File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96827ms, 87.98% of 110060ms total Dropped 1177 nodes (cum <= 550.30ms) flat flat% sum% cum cum% 0 0% 0% 109719ms 99.69% __libc_start_call_main 0 0% 0% 109719ms 99.69% __libc_start_main_impl 0 0% 0% 109719ms 99.69% _start 0 0% 0% 109695ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109695ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109695ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109695ms 99.67% main 0 0% 0% 109653ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109653ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109653ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0045% 0.0045% 109646ms 99.62% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.017% 57083ms 51.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.016% 0.034% 53776ms 48.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 153ms 0.14% 0.17% 52233ms 47.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 334ms 0.3% 0.48% 40040ms 36.38% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.48% 39208ms 35.62% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.48% 24174ms 21.96% VertexBasedCellPopulation::Update 0 0% 0.48% 23997ms 21.80% MutableVertexMesh::ReMesh 14643ms 13.30% 13.78% 23336ms 21.20% Cylindrical2dVertexMesh::GetVectorFromAtoB 102ms 0.093% 13.88% 17701ms 16.08% Cell::ReadyToDivide 76ms 0.069% 13.94% 16353ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 313ms 0.28% 14.23% 14468ms 13.15% NagaiHondaForce::GetAdhesionParameter 174ms 0.16% 14.39% 14065ms 12.78% SimpleWntCellCycleModel::UpdateCellCyclePhase 92ms 0.084% 14.47% 13976ms 12.70% CellPropertyCollection::GetPropertiesType (inline) 471ms 0.43% 14.90% 13855ms 12.59% boost::numeric::ublas::c_vector::c_vector (partial-inline) 289ms 0.26% 15.16% 12376ms 11.24% boost::numeric::ublas::vector_assign (inline) 3476ms 3.16% 18.32% 11999ms 10.90% __dynamic_cast 143ms 0.13% 18.45% 11850ms 10.77% MutableVertexMesh::CheckForIntersections 54ms 0.049% 18.50% 11848ms 10.77% AbstractCellProperty::IsSubType (inline) 70ms 0.064% 18.56% 11595ms 10.54% VertexBasedCellPopulation::GetDampingConstant 82ms 0.075% 18.64% 10834ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 43ms 0.039% 18.68% 10711ms 9.73% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 18.70% 10356ms 9.41% AbstractCellBasedSimulation::DoCellBirth 1483ms 1.35% 20.05% 10176ms 9.25% std::__new_allocator::allocate (inline) 0 0% 20.05% 9626ms 8.75% std::_Rb_tree::_M_create_node (inline) 0 0% 20.05% 9612ms 8.73% std::allocator_traits::allocate (inline) 2833ms 2.57% 22.62% 9462ms 8.60% boost::numeric::ublas::indexing_vector_assign 367ms 0.33% 22.95% 9458ms 8.59% VertexMesh::GetNextEdgeGradientOfElementAtNode 1316ms 1.20% 24.15% 9148ms 8.31% std::_Rb_tree::_M_erase 0 0% 24.15% 8913ms 8.10% std::_Rb_tree::_M_get_node (inline) 36ms 0.033% 24.18% 8749ms 7.95% VertexBasedCellPopulation::GetLocationOfCellCentre 823ms 0.75% 24.93% 8748ms 7.95% operator new 827ms 0.75% 25.68% 8665ms 7.87% VertexMesh::ElementIncludesPoint 90ms 0.082% 25.76% 8608ms 7.82% Cell::GetMutationState 0 0% 25.76% 8479ms 7.70% std::_Rb_tree::_Alloc_node::operator() (inline) 236ms 0.21% 25.98% 8219ms 7.47% std::_Rb_tree::~_Rb_tree (inline) 433ms 0.39% 26.37% 8205ms 7.46% VertexMesh::GetCentroidOfElement 0 0% 26.37% 8114ms 7.37% std::_Rb_tree::_M_drop_node (inline) 233ms 0.21% 26.58% 7876ms 7.16% std::__new_allocator::deallocate (inline) 0 0% 26.58% 7869ms 7.15% std::allocator_traits::deallocate (inline) 13ms 0.012% 26.59% 7840ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.59% 7788ms 7.08% std::set::~set (inline) 0 0% 26.59% 7774ms 7.06% std::_Rb_tree::_M_put_node (inline) 438ms 0.4% 26.99% 7752ms 7.04% std::map::operator[] (partial-inline) 2931ms 2.66% 29.65% 7715ms 7.01% __GI___libc_malloc 1502ms 1.36% 31.02% 7467ms 6.78% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2393ms 2.17% 33.19% 7299ms 6.63% __GI___libc_free 170ms 0.15% 33.35% 7174ms 6.52% std::_Rb_tree::_Rb_tree (partial-inline) 6997ms 6.36% 39.71% 6997ms 6.36% __strcmp_avx2 707ms 0.64% 40.35% 6761ms 6.14% std::_Rb_tree::_M_copy (inline) 8ms 0.0073% 40.36% 6728ms 6.11% std::set::set (inline) 122ms 0.11% 40.47% 6343ms 5.76% SimpleWntCellCycleModel::GetWntLevel 6246ms 5.68% 46.14% 6246ms 5.68% boost::numeric::ublas::c_vector::operator() 2474ms 2.25% 48.39% 6209ms 5.64% std::_Rb_tree::_M_lower_bound (inline) 182ms 0.17% 48.55% 6141ms 5.58% WntConcentration::GetWntLevel 2850ms 2.59% 51.14% 5846ms 5.31% __cxxabiv1::__si_class_type_info::__do_dyncast 773ms 0.7% 51.85% 5823ms 5.29% std::_Rb_tree::_M_clone_node (inline) 19ms 0.017% 51.86% 5545ms 5.04% MutableVertexMesh::RemoveDeletedNodes 47ms 0.043% 51.91% 5357ms 4.87% EdgeHelper::RemoveDeletedEdges 1976ms 1.80% 53.70% 5342ms 4.85% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.70% 5205ms 4.73% std::set::insert (inline) 0 0% 53.70% 5049ms 4.59% std::_Rb_tree::lower_bound (inline) 0 0% 53.70% 5049ms 4.59% std::map::lower_bound (inline) 39ms 0.035% 53.74% 4993ms 4.54% EdgeHelper::UpdateEdgesMapKey 4498ms 4.09% 57.82% 4896ms 4.45% _int_free 215ms 0.2% 58.02% 4713ms 4.28% MutableElement::ResetIndex 1ms 0.00091% 58.02% 4663ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 152ms 0.14% 58.16% 4495ms 4.08% AbstractCellPopulation::GetCellUsingLocationIndex 475ms 0.43% 58.59% 4392ms 3.99% std::_Rb_tree::_M_insert_ (inline) 147ms 0.13% 58.72% 4294ms 3.90% std::set_intersection (inline) 243ms 0.22% 58.94% 4147ms 3.77% std::__set_intersection 55ms 0.05% 58.99% 4117ms 3.74% Cell::GetCellProliferativeType 54ms 0.049% 59.04% 3870ms 3.52% AbstractCellProperty::IsType (inline) 3683ms 3.35% 62.39% 3683ms 3.35% boost::numeric::ublas::same_impl_ex 13ms 0.012% 62.40% 3523ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2262ms 2.06% 64.46% 3252ms 2.95% _int_malloc 44ms 0.04% 64.50% 3192ms 2.90% Cell::SetCellProliferativeType 0 0% 64.50% 3135ms 2.85% std::insert_iterator::operator= (inline) 3094ms 2.81% 67.31% 3094ms 2.81% std::_Rb_tree::_S_right (inline) 906ms 0.82% 68.13% 3036ms 2.76% AbstractElement::GetNodeLocation 72ms 0.065% 68.20% 2991ms 2.72% std::_Rb_tree::erase 41ms 0.037% 68.23% 2802ms 2.55% CellPropertyCollection::HasProperty 678ms 0.62% 68.85% 2797ms 2.54% AbstractCellProperty::IsSame 7ms 0.0064% 68.86% 2735ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 68.86% 2723ms 2.47% Cell::HasCellProperty (inline) 38ms 0.035% 68.89% 2584ms 2.35% Cell::GetCellData 226ms 0.21% 69.10% 2576ms 2.34% VertexMesh::GetAreaGradientOfElementAtNode 266ms 0.24% 69.34% 2573ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.34% 2535ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 659ms 0.6% 69.94% 2534ms 2.30% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.94% 2502ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.94% 2478ms 2.25% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0018% 69.94% 2470ms 2.24% std::_Rb_tree::_M_insert_unique 83ms 0.075% 70.01% 2300ms 2.09% VertexMesh::GetVolumeOfElement 5ms 0.0045% 70.02% 2237ms 2.03% AbstractCellPopulation::Iterator::operator++ (inline) 186ms 0.17% 70.19% 2227ms 2.02% AbstractCellPopulation::Iterator::IsRealCell (inline) 44ms 0.04% 70.23% 2214ms 2.01% std::_Rb_tree::_M_emplace_hint_unique 50ms 0.045% 70.27% 2190ms 1.99% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 489ms 0.44% 70.72% 2119ms 1.93% std::type_info::operator== (inline) 2075ms 1.89% 72.60% 2075ms 1.89% std::_Rb_tree_increment 1ms 0.00091% 72.60% 2046ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.60% 2046ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.60% 2041ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.60% 2030ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1301ms 1.18% 73.79% 1952ms 1.77% std::_Rb_tree::equal_range (inline) 65ms 0.059% 73.84% 1825ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00091% 73.85% 1812ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 27ms 0.025% 73.87% 1751ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 43ms 0.039% 73.91% 1603ms 1.46% AbstractCellPopulation::GetLocationIndexUsingCell 30ms 0.027% 73.94% 1574ms 1.43% VertexMesh::GetSurfaceAreaOfElement 75ms 0.068% 74.00% 1553ms 1.41% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 64ms 0.058% 74.06% 1473ms 1.34% boost::numeric::ublas::vector_reference::operator() (inline) 44ms 0.04% 74.10% 1452ms 1.32% Node::RemoveElement 0 0% 74.10% 1422ms 1.29% boost::numeric::ublas::vector_binary::operator() (inline) 12ms 0.011% 74.11% 1410ms 1.28% std::set::erase (inline) 149ms 0.14% 74.25% 1396ms 1.27% CellPropertyCollection::AddProperty 2ms 0.0018% 74.25% 1392ms 1.26% OffLatticeSimulation::ApplyBoundaries 0 0% 74.25% 1370ms 1.24% boost::numeric::ublas::norm_2 (inline) 584ms 0.53% 74.78% 1359ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 100ms 0.091% 74.87% 1349ms 1.23% std::less::operator() (inline) 0 0% 74.87% 1342ms 1.22% tcache_get (inline) 1342ms 1.22% 76.09% 1342ms 1.22% tcache_get_n (inline) 1329ms 1.21% 77.30% 1329ms 1.21% [libchaste_cell_based.so] 999ms 0.91% 78.21% 1249ms 1.13% std::operator< (inline) 21ms 0.019% 78.23% 1201ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 96ms 0.087% 78.31% 1194ms 1.08% std::_Rb_tree::find (inline) 0 0% 78.31% 1170ms 1.06% std::_Rb_tree::clear (inline) 20ms 0.018% 78.33% 1157ms 1.05% CellPropertyRegistry::Get 0 0% 78.33% 1152ms 1.05% std::map::clear (inline) 0 0% 78.33% 1147ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 78ms 0.071% 78.40% 1144ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 1104ms 1.00% 79.40% 1104ms 1.00% std::_Rb_tree_insert_and_rebalance 6ms 0.0055% 79.41% 1102ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 111ms 0.1% 79.51% 1056ms 0.96% boost::detail::shared_count::~shared_count (inline) 0 0% 79.51% 1056ms 0.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.51% 1037ms 0.94% std::map::find (inline) 0 0% 79.51% 1009ms 0.92% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0091% 79.52% 1009ms 0.92% boost::numeric::ublas::c_vector::swap (inline) 69ms 0.063% 79.58% 999ms 0.91% std::swap_ranges (inline) 994ms 0.9% 80.49% 994ms 0.9% Node::rGetLocation 12ms 0.011% 80.50% 968ms 0.88% boost::numeric::ublas::detail::expression_type_check (inline) 206ms 0.19% 80.68% 948ms 0.86% boost::numeric::ublas::detail::equals 932ms 0.85% 81.53% 932ms 0.85% std::swap (inline) 0 0% 81.53% 930ms 0.84% std::iter_swap (inline) 868ms 0.79% 82.32% 895ms 0.81% boost::detail::sp_counted_base::release 1ms 0.00091% 82.32% 864ms 0.79% VertexMeshWriter::MakeVtkMesh 859ms 0.78% 83.10% 859ms 0.78% std::vector::size (inline) 20ms 0.018% 83.12% 789ms 0.72% Edge::AddElement 16ms 0.015% 83.13% 780ms 0.71% MutableElement::RegisterWithEdges (inline) 402ms 0.37% 83.50% 776ms 0.71% Edge::GetMapIndex 72ms 0.065% 83.56% 768ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 226ms 0.21% 83.77% 766ms 0.7% std::__new_allocator::construct (inline) 0 0% 83.77% 766ms 0.7% std::allocator_traits::construct (inline) 761ms 0.69% 84.46% 761ms 0.69% [libchaste_mesh.so] 27ms 0.025% 84.49% 760ms 0.69% AbstractNumericalMethod::DetectStepSizeExceptions 406ms 0.37% 84.85% 758ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 126ms 0.11% 84.97% 733ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 162ms 0.15% 85.12% 727ms 0.66% boost::shared_ptr::shared_ptr (inline) 154ms 0.14% 85.26% 725ms 0.66% MutableElement::GetNodeLocalIndex 721ms 0.66% 85.91% 721ms 0.66% [libstdc++.so.6.0.33] 0 0% 85.91% 713ms 0.65% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.91% 703ms 0.64% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.91% 698ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 85.91% 696ms 0.63% std::_Vector_base::_M_allocate (inline) 0 0% 85.91% 694ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 24ms 0.022% 85.93% 694ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.93% 676ms 0.61% boost::numeric::ublas::norm_inf (inline) 397ms 0.36% 86.29% 676ms 0.61% boost::numeric::ublas::vector_norm_inf::apply (inline) 648ms 0.59% 86.88% 648ms 0.59% Node::GetIndex 1ms 0.00091% 86.88% 628ms 0.57% vtkPolygon::New 0 0% 86.88% 626ms 0.57% vtkPolygon::vtkPolygon 33ms 0.03% 86.91% 597ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.91% 597ms 0.54% boost::numeric::ublas::vector::vector (inline) 29ms 0.026% 86.94% 592ms 0.54% MutableElement::RegisterWithNodes (inline) 12ms 0.011% 86.95% 581ms 0.53% std::vector::_M_default_append (inline) 544ms 0.49% 87.45% 565ms 0.51% boost::detail::shared_count::shared_count (inline) 27ms 0.025% 87.47% 559ms 0.51% Node::AddElement 558ms 0.51% 87.98% 558ms 0.51% operator delete