File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 98485ms, 88.84% of 110860ms total Dropped 1047 nodes (cum <= 554.30ms) flat flat% sum% cum cum% 0 0% 0% 110374ms 99.56% __libc_start_call_main 0 0% 0% 110374ms 99.56% __libc_start_main_impl 0 0% 0% 110374ms 99.56% _start 0 0% 0% 110355ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110355ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110355ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110355ms 99.54% main 0 0% 0% 110321ms 99.51% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110321ms 99.51% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110321ms 99.51% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 110314ms 99.51% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.02% 57437ms 51.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 19ms 0.017% 0.037% 54218ms 48.91% ForwardEulerNumericalMethod::UpdateAllNodePositions 107ms 0.097% 0.13% 53179ms 47.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 340ms 0.31% 0.44% 40617ms 36.64% NagaiHondaForce::AddForceContribution 1ms 0.0009% 0.44% 39748ms 35.85% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0009% 0.44% 24502ms 22.10% VertexBasedCellPopulation::Update 1ms 0.0009% 0.44% 24385ms 22.00% MutableVertexMesh::ReMesh 14387ms 12.98% 13.42% 22894ms 20.65% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.073% 13.49% 17917ms 16.16% Cell::ReadyToDivide 79ms 0.071% 13.56% 16718ms 15.08% AbstractPhaseBasedCellCycleModel::ReadyToDivide 307ms 0.28% 13.84% 15399ms 13.89% NagaiHondaForce::GetAdhesionParameter 107ms 0.097% 13.94% 14286ms 12.89% SimpleWntCellCycleModel::UpdateCellCyclePhase 111ms 0.1% 14.04% 14283ms 12.88% CellPropertyCollection::GetPropertiesType (inline) 399ms 0.36% 14.40% 14246ms 12.85% boost::numeric::ublas::c_vector::c_vector (partial-inline) 410ms 0.37% 14.77% 12731ms 11.48% boost::numeric::ublas::vector_assign (inline) 93ms 0.084% 14.85% 12081ms 10.90% VertexBasedCellPopulation::GetDampingConstant 144ms 0.13% 14.98% 11988ms 10.81% MutableVertexMesh::CheckForIntersections 3601ms 3.25% 18.23% 11914ms 10.75% __dynamic_cast 111ms 0.1% 18.33% 11832ms 10.67% AbstractCellProperty::IsSubType (inline) 76ms 0.069% 18.40% 10753ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 48ms 0.043% 18.44% 10655ms 9.61% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1376ms 1.24% 19.68% 10513ms 9.48% std::__new_allocator::allocate (inline) 27ms 0.024% 19.71% 10506ms 9.48% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.71% 9942ms 8.97% std::_Rb_tree::_M_create_node (inline) 0 0% 19.71% 9926ms 8.95% std::allocator_traits::allocate (inline) 1491ms 1.34% 21.05% 9511ms 8.58% std::_Rb_tree::_M_erase 2581ms 2.33% 23.38% 9376ms 8.46% boost::numeric::ublas::indexing_vector_assign 0 0% 23.38% 9303ms 8.39% std::_Rb_tree::_M_get_node (inline) 852ms 0.77% 24.15% 9254ms 8.35% operator new 72ms 0.065% 24.21% 9241ms 8.34% Cell::GetMutationState 27ms 0.024% 24.24% 9033ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 779ms 0.7% 24.94% 8850ms 7.98% VertexMesh::ElementIncludesPoint 369ms 0.33% 25.27% 8763ms 7.90% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.27% 8746ms 7.89% std::_Rb_tree::_Alloc_node::operator() (inline) 227ms 0.2% 25.48% 8684ms 7.83% std::_Rb_tree::~_Rb_tree (inline) 478ms 0.43% 25.91% 8493ms 7.66% VertexMesh::GetCentroidOfElement 0 0% 25.91% 8317ms 7.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 25.91% 8220ms 7.41% std::set::~set (inline) 3219ms 2.90% 28.81% 8218ms 7.41% __GI___libc_malloc 268ms 0.24% 29.06% 8088ms 7.30% std::__new_allocator::deallocate (inline) 0 0% 29.06% 8061ms 7.27% std::allocator_traits::deallocate (inline) 0 0% 29.06% 8006ms 7.22% std::_Rb_tree::_M_put_node (inline) 3162ms 2.85% 31.91% 7766ms 7.01% __GI___libc_free 456ms 0.41% 32.32% 7766ms 7.01% std::map::operator[] (partial-inline) 20ms 0.018% 32.34% 7758ms 7.00% MutableVertexMesh::RemoveDeletedNodesAndElements 125ms 0.11% 32.45% 7139ms 6.44% std::_Rb_tree::_Rb_tree (partial-inline) 1370ms 1.24% 33.69% 7133ms 6.43% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 653ms 0.59% 34.27% 6741ms 6.08% std::_Rb_tree::_M_copy (inline) 10ms 0.009% 34.28% 6697ms 6.04% std::set::set (inline) 6535ms 5.89% 40.18% 6535ms 5.89% __strcmp_avx2 98ms 0.088% 40.27% 6512ms 5.87% SimpleWntCellCycleModel::GetWntLevel 6316ms 5.70% 45.96% 6316ms 5.70% boost::numeric::ublas::c_vector::operator() 150ms 0.14% 46.10% 6284ms 5.67% WntConcentration::GetWntLevel 2501ms 2.26% 48.36% 6272ms 5.66% std::_Rb_tree::_M_lower_bound (inline) 720ms 0.65% 49.01% 5814ms 5.24% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.01% 5646ms 5.09% std::set::insert (inline) 2740ms 2.47% 51.48% 5633ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 33ms 0.03% 51.51% 5558ms 5.01% MutableVertexMesh::RemoveDeletedNodes 44ms 0.04% 51.55% 5375ms 4.85% EdgeHelper::RemoveDeletedEdges 47ms 0.042% 51.59% 5079ms 4.58% EdgeHelper::UpdateEdgesMapKey 0 0% 51.59% 5048ms 4.55% std::_Rb_tree::lower_bound (inline) 0 0% 51.59% 5048ms 4.55% std::map::lower_bound (inline) 1519ms 1.37% 52.96% 4978ms 4.49% boost::numeric::ublas::c_vector::operator[] (inline) 221ms 0.2% 53.16% 4881ms 4.40% MutableElement::ResetIndex 558ms 0.5% 53.66% 4756ms 4.29% std::_Rb_tree::_M_insert_ (inline) 2ms 0.0018% 53.66% 4730ms 4.27% AbstractCellBasedSimulation::DoCellRemoval (inline) 4248ms 3.83% 57.50% 4595ms 4.14% _int_free 49ms 0.044% 57.54% 4593ms 4.14% std::set_intersection (inline) 284ms 0.26% 57.80% 4544ms 4.10% std::__set_intersection 96ms 0.087% 57.88% 4227ms 3.81% AbstractCellPopulation::GetCellUsingLocationIndex 69ms 0.062% 57.94% 4068ms 3.67% Cell::GetCellProliferativeType 3900ms 3.52% 61.46% 3900ms 3.52% boost::numeric::ublas::same_impl_ex 52ms 0.047% 61.51% 3780ms 3.41% AbstractCellProperty::IsType (inline) 5ms 0.0045% 61.51% 3682ms 3.32% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 50ms 0.045% 61.56% 3376ms 3.05% Cell::SetCellProliferativeType 0 0% 61.56% 3368ms 3.04% std::insert_iterator::operator= (inline) 2398ms 2.16% 63.72% 3258ms 2.94% _int_malloc 3257ms 2.94% 66.66% 3257ms 2.94% std::_Rb_tree::_S_right (inline) 776ms 0.7% 67.36% 3207ms 2.89% AbstractElement::GetNodeLocation 34ms 0.031% 67.39% 2997ms 2.70% std::_Rb_tree::erase 8ms 0.0072% 67.40% 2943ms 2.65% std::_Rb_tree::_M_insert_unique_ (inline) 429ms 0.39% 67.78% 2875ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 631ms 0.57% 68.35% 2852ms 2.57% boost::numeric::ublas::vector_binary::size (inline) 0 0% 68.35% 2703ms 2.44% std::_Rb_tree::_M_insert_unique 797ms 0.72% 69.07% 2658ms 2.40% AbstractCellProperty::IsSame 47ms 0.042% 69.12% 2623ms 2.37% CellPropertyCollection::HasProperty 19ms 0.017% 69.13% 2532ms 2.28% Cell::GetCellData 0 0% 69.13% 2504ms 2.26% Cell::HasCellProperty (inline) 0 0% 69.13% 2418ms 2.18% boost::numeric::ublas::c_vector::operator-= (inline) 260ms 0.23% 69.37% 2416ms 2.18% VertexMesh::GetAreaGradientOfElementAtNode 9ms 0.0081% 69.37% 2396ms 2.16% AbstractCellPopulation::Iterator::operator++ (inline) 224ms 0.2% 69.58% 2368ms 2.14% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.58% 2354ms 2.12% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.58% 2333ms 2.10% boost::numeric::ublas::c_vector::assign (inline) 109ms 0.098% 69.68% 2330ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 86ms 0.078% 69.75% 2310ms 2.08% VertexMesh::GetVolumeOfElement 2243ms 2.02% 71.78% 2243ms 2.02% std::_Rb_tree_increment 28ms 0.025% 71.80% 2200ms 1.98% std::_Rb_tree::_M_emplace_hint_unique 1370ms 1.24% 73.04% 2057ms 1.86% std::_Rb_tree::equal_range (inline) 0 0% 73.04% 1940ms 1.75% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0009% 73.04% 1930ms 1.74% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 73.04% 1929ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.04% 1929ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 67ms 0.06% 73.10% 1893ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 29ms 0.026% 73.12% 1880ms 1.70% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 481ms 0.43% 73.56% 1861ms 1.68% std::type_info::operator== (inline) 0 0% 73.56% 1727ms 1.56% VertexMeshWriter::WriteVtkUsingMesh 24ms 0.022% 73.58% 1685ms 1.52% VertexMesh::GetSurfaceAreaOfElement 49ms 0.044% 73.62% 1627ms 1.47% Node::RemoveElement 30ms 0.027% 73.65% 1618ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.068% 73.72% 1592ms 1.44% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 15ms 0.014% 73.73% 1586ms 1.43% std::set::erase (inline) 0 0% 73.73% 1542ms 1.39% tcache_get (inline) 1542ms 1.39% 75.12% 1542ms 1.39% tcache_get_n (inline) 162ms 0.15% 75.27% 1540ms 1.39% CellPropertyCollection::AddProperty 140ms 0.13% 75.40% 1527ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.40% 1416ms 1.28% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.0009% 75.40% 1331ms 1.20% OffLatticeSimulation::ApplyBoundaries 1245ms 1.12% 76.52% 1245ms 1.12% Node::rGetLocation 57ms 0.051% 76.57% 1229ms 1.11% std::less::operator() (inline) 0 0% 76.57% 1196ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.57% 1183ms 1.07% boost::numeric::ublas::norm_2 (inline) 100ms 0.09% 76.66% 1180ms 1.06% std::_Rb_tree::find (inline) 524ms 0.47% 77.13% 1178ms 1.06% boost::numeric::ublas::vector_norm_2::apply 986ms 0.89% 78.02% 1172ms 1.06% std::operator< (inline) 119ms 0.11% 78.13% 1152ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 1139ms 1.03% 79.16% 1139ms 1.03% std::_Rb_tree_insert_and_rebalance 1134ms 1.02% 80.18% 1134ms 1.02% [libchaste_cell_based.so] 17ms 0.015% 80.20% 1111ms 1.00% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 41ms 0.037% 80.23% 1082ms 0.98% CellPropertyRegistry::Get 0 0% 80.23% 1058ms 0.95% std::_Rb_tree::clear (inline) 1046ms 0.94% 81.18% 1046ms 0.94% std::vector::size (inline) 0 0% 81.18% 1045ms 0.94% std::map::clear (inline) 172ms 0.16% 81.33% 1010ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 81.33% 1010ms 0.91% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0081% 81.34% 999ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 24ms 0.022% 81.36% 986ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.36% 970ms 0.87% std::map::find (inline) 165ms 0.15% 81.51% 950ms 0.86% boost::numeric::ublas::detail::equals 0 0% 81.51% 948ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 14ms 0.013% 81.52% 948ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 362ms 0.33% 81.85% 945ms 0.85% Edge::GetMapIndex 936ms 0.84% 82.69% 936ms 0.84% [libchaste_mesh.so] 103ms 0.093% 82.79% 934ms 0.84% std::swap_ranges (inline) 107ms 0.097% 82.88% 884ms 0.8% MutableElement::GetNodeLocalIndex 0 0% 82.88% 861ms 0.78% VertexMeshWriter::MakeVtkMesh 142ms 0.13% 83.01% 859ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 28ms 0.025% 83.04% 847ms 0.76% Edge::AddElement 17ms 0.015% 83.05% 845ms 0.76% MutableElement::RegisterWithEdges (inline) 0 0% 83.05% 831ms 0.75% std::iter_swap (inline) 831ms 0.75% 83.80% 831ms 0.75% std::swap (inline) 0 0% 83.80% 815ms 0.74% CellPropertyCollection::~CellPropertyCollection (inline) 803ms 0.72% 84.53% 808ms 0.73% boost::detail::sp_counted_base::release 794ms 0.72% 85.24% 794ms 0.72% Node::GetIndex 473ms 0.43% 85.67% 771ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.67% 746ms 0.67% boost::numeric::ublas::norm_inf (inline) 387ms 0.35% 86.02% 746ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 145ms 0.13% 86.15% 709ms 0.64% boost::shared_ptr::shared_ptr (inline) 115ms 0.1% 86.25% 679ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.25% 679ms 0.61% std::allocator_traits::construct (inline) 0 0% 86.25% 678ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.023% 86.28% 678ms 0.61% std::_Rb_tree::_M_insert_node (inline) 26ms 0.023% 86.30% 669ms 0.6% MutableElement::RegisterWithNodes (inline) 648ms 0.58% 86.88% 648ms 0.58% operator delete 38ms 0.034% 86.92% 643ms 0.58% Node::AddElement 0 0% 86.92% 639ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.92% 638ms 0.58% vtkPolygon::New 0 0% 86.92% 637ms 0.57% vtkPolygon::vtkPolygon 1ms 0.0009% 86.92% 621ms 0.56% std::_Vector_base::_M_allocate (inline) 606ms 0.55% 87.47% 606ms 0.55% [libstdc++.so.6.0.33] 15ms 0.014% 87.48% 602ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.48% 602ms 0.54% boost::numeric::ublas::vector::vector (inline) 584ms 0.53% 88.01% 584ms 0.53% boost::shared_ptr::operator-> (inline) 541ms 0.49% 88.49% 564ms 0.51% boost::detail::shared_count::shared_count (inline) 380ms 0.34% 88.84% 556ms 0.5% CellPropertyCollection::GetProperty