File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97581ms, 88.13% of 110729ms total Dropped 1038 nodes (cum <= 553.64ms) flat flat% sum% cum cum% 0 0% 0% 110250ms 99.57% __libc_start_call_main 0 0% 0% 110250ms 99.57% __libc_start_main_impl 0 0% 0% 110250ms 99.57% _start 0 0% 0% 110231ms 99.55% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110231ms 99.55% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110231ms 99.55% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110231ms 99.55% main 0 0% 0% 110194ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110194ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110194ms 99.52% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 110187ms 99.51% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.021% 57231ms 51.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.014% 0.035% 54041ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 159ms 0.14% 0.18% 52996ms 47.86% AbstractNumericalMethod::ComputeForcesIncludingDamping 416ms 0.38% 0.55% 40708ms 36.76% NagaiHondaForce::AddForceContribution 0 0% 0.55% 39901ms 36.03% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.56% 24639ms 22.25% VertexBasedCellPopulation::Update 1ms 0.0009% 0.56% 24486ms 22.11% MutableVertexMesh::ReMesh 14530ms 13.12% 13.68% 23036ms 20.80% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.073% 13.75% 17895ms 16.16% Cell::ReadyToDivide 74ms 0.067% 13.82% 16765ms 15.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 324ms 0.29% 14.11% 15320ms 13.84% NagaiHondaForce::GetAdhesionParameter 159ms 0.14% 14.26% 14382ms 12.99% SimpleWntCellCycleModel::UpdateCellCyclePhase 429ms 0.39% 14.64% 14284ms 12.90% boost::numeric::ublas::c_vector::c_vector (partial-inline) 138ms 0.12% 14.77% 13716ms 12.39% CellPropertyCollection::GetPropertiesType (inline) 444ms 0.4% 15.17% 12735ms 11.50% boost::numeric::ublas::vector_assign (inline) 127ms 0.11% 15.28% 12090ms 10.92% MutableVertexMesh::CheckForIntersections 82ms 0.074% 15.36% 11763ms 10.62% VertexBasedCellPopulation::GetDampingConstant 3605ms 3.26% 18.61% 11298ms 10.20% __dynamic_cast 103ms 0.093% 18.71% 11228ms 10.14% AbstractCellProperty::IsSubType (inline) 71ms 0.064% 18.77% 10626ms 9.60% AbstractTargetAreaModifier::UpdateTargetAreas 1439ms 1.30% 20.07% 10555ms 9.53% std::__new_allocator::allocate (inline) 48ms 0.043% 20.11% 10529ms 9.51% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 28ms 0.025% 20.14% 10486ms 9.47% AbstractCellBasedSimulation::DoCellBirth 0 0% 20.14% 9904ms 8.94% std::allocator_traits::allocate (inline) 0 0% 20.14% 9855ms 8.90% std::_Rb_tree::_M_create_node (inline) 1367ms 1.23% 21.37% 9441ms 8.53% std::_Rb_tree::_M_erase 2648ms 2.39% 23.76% 9391ms 8.48% boost::numeric::ublas::indexing_vector_assign 861ms 0.78% 24.54% 9224ms 8.33% operator new 0 0% 24.54% 9214ms 8.32% std::_Rb_tree::_M_get_node (inline) 31ms 0.028% 24.57% 9005ms 8.13% VertexBasedCellPopulation::GetLocationOfCellCentre 397ms 0.36% 24.93% 8994ms 8.12% VertexMesh::GetNextEdgeGradientOfElementAtNode 792ms 0.72% 25.64% 8887ms 8.03% VertexMesh::ElementIncludesPoint 76ms 0.069% 25.71% 8824ms 7.97% Cell::GetMutationState 0 0% 25.71% 8669ms 7.83% std::_Rb_tree::_Alloc_node::operator() (inline) 214ms 0.19% 25.91% 8647ms 7.81% std::_Rb_tree::~_Rb_tree (inline) 515ms 0.47% 26.37% 8414ms 7.60% VertexMesh::GetCentroidOfElement 0 0% 26.37% 8356ms 7.55% std::_Rb_tree::_M_drop_node (inline) 3177ms 2.87% 29.24% 8180ms 7.39% __GI___libc_malloc 0 0% 29.24% 8166ms 7.37% std::set::~set (inline) 249ms 0.22% 29.46% 8122ms 7.34% std::__new_allocator::deallocate (inline) 0 0% 29.46% 8091ms 7.31% std::allocator_traits::deallocate (inline) 0 0% 29.46% 8028ms 7.25% std::_Rb_tree::_M_put_node (inline) 516ms 0.47% 29.93% 7968ms 7.20% std::map::operator[] (partial-inline) 3056ms 2.76% 32.69% 7850ms 7.09% __GI___libc_free 17ms 0.015% 32.71% 7834ms 7.07% MutableVertexMesh::RemoveDeletedNodesAndElements 1300ms 1.17% 33.88% 7172ms 6.48% AbstractMesh::GetDistanceBetweenNodes 160ms 0.14% 34.02% 7169ms 6.47% std::_Rb_tree::_Rb_tree (partial-inline) 685ms 0.62% 34.64% 6778ms 6.12% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 34.66% 6762ms 6.11% std::set::set (inline) 159ms 0.14% 34.80% 6651ms 6.01% SimpleWntCellCycleModel::GetWntLevel 2507ms 2.26% 37.06% 6496ms 5.87% std::_Rb_tree::_M_lower_bound (inline) 206ms 0.19% 37.25% 6366ms 5.75% WntConcentration::GetWntLevel 6244ms 5.64% 42.89% 6244ms 5.64% boost::numeric::ublas::c_vector::operator() 6125ms 5.53% 48.42% 6125ms 5.53% __strcmp_avx2 813ms 0.73% 49.16% 5826ms 5.26% std::_Rb_tree::_M_clone_node (inline) 28ms 0.025% 49.18% 5550ms 5.01% MutableVertexMesh::RemoveDeletedNodes 0 0% 49.18% 5419ms 4.89% std::set::insert (inline) 40ms 0.036% 49.22% 5401ms 4.88% EdgeHelper::RemoveDeletedEdges 2545ms 2.30% 51.51% 5211ms 4.71% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 51.51% 5209ms 4.70% std::_Rb_tree::lower_bound (inline) 0 0% 51.51% 5209ms 4.70% std::map::lower_bound (inline) 38ms 0.034% 51.55% 5116ms 4.62% EdgeHelper::UpdateEdgesMapKey 221ms 0.2% 51.75% 4911ms 4.44% MutableElement::ResetIndex 1504ms 1.36% 53.11% 4874ms 4.40% boost::numeric::ublas::c_vector::operator[] (inline) 4449ms 4.02% 57.13% 4788ms 4.32% _int_free 0 0% 57.13% 4770ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 497ms 0.45% 57.57% 4642ms 4.19% std::_Rb_tree::_M_insert_ (inline) 58ms 0.052% 57.63% 4642ms 4.19% std::set_intersection (inline) 266ms 0.24% 57.87% 4584ms 4.14% std::__set_intersection 118ms 0.11% 57.97% 4445ms 4.01% AbstractCellPopulation::GetCellUsingLocationIndex 46ms 0.042% 58.01% 3979ms 3.59% Cell::GetCellProliferativeType 3848ms 3.48% 61.49% 3848ms 3.48% boost::numeric::ublas::same_impl_ex 8ms 0.0072% 61.50% 3637ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 69ms 0.062% 61.56% 3624ms 3.27% AbstractCellProperty::IsType (inline) 3334ms 3.01% 64.57% 3334ms 3.01% std::_Rb_tree::_S_right (inline) 849ms 0.77% 65.34% 3292ms 2.97% AbstractElement::GetNodeLocation 53ms 0.048% 65.38% 3249ms 2.93% Cell::SetCellProliferativeType 0 0% 65.38% 3246ms 2.93% std::insert_iterator::operator= (inline) 2354ms 2.13% 67.51% 3245ms 2.93% _int_malloc 56ms 0.051% 67.56% 3174ms 2.87% std::_Rb_tree::erase 406ms 0.37% 67.93% 2962ms 2.67% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.0063% 67.93% 2822ms 2.55% std::_Rb_tree::_M_insert_unique_ (inline) 629ms 0.57% 68.50% 2700ms 2.44% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 68.50% 2597ms 2.35% std::_Rb_tree::_M_insert_unique (inline) 748ms 0.68% 69.18% 2555ms 2.31% AbstractCellProperty::IsSame 211ms 0.19% 69.37% 2457ms 2.22% VertexMesh::GetAreaGradientOfElementAtNode 48ms 0.043% 69.41% 2455ms 2.22% CellPropertyCollection::HasProperty 0 0% 69.41% 2421ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.41% 2405ms 2.17% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.41% 2401ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 232ms 0.21% 69.62% 2359ms 2.13% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0009% 69.62% 2358ms 2.13% AbstractCellPopulation::Iterator::operator++ (inline) 2342ms 2.12% 71.74% 2342ms 2.12% std::_Rb_tree_increment 0 0% 71.74% 2339ms 2.11% Cell::HasCellProperty (inline) 20ms 0.018% 71.76% 2331ms 2.11% Cell::GetCellData 89ms 0.08% 71.84% 2307ms 2.08% VertexMesh::GetVolumeOfElement 117ms 0.11% 71.94% 2290ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1525ms 1.38% 73.32% 2227ms 2.01% std::_Rb_tree::equal_range (inline) 25ms 0.023% 73.34% 2188ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 0 0% 73.34% 1963ms 1.77% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 73.34% 1956ms 1.77% VertexBasedCellPopulation::WriteCellVtkResultsToFile 78ms 0.07% 73.41% 1865ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 27ms 0.024% 73.44% 1848ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 480ms 0.43% 73.87% 1807ms 1.63% std::type_info::operator== (inline) 0 0% 73.87% 1773ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 0 0% 73.87% 1766ms 1.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.87% 1766ms 1.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 46ms 0.042% 73.91% 1712ms 1.55% Node::RemoveElement 25ms 0.023% 73.94% 1680ms 1.52% std::set::erase (inline) 19ms 0.017% 73.95% 1652ms 1.49% VertexMesh::GetSurfaceAreaOfElement 20ms 0.018% 73.97% 1637ms 1.48% AbstractCellPopulation::GetLocationIndexUsingCell 94ms 0.085% 74.06% 1626ms 1.47% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.06% 1571ms 1.42% tcache_get (inline) 1571ms 1.42% 75.47% 1571ms 1.42% tcache_get_n (inline) 164ms 0.15% 75.62% 1561ms 1.41% CellPropertyCollection::AddProperty 131ms 0.12% 75.74% 1431ms 1.29% boost::numeric::ublas::vector_reference::operator() (inline) 73ms 0.066% 75.81% 1335ms 1.21% std::less::operator() (inline) 0 0% 75.81% 1310ms 1.18% OffLatticeSimulation::ApplyBoundaries 0 0% 75.81% 1292ms 1.17% boost::numeric::ublas::vector_binary::operator() (inline) 111ms 0.1% 75.91% 1264ms 1.14% std::_Rb_tree::find (inline) 1024ms 0.92% 76.83% 1262ms 1.14% std::operator< (inline) 1196ms 1.08% 77.91% 1196ms 1.08% Node::rGetLocation 0 0% 77.91% 1186ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 77.91% 1151ms 1.04% boost::numeric::ublas::norm_2 (inline) 487ms 0.44% 78.35% 1145ms 1.03% boost::numeric::ublas::vector_norm_2::apply 28ms 0.025% 78.38% 1126ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 60ms 0.054% 78.43% 1100ms 0.99% CellPropertyRegistry::Get 1094ms 0.99% 79.42% 1094ms 0.99% std::_Rb_tree_insert_and_rebalance 93ms 0.084% 79.50% 1092ms 0.99% std::_Rb_tree::_M_erase_aux (partial-inline) 1091ms 0.99% 80.49% 1091ms 0.99% [libchaste_cell_based.so] 3ms 0.0027% 80.49% 1085ms 0.98% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 400ms 0.36% 80.85% 1019ms 0.92% Edge::GetMapIndex 0 0% 80.85% 1011ms 0.91% std::_Rb_tree::clear (inline) 0 0% 80.85% 1008ms 0.91% std::map::find (inline) 0 0% 80.85% 994ms 0.9% std::map::clear (inline) 146ms 0.13% 80.98% 986ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.98% 986ms 0.89% boost::shared_ptr::~shared_ptr (inline) 972ms 0.88% 81.86% 972ms 0.88% [libchaste_mesh.so] 0 0% 81.86% 971ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 6ms 0.0054% 81.87% 971ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 970ms 0.88% 82.74% 970ms 0.88% std::vector::size (inline) 74ms 0.067% 82.81% 965ms 0.87% std::swap_ranges (inline) 0 0% 82.81% 891ms 0.8% std::iter_swap (inline) 891ms 0.8% 83.61% 891ms 0.8% std::swap (inline) 1ms 0.0009% 83.62% 872ms 0.79% VertexMeshWriter::MakeVtkMesh 24ms 0.022% 83.64% 839ms 0.76% boost::numeric::ublas::detail::expression_type_check (inline) 809ms 0.73% 84.37% 814ms 0.74% boost::detail::sp_counted_base::release 159ms 0.14% 84.51% 813ms 0.73% boost::numeric::ublas::detail::equals 22ms 0.02% 84.53% 799ms 0.72% MutableElement::RegisterWithEdges (inline) 799ms 0.72% 85.25% 799ms 0.72% Node::GetIndex 151ms 0.14% 85.39% 798ms 0.72% boost::shared_ptr::shared_ptr (inline) 31ms 0.028% 85.42% 793ms 0.72% Edge::AddElement 81ms 0.073% 85.49% 792ms 0.72% MutableElement::GetNodeLocalIndex 96ms 0.087% 85.58% 768ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.58% 724ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 107ms 0.097% 85.67% 692ms 0.62% std::__new_allocator::construct (inline) 0 0% 85.67% 692ms 0.62% std::allocator_traits::construct (inline) 2ms 0.0018% 85.68% 691ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 85.68% 690ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 31ms 0.028% 85.70% 690ms 0.62% std::_Rb_tree::_M_insert_node (inline) 404ms 0.36% 86.07% 688ms 0.62% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 24ms 0.022% 86.09% 675ms 0.61% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.09% 675ms 0.61% boost::numeric::ublas::vector::vector (inline) 670ms 0.61% 86.70% 670ms 0.61% operator delete 618ms 0.56% 87.25% 647ms 0.58% boost::detail::shared_count::shared_count (inline) 0 0% 87.25% 641ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.25% 615ms 0.56% boost::numeric::ublas::norm_inf (inline) 334ms 0.3% 87.56% 615ms 0.56% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 87.56% 602ms 0.54% vtkPolygon::New 0 0% 87.56% 602ms 0.54% vtkPolygon::vtkPolygon 27ms 0.024% 87.58% 589ms 0.53% MutableElement::RegisterWithNodes (inline) 8ms 0.0072% 87.59% 584ms 0.53% std::vector::_M_default_append (inline) 570ms 0.51% 88.10% 570ms 0.51% [libstdc++.so.6.0.33] 27ms 0.024% 88.13% 561ms 0.51% Node::AddElement