.14% 82.85% 882ms 0.81% boost::numeric::ublas::detail::equals 0 0% 82.85% 843ms 0.77% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0055% 82.86% 843ms 0.77% boost::numeric::ublas::c_vector::swap (inline) 69ms 0.063% 82.92% 837ms 0.77% std::swap_ranges (inline) 106ms 0.097% 83.02% 795ms 0.73% MutableElement::GetNodeLocalIndex 791ms 0.73% 83.74% 795ms 0.73% boost::detail::sp_counted_base::release 17ms 0.016% 83.76% 790ms 0.73% MutableElement::RegisterWithEdges (inline) 21ms 0.019% 83.78% 781ms 0.72% Edge::AddElement 770ms 0.71% 84.49% 770ms 0.71% std::swap (inline) 0 0% 84.49% 768ms 0.71% std::iter_swap (inline) 16ms 0.015% 84.50% 726ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 725ms 0.67% 85.17% 725ms 0.67% Node::GetIndex 104ms 0.095% 85.26% 719ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 100ms 0.092% 85.35% 710ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 422ms 0.39% 85.74% 710ms 0.65% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 135ms 0.12% 85.86% 708ms 0.65% boost::shared_ptr::shared_ptr (inline) 0 0% 85.86% 703ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 115ms 0.11% 85.97% 682ms 0.63% std::__new_allocator::construct (inline) 0 0% 85.97% 682ms 0.63% std::allocator_traits::construct (inline) 0 0% 85.97% 676ms 0.62% boost::numeric::ublas::norm_inf (inline) 356ms 0.33% 86.30% 676ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00092% 86.30% 672ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.30% 667ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 32ms 0.029% 86.33% 667ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.33% 661ms 0.61% vtkPolygon::New 0 0% 86.33% 658ms 0.6% vtkPolygon::vtkPolygon 0 0% 86.33% 618ms 0.57% std::_Rb_tree::_M_construct_node (inline) 30ms 0.028% 86.36% 610ms 0.56% MutableElement::RegisterWithNodes (inline) 603ms 0.55% 86.91% 603ms 0.55% [libstdc++.so.6.0.33] 30ms 0.028% 86.94% 579ms 0.53% Node::AddElement 0 0% 86.94% 574ms 0.53% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 541ms 0.5% 87.43% 573ms 0.53% boost::detail::shared_count::shared_count (inline) 567ms 0.52% 87.95% 567ms 0.52% operator delete 5ms 0.0046% 87.96% 564ms 0.52% std::vector::_M_default_append (inline) 554ms 0.51% 88.47% 554ms 0.51% boost::shared_ptr::operator-> (inline) 29ms 0.027% 88.49% 547ms 0.5% AbstractNumericalMethod::SafeNodePositionUpdate