File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96680ms, 88.30% of 109486ms total Dropped 1089 nodes (cum <= 547.43ms) flat flat% sum% cum cum% 0 0% 0% 109045ms 99.60% __libc_start_call_main 0 0% 0% 109045ms 99.60% __libc_start_main_impl 0 0% 0% 109045ms 99.60% _start 0 0% 0% 109027ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109027ms 99.58% CxxTest::TestRunner::runAllTests (inline) 1ms 0.00091% 0.00091% 109027ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0.00091% 109027ms 99.58% main 0 0% 0.00091% 108988ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0.00091% 108988ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0.00091% 108988ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0027% 108980ms 99.54% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.015% 56442ms 51.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 26ms 0.024% 0.038% 53231ms 48.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 121ms 0.11% 0.15% 52131ms 47.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 405ms 0.37% 0.52% 39917ms 36.46% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.52% 39277ms 35.87% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.52% 24146ms 22.05% VertexBasedCellPopulation::Update 1ms 0.00091% 0.52% 24012ms 21.93% MutableVertexMesh::ReMesh 14657ms 13.39% 13.91% 22938ms 20.95% Cylindrical2dVertexMesh::GetVectorFromAtoB 113ms 0.1% 14.01% 17962ms 16.41% Cell::ReadyToDivide 65ms 0.059% 14.07% 16742ms 15.29% AbstractPhaseBasedCellCycleModel::ReadyToDivide 356ms 0.33% 14.40% 15098ms 13.79% NagaiHondaForce::GetAdhesionParameter 127ms 0.12% 14.51% 14597ms 13.33% CellPropertyCollection::GetPropertiesType (inline) 126ms 0.12% 14.63% 14206ms 12.98% SimpleWntCellCycleModel::UpdateCellCyclePhase 462ms 0.42% 15.05% 13835ms 12.64% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3529ms 3.22% 18.27% 12334ms 11.27% __dynamic_cast 67ms 0.061% 18.33% 12224ms 11.16% AbstractCellProperty::IsSubType (inline) 394ms 0.36% 18.69% 12216ms 11.16% boost::numeric::ublas::vector_assign (inline) 134ms 0.12% 18.82% 12080ms 11.03% MutableVertexMesh::CheckForIntersections 87ms 0.079% 18.90% 11728ms 10.71% VertexBasedCellPopulation::GetDampingConstant 90ms 0.082% 18.98% 10756ms 9.82% AbstractTargetAreaModifier::UpdateTargetAreas 46ms 0.042% 19.02% 10622ms 9.70% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 27ms 0.025% 19.05% 10493ms 9.58% AbstractCellBasedSimulation::DoCellBirth 1325ms 1.21% 20.26% 10289ms 9.40% std::__new_allocator::allocate (inline) 0 0% 20.26% 9758ms 8.91% std::allocator_traits::allocate (inline) 0 0% 20.26% 9641ms 8.81% std::_Rb_tree::_M_create_node (inline) 1442ms 1.32% 21.57% 9336ms 8.53% std::_Rb_tree::_M_erase 85ms 0.078% 21.65% 9227ms 8.43% Cell::GetMutationState 0 0% 21.65% 9075ms 8.29% std::_Rb_tree::_M_get_node (inline) 822ms 0.75% 22.40% 9062ms 8.28% operator new 2657ms 2.43% 24.83% 9039ms 8.26% boost::numeric::ublas::indexing_vector_assign 759ms 0.69% 25.52% 8977ms 8.20% VertexMesh::ElementIncludesPoint 360ms 0.33% 25.85% 8808ms 8.04% VertexMesh::GetNextEdgeGradientOfElementAtNode 29ms 0.026% 25.88% 8717ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.88% 8466ms 7.73% std::_Rb_tree::_Alloc_node::operator() (inline) 217ms 0.2% 26.07% 8435ms 7.70% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.07% 8261ms 7.55% std::_Rb_tree::_M_drop_node (inline) 529ms 0.48% 26.56% 8232ms 7.52% VertexMesh::GetCentroidOfElement 274ms 0.25% 26.81% 8033ms 7.34% std::__new_allocator::deallocate (inline) 3165ms 2.89% 29.70% 8022ms 7.33% __GI___libc_malloc 0 0% 29.70% 8004ms 7.31% std::set::~set (inline) 0 0% 29.70% 7999ms 7.31% std::allocator_traits::deallocate (inline) 0 0% 29.70% 7948ms 7.26% std::_Rb_tree::_M_put_node (inline) 3230ms 2.95% 32.65% 7740ms 7.07% __GI___libc_free 17ms 0.016% 32.66% 7586ms 6.93% MutableVertexMesh::RemoveDeletedNodesAndElements 450ms 0.41% 33.08% 7449ms 6.80% std::map::operator[] (partial-inline) 1395ms 1.27% 34.35% 7149ms 6.53% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 7005ms 6.40% 40.75% 7005ms 6.40% __strcmp_avx2 133ms 0.12% 40.87% 7005ms 6.40% std::_Rb_tree::_Rb_tree (partial-inline) 667ms 0.61% 41.48% 6618ms 6.04% std::_Rb_tree::_M_copy (inline) 10ms 0.0091% 41.49% 6580ms 6.01% std::set::set (inline) 101ms 0.092% 41.58% 6294ms 5.75% SimpleWntCellCycleModel::GetWntLevel 140ms 0.13% 41.71% 6099ms 5.57% WntConcentration::GetWntLevel 2815ms 2.57% 44.28% 5942ms 5.43% __cxxabiv1::__si_class_type_info::__do_dyncast 2428ms 2.22% 46.50% 5911ms 5.40% std::_Rb_tree::_M_lower_bound (inline) 5905ms 5.39% 51.89% 5905ms 5.39% boost::numeric::ublas::c_vector::operator() 743ms 0.68% 52.57% 5690ms 5.20% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.57% 5375ms 4.91% std::set::insert (inline) 37ms 0.034% 52.60% 5329ms 4.87% MutableVertexMesh::RemoveDeletedNodes 42ms 0.038% 52.64% 5166ms 4.72% EdgeHelper::RemoveDeletedEdges 32ms 0.029% 52.67% 4851ms 4.43% EdgeHelper::UpdateEdgesMapKey 0 0% 52.67% 4787ms 4.37% std::_Rb_tree::lower_bound (inline) 0 0% 52.67% 4787ms 4.37% std::map::lower_bound (inline) 1429ms 1.31% 53.97% 4762ms 4.35% boost::numeric::ublas::c_vector::operator[] (inline) 192ms 0.18% 54.15% 4693ms 4.29% MutableElement::ResetIndex 1ms 0.00091% 54.15% 4629ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 504ms 0.46% 54.61% 4520ms 4.13% std::_Rb_tree::_M_insert_ (inline) 4176ms 3.81% 58.43% 4507ms 4.12% _int_free 50ms 0.046% 58.47% 4436ms 4.05% std::set_intersection (inline) 265ms 0.24% 58.71% 4386ms 4.01% std::__set_intersection 138ms 0.13% 58.84% 4182ms 3.82% AbstractCellPopulation::GetCellUsingLocationIndex 33ms 0.03% 58.87% 4137ms 3.78% Cell::GetCellProliferativeType 3929ms 3.59% 62.46% 3929ms 3.59% boost::numeric::ublas::same_impl_ex 59ms 0.054% 62.51% 3705ms 3.38% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.52% 3527ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 58ms 0.053% 62.57% 3323ms 3.04% Cell::SetCellProliferativeType 849ms 0.78% 63.35% 3257ms 2.97% AbstractElement::GetNodeLocation 0 0% 63.35% 3203ms 2.93% std::insert_iterator::operator= (inline) 2265ms 2.07% 65.42% 3159ms 2.89% _int_malloc 42ms 0.038% 65.45% 2979ms 2.72% std::_Rb_tree::erase 2919ms 2.67% 68.12% 2919ms 2.67% std::_Rb_tree::_S_right (inline) 648ms 0.59% 68.71% 2826ms 2.58% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 68.71% 2819ms 2.57% std::_Rb_tree::_M_insert_unique_ (inline) 403ms 0.37% 69.08% 2769ms 2.53% std::_Rb_tree_const_iterator::operator++ (inline) 716ms 0.65% 69.74% 2624ms 2.40% AbstractCellProperty::IsSame 2ms 0.0018% 69.74% 2556ms 2.33% std::_Rb_tree::_M_insert_unique 49ms 0.045% 69.78% 2546ms 2.33% CellPropertyCollection::HasProperty 22ms 0.02% 69.80% 2536ms 2.32% Cell::GetCellData 0 0% 69.80% 2478ms 2.26% AbstractCellPopulation::WriteResultsToFiles 217ms 0.2% 70.00% 2473ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.00% 2463ms 2.25% Cell::HasCellProperty (inline) 137ms 0.13% 70.13% 2435ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.13% 2313ms 2.11% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.13% 2263ms 2.07% boost::numeric::ublas::c_vector::operator-= (inline) 87ms 0.079% 70.21% 2207ms 2.02% VertexMesh::GetVolumeOfElement 6ms 0.0055% 70.21% 2204ms 2.01% AbstractCellPopulation::Iterator::operator++ (inline) 2175ms 1.99% 72.20% 2175ms 1.99% std::_Rb_tree_increment 227ms 0.21% 72.41% 2169ms 1.98% AbstractCellPopulation::Iterator::IsRealCell (inline) 34ms 0.031% 72.44% 2156ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.44% 2037ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.44% 2025ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1303ms 1.19% 73.63% 1970ms 1.80% std::_Rb_tree::equal_range (inline) 448ms 0.41% 74.04% 1908ms 1.74% std::type_info::operator== (inline) 67ms 0.061% 74.10% 1834ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 2ms 0.0018% 74.10% 1829ms 1.67% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.10% 1829ms 1.67% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.10% 1806ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 39ms 0.036% 74.14% 1691ms 1.54% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 20ms 0.018% 74.15% 1670ms 1.53% VertexMesh::GetSurfaceAreaOfElement 46ms 0.042% 74.20% 1561ms 1.43% Node::RemoveElement 178ms 0.16% 74.36% 1544ms 1.41% CellPropertyCollection::AddProperty 26ms 0.024% 74.38% 1531ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.016% 74.40% 1528ms 1.40% std::set::erase (inline) 0 0% 74.40% 1526ms 1.39% tcache_get (inline) 1526ms 1.39% 75.79% 1526ms 1.39% tcache_get_n (inline) 85ms 0.078% 75.87% 1467ms 1.34% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 83ms 0.076% 75.95% 1431ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.95% 1314ms 1.20% OffLatticeSimulation::ApplyBoundaries 1245ms 1.14% 77.08% 1245ms 1.14% Node::rGetLocation 99ms 0.09% 77.17% 1239ms 1.13% std::less::operator() (inline) 0 0% 77.17% 1221ms 1.12% boost::numeric::ublas::vector_binary::operator() (inline) 100ms 0.091% 77.27% 1195ms 1.09% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 77.27% 1175ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 921ms 0.84% 78.11% 1140ms 1.04% std::operator< (inline) 0 0% 78.11% 1126ms 1.03% boost::numeric::ublas::norm_2 (inline) 0 0% 78.11% 1125ms 1.03% std::_Rb_tree::clear (inline) 496ms 0.45% 78.56% 1116ms 1.02% boost::numeric::ublas::vector_norm_2::apply 1111ms 1.01% 79.57% 1111ms 1.01% std::_Rb_tree_insert_and_rebalance 16ms 0.015% 79.59% 1104ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 79.59% 1101ms 1.01% std::map::clear (inline) 84ms 0.077% 79.67% 1100ms 1.00% std::_Rb_tree::find (inline) 1082ms 0.99% 80.65% 1082ms 0.99% [libchaste_cell_based.so] 47ms 0.043% 80.70% 1064ms 0.97% CellPropertyRegistry::Get 7ms 0.0064% 80.70% 1055ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 155ms 0.14% 80.85% 979ms 0.89% boost::detail::shared_count::~shared_count (inline) 0 0% 80.85% 979ms 0.89% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.85% 947ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 80.85% 947ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 75ms 0.069% 80.92% 943ms 0.86% std::swap_ranges (inline) 940ms 0.86% 81.78% 940ms 0.86% [libchaste_mesh.so] 939ms 0.86% 82.63% 939ms 0.86% std::vector::size (inline) 24ms 0.022% 82.66% 927ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.66% 919ms 0.84% std::map::find (inline) 143ms 0.13% 82.79% 893ms 0.82% boost::numeric::ublas::detail::equals 371ms 0.34% 83.12% 889ms 0.81% Edge::GetMapIndex 0 0% 83.12% 868ms 0.79% std::iter_swap (inline) 868ms 0.79% 83.92% 868ms 0.79% std::swap (inline) 2ms 0.0018% 83.92% 858ms 0.78% VertexMeshWriter::MakeVtkMesh 97ms 0.089% 84.01% 803ms 0.73% MutableElement::GetNodeLocalIndex 795ms 0.73% 84.73% 801ms 0.73% boost::detail::sp_counted_base::release 128ms 0.12% 84.85% 791ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.016% 84.87% 753ms 0.69% MutableElement::RegisterWithEdges (inline) 33ms 0.03% 84.90% 748ms 0.68% Edge::AddElement 727ms 0.66% 85.56% 727ms 0.66% Node::GetIndex 141ms 0.13% 85.69% 725ms 0.66% boost::shared_ptr::shared_ptr (inline) 0 0% 85.69% 703ms 0.64% boost::numeric::ublas::norm_inf (inline) 364ms 0.33% 86.02% 703ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 433ms 0.4% 86.42% 700ms 0.64% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.42% 680ms 0.62% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.42% 679ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 16ms 0.015% 86.43% 679ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.43% 679ms 0.62% std::_Vector_base::_M_allocate (inline) 657ms 0.6% 87.03% 657ms 0.6% operator delete 640ms 0.58% 87.62% 640ms 0.58% [libstdc++.so.6.0.33] 41ms 0.037% 87.66% 637ms 0.58% MutableElement::RegisterWithNodes (inline) 81ms 0.074% 87.73% 630ms 0.58% std::__new_allocator::construct (inline) 0 0% 87.73% 630ms 0.58% std::allocator_traits::construct (inline) 0 0% 87.73% 605ms 0.55% vtkPolygon::New 1ms 0.00091% 87.73% 605ms 0.55% vtkPolygon::vtkPolygon 33ms 0.03% 87.76% 592ms 0.54% Node::AddElement 553ms 0.51% 88.27% 584ms 0.53% boost::detail::shared_count::shared_count (inline) 11ms 0.01% 88.28% 577ms 0.53% std::vector::_M_default_append (inline) 0 0% 88.28% 566ms 0.52% std::_Rb_tree::_M_construct_node (inline) 31ms 0.028% 88.30% 562ms 0.51% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.30% 562ms 0.51% boost::numeric::ublas::vector::vector (inline)