File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95761ms, 87.77% of 109106ms total Dropped 1140 nodes (cum <= 545.53ms) flat flat% sum% cum cum% 0 0% 0% 108808ms 99.73% __libc_start_call_main 0 0% 0% 108808ms 99.73% __libc_start_main_impl 0 0% 0% 108808ms 99.73% _start 0 0% 0% 108786ms 99.71% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108786ms 99.71% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108786ms 99.71% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108786ms 99.71% main 0 0% 0% 108743ms 99.67% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108743ms 99.67% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108743ms 99.67% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 8ms 0.0073% 0.0073% 108735ms 99.66% AbstractCellBasedSimulation::Solve 16ms 0.015% 0.022% 56800ms 52.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.016% 0.038% 53405ms 48.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 134ms 0.12% 0.16% 52268ms 47.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 316ms 0.29% 0.45% 40173ms 36.82% NagaiHondaForce::AddForceContribution 0 0% 0.45% 38972ms 35.72% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0046% 0.46% 24027ms 22.02% VertexBasedCellPopulation::Update 4ms 0.0037% 0.46% 23868ms 21.88% MutableVertexMesh::ReMesh 14769ms 13.54% 14.00% 23410ms 21.46% Cylindrical2dVertexMesh::GetVectorFromAtoB 99ms 0.091% 14.09% 17507ms 16.05% Cell::ReadyToDivide 72ms 0.066% 14.15% 16188ms 14.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 336ms 0.31% 14.46% 14585ms 13.37% NagaiHondaForce::GetAdhesionParameter 153ms 0.14% 14.60% 13962ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 120ms 0.11% 14.71% 13589ms 12.45% CellPropertyCollection::GetPropertiesType (inline) 483ms 0.44% 15.15% 13586ms 12.45% boost::numeric::ublas::c_vector::c_vector (partial-inline) 344ms 0.32% 15.47% 12178ms 11.16% boost::numeric::ublas::vector_assign (inline) 139ms 0.13% 15.60% 11781ms 10.80% MutableVertexMesh::CheckForIntersections 74ms 0.068% 15.66% 11525ms 10.56% VertexBasedCellPopulation::GetDampingConstant 3570ms 3.27% 18.94% 11522ms 10.56% __dynamic_cast 89ms 0.082% 19.02% 11438ms 10.48% AbstractCellProperty::IsSubType (inline) 59ms 0.054% 19.07% 10434ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.037% 19.11% 10349ms 9.49% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 25ms 0.023% 19.13% 10253ms 9.40% AbstractCellBasedSimulation::DoCellBirth 1369ms 1.25% 20.39% 9809ms 8.99% std::__new_allocator::allocate (inline) 377ms 0.35% 20.73% 9538ms 8.74% VertexMesh::GetNextEdgeGradientOfElementAtNode 2777ms 2.55% 23.28% 9372ms 8.59% boost::numeric::ublas::indexing_vector_assign 0 0% 23.28% 9311ms 8.53% std::_Rb_tree::_M_create_node (inline) 0 0% 23.28% 9240ms 8.47% std::allocator_traits::allocate (inline) 1276ms 1.17% 24.45% 8998ms 8.25% std::_Rb_tree::_M_erase 37ms 0.034% 24.48% 8744ms 8.01% VertexBasedCellPopulation::GetLocationOfCellCentre 108ms 0.099% 24.58% 8685ms 7.96% Cell::GetMutationState 817ms 0.75% 25.33% 8579ms 7.86% VertexMesh::ElementIncludesPoint 0 0% 25.33% 8531ms 7.82% std::_Rb_tree::_M_get_node (inline) 670ms 0.61% 25.94% 8493ms 7.78% operator new 437ms 0.4% 26.34% 8258ms 7.57% VertexMesh::GetCentroidOfElement 0 0% 26.34% 8186ms 7.50% std::_Rb_tree::_Alloc_node::operator() (inline) 227ms 0.21% 26.55% 8122ms 7.44% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.55% 8039ms 7.37% std::_Rb_tree::_M_drop_node (inline) 479ms 0.44% 26.99% 7789ms 7.14% std::map::operator[] (partial-inline) 1458ms 1.34% 28.33% 7755ms 7.11% AbstractMesh::GetDistanceBetweenNodes 222ms 0.2% 28.53% 7744ms 7.10% std::__new_allocator::deallocate (inline) 0 0% 28.53% 7742ms 7.10% std::allocator_traits::deallocate (inline) 11ms 0.01% 28.54% 7726ms 7.08% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 28.54% 7688ms 7.05% std::set::~set (inline) 0 0% 28.54% 7678ms 7.04% std::_Rb_tree::_M_put_node (inline) 2896ms 2.65% 31.19% 7619ms 6.98% __GI___libc_malloc 2395ms 2.20% 33.39% 7236ms 6.63% __GI___libc_free 163ms 0.15% 33.54% 7092ms 6.50% std::_Rb_tree::_Rb_tree (partial-inline) 682ms 0.63% 34.16% 6680ms 6.12% std::_Rb_tree::_M_copy (inline) 22ms 0.02% 34.18% 6603ms 6.05% std::set::set (inline) 139ms 0.13% 34.31% 6298ms 5.77% SimpleWntCellCycleModel::GetWntLevel 6251ms 5.73% 40.04% 6251ms 5.73% __strcmp_avx2 6199ms 5.68% 45.72% 6199ms 5.68% boost::numeric::ublas::c_vector::operator() 2535ms 2.32% 48.05% 6152ms 5.64% std::_Rb_tree::_M_lower_bound (inline) 158ms 0.14% 48.19% 6103ms 5.59% WntConcentration::GetWntLevel 851ms 0.78% 48.97% 5747ms 5.27% std::_Rb_tree::_M_clone_node (inline) 2000ms 1.83% 50.80% 5434ms 4.98% boost::numeric::ublas::c_vector::operator[] (inline) 2920ms 2.68% 53.48% 5419ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 37ms 0.034% 53.51% 5406ms 4.95% MutableVertexMesh::RemoveDeletedNodes 38ms 0.035% 53.55% 5198ms 4.76% EdgeHelper::RemoveDeletedEdges 0 0% 53.55% 5190ms 4.76% std::set::insert (inline) 0 0% 53.55% 5049ms 4.63% std::_Rb_tree::lower_bound (inline) 0 0% 53.55% 5049ms 4.63% std::map::lower_bound (inline) 35ms 0.032% 53.58% 4869ms 4.46% EdgeHelper::UpdateEdgesMapKey 4393ms 4.03% 57.61% 4821ms 4.42% _int_free 205ms 0.19% 57.79% 4698ms 4.31% MutableElement::ResetIndex 2ms 0.0018% 57.80% 4672ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 150ms 0.14% 57.93% 4528ms 4.15% AbstractCellPopulation::GetCellUsingLocationIndex 194ms 0.18% 58.11% 4388ms 4.02% std::set_intersection (inline) 544ms 0.5% 58.61% 4335ms 3.97% std::_Rb_tree::_M_insert_ (inline) 236ms 0.22% 58.83% 4194ms 3.84% std::__set_intersection 46ms 0.042% 58.87% 3847ms 3.53% Cell::GetCellProliferativeType 54ms 0.049% 58.92% 3792ms 3.48% AbstractCellProperty::IsType (inline) 3719ms 3.41% 62.33% 3719ms 3.41% boost::numeric::ublas::same_impl_ex 14ms 0.013% 62.34% 3534ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.34% 3231ms 2.96% std::insert_iterator::operator= (inline) 2236ms 2.05% 64.39% 3206ms 2.94% _int_malloc 66ms 0.06% 64.45% 3109ms 2.85% std::_Rb_tree::erase 51ms 0.047% 64.50% 3099ms 2.84% Cell::SetCellProliferativeType 947ms 0.87% 65.36% 3098ms 2.84% AbstractElement::GetNodeLocation 3055ms 2.80% 68.16% 3055ms 2.80% std::_Rb_tree::_S_right (inline) 4ms 0.0037% 68.17% 2810ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 723ms 0.66% 68.83% 2715ms 2.49% AbstractCellProperty::IsSame 34ms 0.031% 68.86% 2674ms 2.45% CellPropertyCollection::HasProperty 223ms 0.2% 69.07% 2657ms 2.44% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.07% 2627ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.07% 2580ms 2.36% Cell::HasCellProperty (inline) 0 0% 69.07% 2522ms 2.31% boost::numeric::ublas::c_vector::assign (inline) 257ms 0.24% 69.30% 2495ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.30% 2490ms 2.28% AbstractCellPopulation::WriteResultsToFiles 602ms 0.55% 69.85% 2474ms 2.27% boost::numeric::ublas::vector_binary::size (inline) 25ms 0.023% 69.88% 2435ms 2.23% Cell::GetCellData 3ms 0.0027% 69.88% 2380ms 2.18% std::_Rb_tree::_M_insert_unique 74ms 0.068% 69.95% 2247ms 2.06% VertexMesh::GetVolumeOfElement 37ms 0.034% 69.98% 2201ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 37ms 0.034% 70.01% 2145ms 1.97% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0027% 70.02% 2134ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 187ms 0.17% 70.19% 2122ms 1.94% AbstractCellPopulation::Iterator::IsRealCell 2ms 0.0018% 70.19% 2112ms 1.94% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.19% 2112ms 1.94% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1371ms 1.26% 71.45% 2069ms 1.90% std::_Rb_tree::equal_range (inline) 1ms 0.00092% 71.45% 2025ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 71.45% 2011ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 486ms 0.45% 71.89% 1992ms 1.83% std::type_info::operator== (inline) 1957ms 1.79% 73.69% 1957ms 1.79% std::_Rb_tree_increment 63ms 0.058% 73.75% 1933ms 1.77% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.75% 1818ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 42ms 0.038% 73.78% 1668ms 1.53% VertexMesh::GetSurfaceAreaOfElement 23ms 0.021% 73.81% 1656ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 43ms 0.039% 73.84% 1545ms 1.42% Node::RemoveElement 48ms 0.044% 73.89% 1524ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 11ms 0.01% 73.90% 1506ms 1.38% std::set::erase (inline) 61ms 0.056% 73.95% 1476ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 73.95% 1436ms 1.32% boost::numeric::ublas::norm_2 (inline) 643ms 0.59% 74.54% 1424ms 1.31% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 127ms 0.12% 74.66% 1413ms 1.30% CellPropertyCollection::AddProperty 60ms 0.055% 74.72% 1358ms 1.24% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00092% 74.72% 1357ms 1.24% OffLatticeSimulation::ApplyBoundaries 0 0% 74.72% 1334ms 1.22% tcache_get (inline) 1334ms 1.22% 75.94% 1334ms 1.22% tcache_get_n (inline) 0 0% 75.94% 1316ms 1.21% boost::numeric::ublas::vector_binary::operator() (inline) 68ms 0.062% 76.00% 1306ms 1.20% std::less::operator() (inline) 1293ms 1.19% 77.19% 1293ms 1.19% [libchaste_cell_based.so] 1007ms 0.92% 78.11% 1238ms 1.13% std::operator< (inline) 82ms 0.075% 78.18% 1164ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 15ms 0.014% 78.20% 1136ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.20% 1134ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 13ms 0.012% 78.21% 1134ms 1.04% boost::numeric::ublas::c_vector::swap 21ms 0.019% 78.23% 1128ms 1.03% CellPropertyRegistry::Get 0 0% 78.23% 1125ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 63ms 0.058% 78.29% 1121ms 1.03% std::swap_ranges (inline) 1114ms 1.02% 79.31% 1114ms 1.02% std::_Rb_tree_insert_and_rebalance 0 0% 79.31% 1111ms 1.02% std::_Rb_tree::clear (inline) 83ms 0.076% 79.38% 1098ms 1.01% std::_Rb_tree::find (inline) 0 0% 79.38% 1093ms 1.00% std::map::clear (inline) 6ms 0.0055% 79.39% 1085ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1059ms 0.97% 80.36% 1059ms 0.97% std::swap (inline) 0 0% 80.36% 1058ms 0.97% std::iter_swap (inline) 120ms 0.11% 80.47% 1038ms 0.95% boost::detail::shared_count::~shared_count (inline) 0 0% 80.47% 1038ms 0.95% boost::shared_ptr::~shared_ptr (inline) 999ms 0.92% 81.39% 999ms 0.92% Node::rGetLocation 1ms 0.00092% 81.39% 926ms 0.85% std::map::find (inline) 5ms 0.0046% 81.39% 920ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 166ms 0.15% 81.54% 897ms 0.82% boost::numeric::ublas::detail::equals 842ms 0.77% 82.32% 880ms 0.81% boost::detail::sp_counted_base::release 2ms 0.0018% 82.32% 857ms 0.79% VertexMeshWriter::MakeVtkMesh 838ms 0.77% 83.09% 838ms 0.77% std::vector::size (inline) 258ms 0.24% 83.32% 831ms 0.76% std::__new_allocator::construct (inline) 0 0% 83.32% 831ms 0.76% std::allocator_traits::construct (inline) 97ms 0.089% 83.41% 813ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 444ms 0.41% 83.82% 805ms 0.74% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 83.82% 780ms 0.71% std::_Rb_tree::_M_construct_node (inline) 156ms 0.14% 83.96% 762ms 0.7% boost::shared_ptr::shared_ptr (inline) 0 0% 83.96% 757ms 0.69% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 746ms 0.68% 84.64% 746ms 0.68% [libchaste_mesh.so] 388ms 0.36% 85.00% 739ms 0.68% Edge::GetMapIndex 29ms 0.027% 85.03% 706ms 0.65% Edge::AddElement 0 0% 85.03% 704ms 0.65% std::_Vector_base::_M_allocate (inline) 16ms 0.015% 85.04% 699ms 0.64% MutableElement::RegisterWithEdges (inline) 0 0% 85.04% 691ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.02% 85.06% 691ms 0.63% std::_Rb_tree::_M_insert_node (inline) 143ms 0.13% 85.19% 688ms 0.63% MutableElement::GetNodeLocalIndex 0 0% 85.19% 677ms 0.62% boost::numeric::ublas::norm_inf (inline) 369ms 0.34% 85.53% 677ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.53% 671ms 0.61% CellPropertyCollection::~CellPropertyCollection (inline) 666ms 0.61% 86.14% 666ms 0.61% [libstdc++.so.6.0.33] 2ms 0.0018% 86.14% 625ms 0.57% vtkPolygon::New 1ms 0.00092% 86.14% 622ms 0.57% vtkPolygon::vtkPolygon 574ms 0.53% 86.67% 606ms 0.56% boost::detail::shared_count::shared_count (inline) 29ms 0.027% 86.70% 598ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.70% 598ms 0.55% boost::numeric::ublas::vector::vector (inline) 8ms 0.0073% 86.70% 595ms 0.55% std::vector::_M_default_append (inline) 34ms 0.031% 86.73% 579ms 0.53% MutableElement::RegisterWithNodes (inline) 568ms 0.52% 87.26% 568ms 0.52% Node::GetIndex 560ms 0.51% 87.77% 560ms 0.51% boost::shared_ptr::operator-> (inline)