File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95210ms, 87.42% of 108905ms total Dropped 1142 nodes (cum <= 544.52ms) flat flat% sum% cum cum% 0 0% 0% 108473ms 99.60% __libc_start_call_main 0 0% 0% 108473ms 99.60% __libc_start_main_impl 0 0% 0% 108473ms 99.60% _start 0 0% 0% 108451ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108451ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108451ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108451ms 99.58% main 0 0% 0% 108407ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108407ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108407ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108398ms 99.53% AbstractCellBasedSimulation::Solve 19ms 0.017% 0.02% 56346ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.015% 0.035% 53068ms 48.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 142ms 0.13% 0.17% 51900ms 47.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 320ms 0.29% 0.46% 40305ms 37.01% NagaiHondaForce::AddForceContribution 3ms 0.0028% 0.46% 38819ms 35.64% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.46% 23964ms 22.00% VertexBasedCellPopulation::Update 0 0% 0.46% 23829ms 21.88% MutableVertexMesh::ReMesh 14685ms 13.48% 13.95% 23302ms 21.40% Cylindrical2dVertexMesh::GetVectorFromAtoB 106ms 0.097% 14.04% 17641ms 16.20% Cell::ReadyToDivide 61ms 0.056% 14.10% 16416ms 15.07% AbstractPhaseBasedCellCycleModel::ReadyToDivide 349ms 0.32% 14.42% 15017ms 13.79% NagaiHondaForce::GetAdhesionParameter 460ms 0.42% 14.84% 14148ms 12.99% boost::numeric::ublas::c_vector::c_vector (partial-inline) 153ms 0.14% 14.98% 14101ms 12.95% SimpleWntCellCycleModel::UpdateCellCyclePhase 125ms 0.11% 15.10% 13537ms 12.43% CellPropertyCollection::GetPropertiesType (inline) 303ms 0.28% 15.38% 12586ms 11.56% boost::numeric::ublas::vector_assign (inline) 144ms 0.13% 15.51% 11807ms 10.84% MutableVertexMesh::CheckForIntersections 3258ms 2.99% 18.50% 11387ms 10.46% __dynamic_cast 60ms 0.055% 18.56% 11267ms 10.35% AbstractCellProperty::IsSubType (inline) 79ms 0.073% 18.63% 11033ms 10.13% VertexBasedCellPopulation::GetDampingConstant 64ms 0.059% 18.69% 10711ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 56ms 0.051% 18.74% 10616ms 9.75% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.028% 18.77% 10225ms 9.39% AbstractCellBasedSimulation::DoCellBirth 1241ms 1.14% 19.91% 10075ms 9.25% std::__new_allocator::allocate (inline) 0 0% 19.91% 9698ms 8.91% std::_Rb_tree::_M_create_node (inline) 2932ms 2.69% 22.60% 9567ms 8.78% boost::numeric::ublas::indexing_vector_assign 0 0% 22.60% 9566ms 8.78% std::allocator_traits::allocate (inline) 321ms 0.29% 22.89% 9192ms 8.44% VertexMesh::GetNextEdgeGradientOfElementAtNode 1290ms 1.18% 24.08% 9114ms 8.37% std::_Rb_tree::_M_erase 0 0% 24.08% 8891ms 8.16% std::_Rb_tree::_M_get_node (inline) 833ms 0.76% 24.84% 8875ms 8.15% operator new 835ms 0.77% 25.61% 8719ms 8.01% VertexMesh::ElementIncludesPoint 38ms 0.035% 25.64% 8672ms 7.96% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.64% 8574ms 7.87% std::_Rb_tree::_Alloc_node::operator() (inline) 97ms 0.089% 25.73% 8458ms 7.77% Cell::GetMutationState 459ms 0.42% 26.15% 8332ms 7.65% VertexMesh::GetCentroidOfElement 246ms 0.23% 26.38% 8273ms 7.60% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.38% 8265ms 7.59% std::_Rb_tree::_M_drop_node (inline) 230ms 0.21% 26.59% 8038ms 7.38% std::__new_allocator::deallocate (inline) 0 0% 26.59% 8035ms 7.38% std::allocator_traits::deallocate (inline) 0 0% 26.59% 7970ms 7.32% std::_Rb_tree::_M_put_node (inline) 0 0% 26.59% 7871ms 7.23% std::set::~set (inline) 3095ms 2.84% 29.43% 7828ms 7.19% __GI___libc_malloc 9ms 0.0083% 29.44% 7786ms 7.15% MutableVertexMesh::RemoveDeletedNodesAndElements 2610ms 2.40% 31.84% 7625ms 7.00% __GI___libc_free 161ms 0.15% 31.99% 7320ms 6.72% std::_Rb_tree::_Rb_tree (partial-inline) 1444ms 1.33% 33.31% 7275ms 6.68% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 470ms 0.43% 33.74% 7063ms 6.49% std::map::operator[] (partial-inline) 759ms 0.7% 34.44% 6899ms 6.33% std::_Rb_tree::_M_copy (inline) 32ms 0.029% 34.47% 6808ms 6.25% std::set::set (inline) 6470ms 5.94% 40.41% 6470ms 5.94% __strcmp_avx2 125ms 0.11% 40.53% 6250ms 5.74% SimpleWntCellCycleModel::GetWntLevel 6093ms 5.59% 46.12% 6093ms 5.59% boost::numeric::ublas::c_vector::operator() 164ms 0.15% 46.27% 6046ms 5.55% WntConcentration::GetWntLevel 862ms 0.79% 47.06% 5881ms 5.40% std::_Rb_tree::_M_clone_node (inline) 2872ms 2.64% 49.70% 5714ms 5.25% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 49.70% 5600ms 5.14% std::set::insert (inline) 2398ms 2.20% 51.90% 5343ms 4.91% std::_Rb_tree::_M_lower_bound (inline) 1914ms 1.76% 53.66% 5250ms 4.82% boost::numeric::ublas::c_vector::operator[] (inline) 18ms 0.017% 53.68% 5210ms 4.78% MutableVertexMesh::RemoveDeletedNodes 34ms 0.031% 53.71% 5031ms 4.62% EdgeHelper::RemoveDeletedEdges 4569ms 4.20% 57.90% 4996ms 4.59% _int_free 203ms 0.19% 58.09% 4861ms 4.46% MutableElement::ResetIndex 234ms 0.21% 58.30% 4707ms 4.32% std::set_intersection (inline) 574ms 0.53% 58.83% 4693ms 4.31% std::_Rb_tree::_M_insert_ (inline) 30ms 0.028% 58.86% 4681ms 4.30% EdgeHelper::UpdateEdgesMapKey 2ms 0.0018% 58.86% 4617ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 234ms 0.21% 59.07% 4473ms 4.11% std::__set_intersection 0 0% 59.07% 4414ms 4.05% std::_Rb_tree::lower_bound (inline) 0 0% 59.07% 4414ms 4.05% std::map::lower_bound (inline) 116ms 0.11% 59.18% 4145ms 3.81% AbstractCellPopulation::GetCellUsingLocationIndex 47ms 0.043% 59.22% 4096ms 3.76% Cell::GetCellProliferativeType 3899ms 3.58% 62.80% 3899ms 3.58% boost::numeric::ublas::same_impl_ex 54ms 0.05% 62.85% 3677ms 3.38% AbstractCellProperty::IsType (inline) 7ms 0.0064% 62.86% 3514ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.86% 3422ms 3.14% std::insert_iterator::operator= (inline) 112ms 0.1% 62.96% 3268ms 3.00% Cell::SetCellProliferativeType 2173ms 2.00% 64.96% 3111ms 2.86% _int_malloc 883ms 0.81% 65.77% 3094ms 2.84% AbstractElement::GetNodeLocation 82ms 0.075% 65.84% 3071ms 2.82% std::_Rb_tree::erase 7ms 0.0064% 65.85% 3018ms 2.77% std::_Rb_tree::_M_insert_unique_ (inline) 639ms 0.59% 66.44% 2735ms 2.51% boost::numeric::ublas::vector_binary::size (inline) 221ms 0.2% 66.64% 2674ms 2.46% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 66.64% 2672ms 2.45% boost::numeric::ublas::c_vector::assign (inline) 693ms 0.64% 67.28% 2664ms 2.45% AbstractCellProperty::IsSame 264ms 0.24% 67.52% 2645ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 39ms 0.036% 67.56% 2641ms 2.43% CellPropertyCollection::HasProperty 0 0% 67.56% 2618ms 2.40% boost::numeric::ublas::c_vector::operator-= (inline) 3ms 0.0028% 67.56% 2582ms 2.37% std::_Rb_tree::_M_insert_unique 0 0% 67.56% 2533ms 2.33% Cell::HasCellProperty (inline) 0 0% 67.56% 2478ms 2.28% AbstractCellPopulation::WriteResultsToFiles 2471ms 2.27% 69.83% 2471ms 2.27% std::_Rb_tree::_S_right (inline) 32ms 0.029% 69.86% 2445ms 2.25% Cell::GetCellData 94ms 0.086% 69.94% 2339ms 2.15% VertexMesh::GetVolumeOfElement 40ms 0.037% 69.98% 2246ms 2.06% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 32ms 0.029% 70.01% 2123ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 2121ms 1.95% 71.96% 2121ms 1.95% std::_Rb_tree_increment 5ms 0.0046% 71.96% 2088ms 1.92% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.96% 2088ms 1.92% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 4ms 0.0037% 71.96% 2085ms 1.91% AbstractCellPopulation::Iterator::operator++ (inline) 145ms 0.13% 72.10% 2029ms 1.86% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 72.10% 2025ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 72.10% 2012ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 449ms 0.41% 72.51% 1971ms 1.81% std::type_info::operator== (inline) 1286ms 1.18% 73.69% 1936ms 1.78% std::_Rb_tree::equal_range (inline) 73ms 0.067% 73.76% 1890ms 1.74% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.76% 1811ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 36ms 0.033% 73.79% 1572ms 1.44% VertexMesh::GetSurfaceAreaOfElement 34ms 0.031% 73.82% 1567ms 1.44% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 172ms 0.16% 73.98% 1514ms 1.39% CellPropertyCollection::AddProperty 60ms 0.055% 74.04% 1502ms 1.38% Node::RemoveElement 9ms 0.0083% 74.04% 1446ms 1.33% std::set::erase (inline) 24ms 0.022% 74.07% 1429ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.07% 1405ms 1.29% tcache_get (inline) 1405ms 1.29% 75.36% 1405ms 1.29% tcache_get_n (inline) 91ms 0.084% 75.44% 1378ms 1.27% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 54ms 0.05% 75.49% 1362ms 1.25% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.49% 1320ms 1.21% boost::numeric::ublas::norm_2 (inline) 1306ms 1.20% 76.69% 1306ms 1.20% [libchaste_cell_based.so] 572ms 0.53% 77.21% 1304ms 1.20% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 77.21% 1296ms 1.19% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 77.22% 1273ms 1.17% OffLatticeSimulation::ApplyBoundaries 56ms 0.051% 77.27% 1250ms 1.15% std::_Rb_tree::_M_erase_aux (partial-inline) 18ms 0.017% 77.28% 1183ms 1.09% CellPropertyRegistry::Get 45ms 0.041% 77.32% 1180ms 1.08% std::less::operator() (inline) 0 0% 77.32% 1139ms 1.05% boost::numeric::ublas::c_vector::assign_temporary (inline) 5ms 0.0046% 77.33% 1139ms 1.05% boost::numeric::ublas::c_vector::swap (inline) 891ms 0.82% 78.15% 1135ms 1.04% std::operator< (inline) 105ms 0.096% 78.24% 1134ms 1.04% std::swap_ranges (inline) 0 0% 78.24% 1124ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1122ms 1.03% 79.27% 1122ms 1.03% std::_Rb_tree_insert_and_rebalance 0 0% 79.27% 1090ms 1.00% std::_Rb_tree::clear (inline) 27ms 0.025% 79.30% 1083ms 0.99% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 10ms 0.0092% 79.31% 1082ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.31% 1070ms 0.98% std::map::clear (inline) 8ms 0.0073% 79.31% 1059ms 0.97% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 219ms 0.2% 79.52% 1056ms 0.97% boost::numeric::ublas::detail::equals 0 0% 79.52% 1029ms 0.94% std::iter_swap (inline) 1029ms 0.94% 80.46% 1029ms 0.94% std::swap (inline) 105ms 0.096% 80.56% 957ms 0.88% std::_Rb_tree::find (inline) 927ms 0.85% 81.41% 927ms 0.85% Node::rGetLocation 109ms 0.1% 81.51% 924ms 0.85% boost::detail::shared_count::~shared_count (inline) 0 0% 81.51% 924ms 0.85% boost::shared_ptr::~shared_ptr (inline) 268ms 0.25% 81.75% 894ms 0.82% std::__new_allocator::construct (inline) 0 0% 81.75% 894ms 0.82% std::allocator_traits::construct (inline) 2ms 0.0018% 81.76% 856ms 0.79% VertexMeshWriter::MakeVtkMesh 117ms 0.11% 81.86% 854ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 836ms 0.77% 82.63% 836ms 0.77% std::vector::size (inline) 212ms 0.19% 82.83% 834ms 0.77% boost::shared_ptr::shared_ptr (inline) 0 0% 82.83% 807ms 0.74% std::_Rb_tree::_M_construct_node (inline) 805ms 0.74% 83.57% 805ms 0.74% [libchaste_mesh.so] 0 0% 83.57% 796ms 0.73% std::map::find (inline) 765ms 0.7% 84.27% 789ms 0.72% boost::detail::sp_counted_base::release 470ms 0.43% 84.70% 785ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 28ms 0.026% 84.73% 781ms 0.72% MutableElement::RegisterWithEdges (inline) 14ms 0.013% 84.74% 778ms 0.71% Edge::AddElement 0 0% 84.74% 769ms 0.71% boost::numeric::ublas::norm_inf (inline) 379ms 0.35% 85.09% 769ms 0.71% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.09% 752ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 400ms 0.37% 85.45% 752ms 0.69% Edge::GetMapIndex 702ms 0.64% 86.10% 702ms 0.64% [libstdc++.so.6.0.33] 1ms 0.00092% 86.10% 670ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.10% 661ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 86.10% 657ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 86.12% 657ms 0.6% std::_Rb_tree::_M_insert_node (inline) 149ms 0.14% 86.26% 656ms 0.6% MutableElement::GetNodeLocalIndex 43ms 0.039% 86.30% 650ms 0.6% MutableElement::RegisterWithNodes (inline) 596ms 0.55% 86.84% 622ms 0.57% boost::detail::shared_count::shared_count (inline) 0 0% 86.84% 618ms 0.57% vtkPolygon::New 0 0% 86.84% 618ms 0.57% vtkPolygon::vtkPolygon 30ms 0.028% 86.87% 610ms 0.56% Node::AddElement 594ms 0.55% 87.42% 594ms 0.55% Node::GetIndex 10ms 0.0092% 87.42% 563ms 0.52% std::vector::_M_default_append (inline) 0 0% 87.42% 553ms 0.51% std::map::map (inline)