File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96672ms, 88.71% of 108975ms total Dropped 1085 nodes (cum <= 544.88ms) flat flat% sum% cum cum% 0 0% 0% 108546ms 99.61% __libc_start_call_main 0 0% 0% 108546ms 99.61% __libc_start_main_impl 0 0% 0% 108546ms 99.61% _start 0 0% 0% 108528ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108528ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108528ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108528ms 99.59% main 0 0% 0% 108492ms 99.56% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108492ms 99.56% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108492ms 99.56% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108484ms 99.55% AbstractCellBasedSimulation::Solve 20ms 0.018% 0.021% 56175ms 51.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.038% 52962ms 48.60% ForwardEulerNumericalMethod::UpdateAllNodePositions 116ms 0.11% 0.14% 51931ms 47.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 356ms 0.33% 0.47% 40252ms 36.94% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.47% 39122ms 35.90% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.47% 24232ms 22.24% VertexBasedCellPopulation::Update 3ms 0.0028% 0.48% 24104ms 22.12% MutableVertexMesh::ReMesh 14673ms 13.46% 13.94% 23211ms 21.30% Cylindrical2dVertexMesh::GetVectorFromAtoB 97ms 0.089% 14.03% 17747ms 16.29% Cell::ReadyToDivide 75ms 0.069% 14.10% 16500ms 15.14% AbstractPhaseBasedCellCycleModel::ReadyToDivide 360ms 0.33% 14.43% 14880ms 13.65% NagaiHondaForce::GetAdhesionParameter 439ms 0.4% 14.83% 14330ms 13.15% boost::numeric::ublas::c_vector::c_vector (partial-inline) 111ms 0.1% 14.93% 13996ms 12.84% SimpleWntCellCycleModel::UpdateCellCyclePhase 147ms 0.13% 15.07% 13733ms 12.60% CellPropertyCollection::GetPropertiesType (inline) 408ms 0.37% 15.44% 12765ms 11.71% boost::numeric::ublas::vector_assign (inline) 163ms 0.15% 15.59% 12108ms 11.11% MutableVertexMesh::CheckForIntersections 3295ms 3.02% 18.62% 11376ms 10.44% __dynamic_cast 93ms 0.085% 18.70% 11283ms 10.35% AbstractCellProperty::IsSubType (inline) 87ms 0.08% 18.78% 11202ms 10.28% VertexBasedCellPopulation::GetDampingConstant 90ms 0.083% 18.86% 10723ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 57ms 0.052% 18.92% 10607ms 9.73% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 34ms 0.031% 18.95% 10315ms 9.47% AbstractCellBasedSimulation::DoCellBirth 1247ms 1.14% 20.09% 9871ms 9.06% std::__new_allocator::allocate (inline) 2736ms 2.51% 22.60% 9533ms 8.75% boost::numeric::ublas::indexing_vector_assign 1468ms 1.35% 23.95% 9387ms 8.61% std::_Rb_tree::_M_erase 0 0% 23.95% 9357ms 8.59% std::allocator_traits::allocate (inline) 0 0% 23.95% 9305ms 8.54% std::_Rb_tree::_M_create_node (inline) 417ms 0.38% 24.33% 9038ms 8.29% VertexMesh::GetNextEdgeGradientOfElementAtNode 723ms 0.66% 24.99% 8948ms 8.21% VertexMesh::ElementIncludesPoint 25ms 0.023% 25.02% 8873ms 8.14% VertexBasedCellPopulation::GetLocationOfCellCentre 794ms 0.73% 25.75% 8727ms 8.01% operator new 0 0% 25.75% 8700ms 7.98% std::_Rb_tree::_M_get_node (inline) 95ms 0.087% 25.83% 8623ms 7.91% Cell::GetMutationState 223ms 0.2% 26.04% 8603ms 7.89% std::_Rb_tree::~_Rb_tree (inline) 482ms 0.44% 26.48% 8462ms 7.77% VertexMesh::GetCentroidOfElement 0 0% 26.48% 8199ms 7.52% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.48% 8129ms 7.46% std::set::~set (inline) 0 0% 26.48% 8113ms 7.44% std::_Rb_tree::_Alloc_node::operator() (inline) 242ms 0.22% 26.70% 7963ms 7.31% std::__new_allocator::deallocate (inline) 0 0% 26.70% 7942ms 7.29% std::allocator_traits::deallocate (inline) 0 0% 26.70% 7893ms 7.24% std::_Rb_tree::_M_put_node (inline) 3091ms 2.84% 29.54% 7810ms 7.17% __GI___libc_free 3000ms 2.75% 32.29% 7714ms 7.08% __GI___libc_malloc 15ms 0.014% 32.31% 7563ms 6.94% MutableVertexMesh::RemoveDeletedNodesAndElements 417ms 0.38% 32.69% 7388ms 6.78% std::map::operator[] (partial-inline) 1407ms 1.29% 33.98% 7215ms 6.62% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 141ms 0.13% 34.11% 6708ms 6.16% std::_Rb_tree::_Rb_tree (partial-inline) 141ms 0.13% 34.24% 6464ms 5.93% SimpleWntCellCycleModel::GetWntLevel 6448ms 5.92% 40.16% 6448ms 5.92% __strcmp_avx2 685ms 0.63% 40.78% 6339ms 5.82% std::_Rb_tree::_M_copy (inline) 14ms 0.013% 40.80% 6287ms 5.77% std::set::set (inline) 6263ms 5.75% 46.54% 6263ms 5.75% boost::numeric::ublas::c_vector::operator() 134ms 0.12% 46.67% 6253ms 5.74% WntConcentration::GetWntLevel 2456ms 2.25% 48.92% 5757ms 5.28% std::_Rb_tree::_M_lower_bound (inline) 2718ms 2.49% 51.41% 5563ms 5.10% __cxxabiv1::__si_class_type_info::__do_dyncast 28ms 0.026% 51.44% 5412ms 4.97% MutableVertexMesh::RemoveDeletedNodes 780ms 0.72% 52.16% 5370ms 4.93% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.16% 5337ms 4.90% std::set::insert (inline) 37ms 0.034% 52.19% 5244ms 4.81% EdgeHelper::RemoveDeletedEdges 33ms 0.03% 52.22% 4961ms 4.55% EdgeHelper::UpdateEdgesMapKey 1488ms 1.37% 53.59% 4879ms 4.48% boost::numeric::ublas::c_vector::operator[] (inline) 4401ms 4.04% 57.62% 4710ms 4.32% _int_free 0 0% 57.62% 4689ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 57.62% 4689ms 4.30% std::map::lower_bound (inline) 242ms 0.22% 57.85% 4683ms 4.30% MutableElement::ResetIndex 562ms 0.52% 58.36% 4594ms 4.22% std::_Rb_tree::_M_insert_ (inline) 3ms 0.0028% 58.36% 4564ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 64ms 0.059% 58.42% 4462ms 4.09% std::set_intersection (inline) 284ms 0.26% 58.68% 4398ms 4.04% std::__set_intersection 49ms 0.045% 58.73% 4074ms 3.74% Cell::GetCellProliferativeType 124ms 0.11% 58.84% 4044ms 3.71% AbstractCellPopulation::GetCellUsingLocationIndex 3956ms 3.63% 62.47% 3956ms 3.63% boost::numeric::ublas::same_impl_ex 64ms 0.059% 62.53% 3766ms 3.46% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.54% 3518ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.54% 3236ms 2.97% std::insert_iterator::operator= (inline) 764ms 0.7% 63.24% 3171ms 2.91% AbstractElement::GetNodeLocation 2248ms 2.06% 65.30% 3113ms 2.86% _int_malloc 46ms 0.042% 65.35% 3103ms 2.85% Cell::SetCellProliferativeType 33ms 0.03% 65.38% 2951ms 2.71% std::_Rb_tree::erase 7ms 0.0064% 65.38% 2826ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 619ms 0.57% 65.95% 2806ms 2.57% boost::numeric::ublas::vector_binary::size (inline) 2802ms 2.57% 68.52% 2802ms 2.57% std::_Rb_tree::_S_right (inline) 436ms 0.4% 68.92% 2734ms 2.51% std::_Rb_tree_const_iterator::operator++ (inline) 722ms 0.66% 69.58% 2662ms 2.44% AbstractCellProperty::IsSame 42ms 0.039% 69.62% 2629ms 2.41% CellPropertyCollection::HasProperty 0 0% 69.62% 2545ms 2.34% Cell::HasCellProperty (inline) 2ms 0.0018% 69.62% 2511ms 2.30% std::_Rb_tree::_M_insert_unique 226ms 0.21% 69.83% 2471ms 2.27% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.83% 2442ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.83% 2436ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.83% 2424ms 2.22% boost::numeric::ublas::c_vector::operator-= (inline) 107ms 0.098% 69.93% 2417ms 2.22% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 22ms 0.02% 69.95% 2381ms 2.18% Cell::GetCellData 42ms 0.039% 69.99% 2229ms 2.05% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.00092% 69.99% 2213ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 93ms 0.085% 70.07% 2207ms 2.03% VertexMesh::GetVolumeOfElement 209ms 0.19% 70.27% 2188ms 2.01% AbstractCellPopulation::Iterator::IsRealCell (inline) 2137ms 1.96% 72.23% 2137ms 1.96% std::_Rb_tree_increment 0 0% 72.23% 2021ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 72.23% 2007ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0018% 72.23% 1994ms 1.83% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.23% 1994ms 1.83% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1308ms 1.20% 73.43% 1975ms 1.81% std::_Rb_tree::equal_range (inline) 450ms 0.41% 73.84% 1940ms 1.78% std::type_info::operator== (inline) 64ms 0.059% 73.90% 1840ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.90% 1787ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 28ms 0.026% 73.93% 1708ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.026% 73.95% 1698ms 1.56% VertexMesh::GetSurfaceAreaOfElement 43ms 0.039% 73.99% 1554ms 1.43% Node::RemoveElement 23ms 0.021% 74.02% 1533ms 1.41% AbstractCellPopulation::GetLocationIndexUsingCell 18ms 0.017% 74.03% 1519ms 1.39% std::set::erase (inline) 76ms 0.07% 74.10% 1511ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 138ms 0.13% 74.23% 1489ms 1.37% boost::numeric::ublas::vector_reference::operator() (inline) 154ms 0.14% 74.37% 1476ms 1.35% CellPropertyCollection::AddProperty 0 0% 74.37% 1404ms 1.29% tcache_get (inline) 1404ms 1.29% 75.66% 1404ms 1.29% tcache_get_n (inline) 0 0% 75.66% 1388ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 75.66% 1273ms 1.17% OffLatticeSimulation::ApplyBoundaries 0 0% 75.66% 1264ms 1.16% boost::numeric::ublas::norm_2 (inline) 566ms 0.52% 76.18% 1250ms 1.15% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 56ms 0.051% 76.23% 1220ms 1.12% std::less::operator() (inline) 0 0% 76.23% 1192ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1170ms 1.07% 77.30% 1170ms 1.07% Node::rGetLocation 943ms 0.87% 78.17% 1164ms 1.07% std::operator< (inline) 107ms 0.098% 78.27% 1159ms 1.06% std::_Rb_tree::_M_erase_aux (partial-inline) 46ms 0.042% 78.31% 1120ms 1.03% CellPropertyRegistry::Get 1114ms 1.02% 79.33% 1114ms 1.02% std::vector::size (inline) 1090ms 1.00% 80.33% 1090ms 1.00% std::_Rb_tree_insert_and_rebalance 103ms 0.095% 80.43% 1076ms 0.99% std::_Rb_tree::find (inline) 22ms 0.02% 80.45% 1071ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1033ms 0.95% 81.39% 1033ms 0.95% [libchaste_cell_based.so] 1ms 0.00092% 81.39% 1015ms 0.93% std::_Rb_tree::clear (inline) 5ms 0.0046% 81.40% 1001ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 81.40% 998ms 0.92% std::map::clear (inline) 164ms 0.15% 81.55% 992ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 81.55% 992ms 0.91% boost::shared_ptr::~shared_ptr (inline) 0 0% 81.55% 987ms 0.91% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0092% 81.56% 987ms 0.91% boost::numeric::ublas::c_vector::swap (inline) 76ms 0.07% 81.63% 977ms 0.9% std::swap_ranges (inline) 948ms 0.87% 82.50% 948ms 0.87% [libchaste_mesh.so] 28ms 0.026% 82.52% 941ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 118ms 0.11% 82.63% 923ms 0.85% MutableElement::GetNodeLocalIndex 342ms 0.31% 82.95% 921ms 0.85% Edge::GetMapIndex 0 0% 82.95% 908ms 0.83% std::map::find (inline) 141ms 0.13% 83.08% 905ms 0.83% boost::numeric::ublas::detail::equals 0 0% 83.08% 901ms 0.83% std::iter_swap (inline) 901ms 0.83% 83.90% 901ms 0.83% std::swap (inline) 0 0% 83.90% 848ms 0.78% VertexMeshWriter::MakeVtkMesh 843ms 0.77% 84.68% 843ms 0.77% Node::GetIndex 106ms 0.097% 84.77% 814ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 799ms 0.73% 85.51% 807ms 0.74% boost::detail::sp_counted_base::release 153ms 0.14% 85.65% 777ms 0.71% boost::shared_ptr::shared_ptr (inline) 27ms 0.025% 85.67% 770ms 0.71% Edge::AddElement 9ms 0.0083% 85.68% 767ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 85.68% 730ms 0.67% boost::numeric::ublas::norm_inf (inline) 370ms 0.34% 86.02% 730ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 390ms 0.36% 86.38% 720ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 86ms 0.079% 86.46% 671ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.46% 671ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.46% 669ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 86.46% 658ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.47% 658ms 0.6% std::_Rb_tree::_M_insert_node (inline) 2ms 0.0018% 86.48% 653ms 0.6% std::_Vector_base::_M_allocate (inline) 601ms 0.55% 87.03% 624ms 0.57% boost::detail::shared_count::shared_count (inline) 616ms 0.57% 87.59% 616ms 0.57% [libstdc++.so.6.0.33] 0 0% 87.59% 605ms 0.56% std::_Rb_tree::_M_construct_node (inline) 0 0% 87.59% 599ms 0.55% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.59% 595ms 0.55% vtkPolygon::New 0 0% 87.59% 595ms 0.55% vtkPolygon::vtkPolygon 36ms 0.033% 87.63% 586ms 0.54% MutableElement::RegisterWithNodes (inline) 585ms 0.54% 88.16% 585ms 0.54% operator delete 567ms 0.52% 88.68% 567ms 0.52% boost::shared_ptr::operator-> (inline) 29ms 0.027% 88.71% 547ms 0.5% Node::AddElement