File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96355ms, 88.83% of 108470ms total Dropped 1072 nodes (cum <= 542.35ms) flat flat% sum% cum cum% 0 0% 0% 108005ms 99.57% __libc_start_call_main 0 0% 0% 108005ms 99.57% __libc_start_main_impl 0 0% 0% 108005ms 99.57% _start 0 0% 0% 107988ms 99.56% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107988ms 99.56% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107988ms 99.56% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107988ms 99.56% main 0 0% 0% 107951ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107951ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107951ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 107944ms 99.52% AbstractCellBasedSimulation::Solve 11ms 0.01% 0.012% 56305ms 51.91% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.022% 53221ms 49.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 134ms 0.12% 0.15% 52141ms 48.07% AbstractNumericalMethod::ComputeForcesIncludingDamping 329ms 0.3% 0.45% 40277ms 37.13% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.45% 38785ms 35.76% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.45% 23924ms 22.06% VertexBasedCellPopulation::Update 0 0% 0.45% 23796ms 21.94% MutableVertexMesh::ReMesh 14620ms 13.48% 13.93% 23070ms 21.27% Cylindrical2dVertexMesh::GetVectorFromAtoB 67ms 0.062% 13.99% 17554ms 16.18% Cell::ReadyToDivide 109ms 0.1% 14.09% 16404ms 15.12% AbstractPhaseBasedCellCycleModel::ReadyToDivide 333ms 0.31% 14.40% 15170ms 13.99% NagaiHondaForce::GetAdhesionParameter 404ms 0.37% 14.77% 14462ms 13.33% boost::numeric::ublas::c_vector::c_vector (partial-inline) 132ms 0.12% 14.89% 13936ms 12.85% SimpleWntCellCycleModel::UpdateCellCyclePhase 156ms 0.14% 15.04% 13841ms 12.76% CellPropertyCollection::GetPropertiesType (inline) 392ms 0.36% 15.40% 12914ms 11.91% boost::numeric::ublas::vector_assign (inline) 134ms 0.12% 15.52% 12048ms 11.11% MutableVertexMesh::CheckForIntersections 3204ms 2.95% 18.48% 11588ms 10.68% __dynamic_cast 86ms 0.079% 18.56% 11521ms 10.62% AbstractCellProperty::IsSubType (inline) 125ms 0.12% 18.67% 11390ms 10.50% VertexBasedCellPopulation::GetDampingConstant 92ms 0.085% 18.76% 10472ms 9.65% AbstractTargetAreaModifier::UpdateTargetAreas 63ms 0.058% 18.81% 10356ms 9.55% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 23ms 0.021% 18.83% 10252ms 9.45% AbstractCellBasedSimulation::DoCellBirth 1188ms 1.10% 19.93% 10103ms 9.31% std::__new_allocator::allocate (inline) 2665ms 2.46% 22.39% 9588ms 8.84% boost::numeric::ublas::indexing_vector_assign 0 0% 22.39% 9543ms 8.80% std::allocator_traits::allocate (inline) 0 0% 22.39% 9532ms 8.79% std::_Rb_tree::_M_create_node (inline) 1412ms 1.30% 23.69% 9334ms 8.61% std::_Rb_tree::_M_erase 871ms 0.8% 24.49% 9016ms 8.31% operator new 352ms 0.32% 24.82% 8958ms 8.26% VertexMesh::GetNextEdgeGradientOfElementAtNode 812ms 0.75% 25.56% 8956ms 8.26% VertexMesh::ElementIncludesPoint 0 0% 25.56% 8918ms 8.22% std::_Rb_tree::_M_get_node (inline) 26ms 0.024% 25.59% 8841ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 86ms 0.079% 25.67% 8789ms 8.10% Cell::GetMutationState 249ms 0.23% 25.90% 8560ms 7.89% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.90% 8413ms 7.76% std::_Rb_tree::_Alloc_node::operator() (inline) 483ms 0.45% 26.34% 8405ms 7.75% VertexMesh::GetCentroidOfElement 0 0% 26.34% 8190ms 7.55% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.34% 8128ms 7.49% std::set::~set (inline) 3277ms 3.02% 29.36% 7982ms 7.36% __GI___libc_malloc 282ms 0.26% 29.62% 7968ms 7.35% std::__new_allocator::deallocate (inline) 0 0% 29.62% 7937ms 7.32% std::allocator_traits::deallocate (inline) 0 0% 29.62% 7889ms 7.27% std::_Rb_tree::_M_put_node (inline) 3132ms 2.89% 32.51% 7757ms 7.15% __GI___libc_free 20ms 0.018% 32.53% 7344ms 6.77% MutableVertexMesh::RemoveDeletedNodesAndElements 467ms 0.43% 32.96% 7295ms 6.73% std::map::operator[] (partial-inline) 1341ms 1.24% 34.20% 7174ms 6.61% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 127ms 0.12% 34.31% 6961ms 6.42% std::_Rb_tree::_Rb_tree (partial-inline) 6823ms 6.29% 40.60% 6823ms 6.29% __strcmp_avx2 677ms 0.62% 41.23% 6575ms 6.06% std::_Rb_tree::_M_copy (inline) 11ms 0.01% 41.24% 6538ms 6.03% std::set::set (inline) 96ms 0.089% 41.33% 6391ms 5.89% SimpleWntCellCycleModel::GetWntLevel 6331ms 5.84% 47.16% 6331ms 5.84% boost::numeric::ublas::c_vector::operator() 137ms 0.13% 47.29% 6183ms 5.70% WntConcentration::GetWntLevel 2634ms 2.43% 49.72% 5769ms 5.32% __cxxabiv1::__si_class_type_info::__do_dyncast 2397ms 2.21% 51.93% 5751ms 5.30% std::_Rb_tree::_M_lower_bound (inline) 714ms 0.66% 52.59% 5618ms 5.18% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.59% 5352ms 4.93% std::set::insert (inline) 26ms 0.024% 52.61% 5264ms 4.85% MutableVertexMesh::RemoveDeletedNodes 42ms 0.039% 52.65% 5116ms 4.72% EdgeHelper::RemoveDeletedEdges 1505ms 1.39% 54.04% 4882ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 32ms 0.03% 54.07% 4841ms 4.46% EdgeHelper::UpdateEdgesMapKey 0 0% 54.07% 4651ms 4.29% std::_Rb_tree::lower_bound (inline) 0 0% 54.07% 4651ms 4.29% std::map::lower_bound (inline) 4320ms 3.98% 58.05% 4612ms 4.25% _int_free 0 0% 58.05% 4598ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 495ms 0.46% 58.50% 4554ms 4.20% std::_Rb_tree::_M_insert_ (inline) 42ms 0.039% 58.54% 4529ms 4.18% std::set_intersection (inline) 173ms 0.16% 58.70% 4528ms 4.17% MutableElement::ResetIndex 335ms 0.31% 59.01% 4487ms 4.14% std::__set_intersection 53ms 0.049% 59.06% 4031ms 3.72% Cell::GetCellProliferativeType 122ms 0.11% 59.17% 3988ms 3.68% AbstractCellPopulation::GetCellUsingLocationIndex 3981ms 3.67% 62.84% 3981ms 3.67% boost::numeric::ublas::same_impl_ex 54ms 0.05% 62.89% 3689ms 3.40% AbstractCellProperty::IsType (inline) 5ms 0.0046% 62.90% 3589ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.90% 3276ms 3.02% std::insert_iterator::operator= (inline) 815ms 0.75% 63.65% 3233ms 2.98% AbstractElement::GetNodeLocation 57ms 0.053% 63.70% 3208ms 2.96% Cell::SetCellProliferativeType 2205ms 2.03% 65.73% 3013ms 2.78% _int_malloc 1ms 0.00092% 65.74% 2869ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 38ms 0.035% 65.77% 2838ms 2.62% std::_Rb_tree::erase 605ms 0.56% 66.33% 2808ms 2.59% boost::numeric::ublas::vector_binary::size (inline) 2778ms 2.56% 68.89% 2778ms 2.56% std::_Rb_tree::_S_right (inline) 435ms 0.4% 69.29% 2703ms 2.49% std::_Rb_tree_const_iterator::operator++ (inline) 685ms 0.63% 69.92% 2588ms 2.39% AbstractCellProperty::IsSame 242ms 0.22% 70.14% 2534ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 35ms 0.032% 70.18% 2499ms 2.30% CellPropertyCollection::HasProperty 1ms 0.00092% 70.18% 2482ms 2.29% std::_Rb_tree::_M_insert_unique 0 0% 70.18% 2453ms 2.26% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.18% 2419ms 2.23% Cell::HasCellProperty (inline) 26ms 0.024% 70.20% 2416ms 2.23% Cell::GetCellData 0 0% 70.20% 2402ms 2.21% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.20% 2360ms 2.18% AbstractCellPopulation::WriteResultsToFiles 104ms 0.096% 70.30% 2343ms 2.16% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 106ms 0.098% 70.40% 2286ms 2.11% VertexMesh::GetVolumeOfElement 6ms 0.0055% 70.40% 2185ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 202ms 0.19% 70.59% 2170ms 2.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 45ms 0.041% 70.63% 2127ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 2086ms 1.92% 72.55% 2086ms 1.92% std::_Rb_tree_increment 1ms 0.00092% 72.55% 1934ms 1.78% VertexBasedCellPopulation::WriteVtkResultsToFile 1304ms 1.20% 73.75% 1927ms 1.78% std::_Rb_tree::equal_range (inline) 1ms 0.00092% 73.76% 1919ms 1.77% VertexBasedCellPopulation::WriteCellVtkResultsToFile 418ms 0.39% 74.14% 1903ms 1.75% std::type_info::operator== (inline) 79ms 0.073% 74.21% 1886ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 74.21% 1866ms 1.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.21% 1866ms 1.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.00092% 74.22% 1725ms 1.59% VertexMeshWriter::WriteVtkUsingMesh 37ms 0.034% 74.25% 1700ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.023% 74.27% 1583ms 1.46% VertexMesh::GetSurfaceAreaOfElement 127ms 0.12% 74.39% 1575ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00092% 74.39% 1503ms 1.39% tcache_get (inline) 1502ms 1.38% 75.78% 1502ms 1.38% tcache_get_n (inline) 33ms 0.03% 75.81% 1495ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 50ms 0.046% 75.85% 1494ms 1.38% Node::RemoveElement 0 0% 75.85% 1475ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 183ms 0.17% 76.02% 1471ms 1.36% CellPropertyCollection::AddProperty 68ms 0.063% 76.08% 1466ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 19ms 0.018% 76.10% 1455ms 1.34% std::set::erase (inline) 1ms 0.00092% 76.10% 1245ms 1.15% OffLatticeSimulation::ApplyBoundaries 72ms 0.066% 76.17% 1193ms 1.10% std::less::operator() (inline) 1168ms 1.08% 77.25% 1168ms 1.08% Node::rGetLocation 0 0% 77.25% 1162ms 1.07% boost::numeric::ublas::norm_2 (inline) 532ms 0.49% 77.74% 1151ms 1.06% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1125ms 1.04% 78.77% 1125ms 1.04% std::_Rb_tree_insert_and_rebalance 927ms 0.85% 79.63% 1121ms 1.03% std::operator< (inline) 0 0% 79.63% 1119ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 85ms 0.078% 79.71% 1058ms 0.98% std::_Rb_tree::find (inline) 163ms 0.15% 79.86% 1052ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 79.86% 1052ms 0.97% boost::shared_ptr::~shared_ptr (inline) 83ms 0.077% 79.93% 1044ms 0.96% std::_Rb_tree::_M_erase_aux (partial-inline) 32ms 0.03% 79.96% 1043ms 0.96% CellPropertyRegistry::Get 1041ms 0.96% 80.92% 1041ms 0.96% [libchaste_cell_based.so] 17ms 0.016% 80.94% 1038ms 0.96% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 80.94% 1025ms 0.94% std::_Rb_tree::clear (inline) 0 0% 80.94% 1013ms 0.93% std::map::clear (inline) 977ms 0.9% 81.84% 977ms 0.9% [libchaste_mesh.so] 13ms 0.012% 81.85% 965ms 0.89% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.022% 81.87% 948ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 921ms 0.85% 82.72% 921ms 0.85% std::vector::size (inline) 161ms 0.15% 82.87% 908ms 0.84% boost::numeric::ublas::detail::equals 381ms 0.35% 83.22% 888ms 0.82% Edge::GetMapIndex 857ms 0.79% 84.01% 865ms 0.8% boost::detail::sp_counted_base::release 0 0% 84.01% 862ms 0.79% boost::numeric::ublas::c_vector::assign_temporary (inline) 11ms 0.01% 84.02% 862ms 0.79% boost::numeric::ublas::c_vector::swap (inline) 1ms 0.00092% 84.02% 860ms 0.79% VertexMeshWriter::MakeVtkMesh 1ms 0.00092% 84.02% 860ms 0.79% std::map::find (inline) 79ms 0.073% 84.10% 851ms 0.78% std::swap_ranges (inline) 98ms 0.09% 84.19% 809ms 0.75% MutableElement::GetNodeLocalIndex 0 0% 84.19% 772ms 0.71% std::iter_swap (inline) 772ms 0.71% 84.90% 772ms 0.71% std::swap (inline) 18ms 0.017% 84.91% 765ms 0.71% MutableElement::RegisterWithEdges (inline) 0 0% 84.91% 762ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 20ms 0.018% 84.93% 760ms 0.7% Edge::AddElement 117ms 0.11% 85.04% 745ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 734ms 0.68% 85.72% 734ms 0.68% Node::GetIndex 147ms 0.14% 85.85% 723ms 0.67% boost::shared_ptr::shared_ptr (inline) 415ms 0.38% 86.24% 716ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.24% 704ms 0.65% boost::numeric::ublas::norm_inf (inline) 340ms 0.31% 86.55% 704ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 125ms 0.12% 86.66% 660ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.66% 660ms 0.61% std::allocator_traits::construct (inline) 0 0% 86.66% 650ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 19ms 0.018% 86.68% 650ms 0.6% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.68% 621ms 0.57% std::_Vector_base::_M_allocate (inline) 620ms 0.57% 87.25% 620ms 0.57% operator delete 0 0% 87.25% 614ms 0.57% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.25% 613ms 0.57% vtkPolygon::New 3ms 0.0028% 87.26% 613ms 0.57% vtkPolygon::vtkPolygon 29ms 0.027% 87.28% 576ms 0.53% MutableElement::RegisterWithNodes (inline) 546ms 0.5% 87.79% 576ms 0.53% boost::detail::shared_count::shared_count (inline) 16ms 0.015% 87.80% 576ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.80% 576ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 87.80% 556ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 549ms 0.51% 88.31% 549ms 0.51% [libstdc++.so.6.0.33] 21ms 0.019% 88.33% 546ms 0.5% Node::AddElement 546ms 0.5% 88.83% 546ms 0.5% boost::shared_ptr::operator-> (inline)