File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96317ms, 88.01% of 109439ms total Dropped 1112 nodes (cum <= 547.20ms) flat flat% sum% cum cum% 0 0% 0% 109097ms 99.69% __libc_start_call_main 0 0% 0% 109097ms 99.69% __libc_start_main_impl 0 0% 0% 109097ms 99.69% _start 0 0% 0% 109075ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109075ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109075ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109075ms 99.67% main 0 0% 0% 109032ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109032ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109032ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109024ms 99.62% AbstractCellBasedSimulation::Solve 18ms 0.016% 0.018% 56803ms 51.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.014% 0.032% 53467ms 48.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 123ms 0.11% 0.14% 52343ms 47.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 284ms 0.26% 0.4% 40266ms 36.79% NagaiHondaForce::AddForceContribution 0 0% 0.4% 39082ms 35.71% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.0027% 0.41% 24032ms 21.96% VertexBasedCellPopulation::Update 1ms 0.00091% 0.41% 23890ms 21.83% MutableVertexMesh::ReMesh 14702ms 13.43% 13.84% 23404ms 21.39% Cylindrical2dVertexMesh::GetVectorFromAtoB 90ms 0.082% 13.92% 17585ms 16.07% Cell::ReadyToDivide 68ms 0.062% 13.99% 16263ms 14.86% AbstractPhaseBasedCellCycleModel::ReadyToDivide 369ms 0.34% 14.32% 14669ms 13.40% NagaiHondaForce::GetAdhesionParameter 154ms 0.14% 14.46% 13984ms 12.78% SimpleWntCellCycleModel::UpdateCellCyclePhase 106ms 0.097% 14.56% 13809ms 12.62% CellPropertyCollection::GetPropertiesType (inline) 440ms 0.4% 14.96% 13767ms 12.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 288ms 0.26% 15.23% 12267ms 11.21% boost::numeric::ublas::vector_assign (inline) 155ms 0.14% 15.37% 11774ms 10.76% MutableVertexMesh::CheckForIntersections 3379ms 3.09% 18.46% 11561ms 10.56% __dynamic_cast 78ms 0.071% 18.53% 11541ms 10.55% VertexBasedCellPopulation::GetDampingConstant 49ms 0.045% 18.57% 11420ms 10.44% AbstractCellProperty::IsSubType (inline) 66ms 0.06% 18.63% 10617ms 9.70% AbstractTargetAreaModifier::UpdateTargetAreas 39ms 0.036% 18.67% 10531ms 9.62% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1310ms 1.20% 19.86% 10358ms 9.46% std::__new_allocator::allocate (inline) 30ms 0.027% 19.89% 10265ms 9.38% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.89% 9873ms 9.02% std::_Rb_tree::_M_create_node (inline) 0 0% 19.89% 9758ms 8.92% std::allocator_traits::allocate (inline) 358ms 0.33% 20.22% 9428ms 8.61% VertexMesh::GetNextEdgeGradientOfElementAtNode 2855ms 2.61% 22.83% 9409ms 8.60% boost::numeric::ublas::indexing_vector_assign 698ms 0.64% 23.47% 9093ms 8.31% operator new 0 0% 23.47% 9037ms 8.26% std::_Rb_tree::_M_get_node (inline) 1238ms 1.13% 24.60% 8988ms 8.21% std::_Rb_tree::_M_erase 105ms 0.096% 24.69% 8854ms 8.09% Cell::GetMutationState 0 0% 24.69% 8744ms 7.99% std::_Rb_tree::_Alloc_node::operator() (inline) 28ms 0.026% 24.72% 8673ms 7.92% VertexBasedCellPopulation::GetLocationOfCellCentre 856ms 0.78% 25.50% 8614ms 7.87% VertexMesh::ElementIncludesPoint 475ms 0.43% 25.93% 8234ms 7.52% VertexMesh::GetCentroidOfElement 3248ms 2.97% 28.90% 8143ms 7.44% __GI___libc_malloc 0 0% 28.90% 8131ms 7.43% std::_Rb_tree::_M_drop_node (inline) 202ms 0.18% 29.09% 8104ms 7.41% std::_Rb_tree::~_Rb_tree (inline) 243ms 0.22% 29.31% 7891ms 7.21% std::__new_allocator::deallocate (inline) 0 0% 29.31% 7888ms 7.21% std::allocator_traits::deallocate (inline) 0 0% 29.31% 7813ms 7.14% std::_Rb_tree::_M_put_node (inline) 451ms 0.41% 29.72% 7743ms 7.08% std::map::operator[] (partial-inline) 17ms 0.016% 29.74% 7705ms 7.04% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.74% 7694ms 7.03% std::set::~set (inline) 1501ms 1.37% 31.11% 7475ms 6.83% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2431ms 2.22% 33.33% 7369ms 6.73% __GI___libc_free 155ms 0.14% 33.47% 7349ms 6.72% std::_Rb_tree::_Rb_tree (partial-inline) 696ms 0.64% 34.11% 6907ms 6.31% std::_Rb_tree::_M_copy (inline) 22ms 0.02% 34.13% 6856ms 6.26% std::set::set (inline) 6675ms 6.10% 40.23% 6675ms 6.10% __strcmp_avx2 136ms 0.12% 40.35% 6253ms 5.71% SimpleWntCellCycleModel::GetWntLevel 2611ms 2.39% 42.74% 6219ms 5.68% std::_Rb_tree::_M_lower_bound (inline) 172ms 0.16% 42.89% 6033ms 5.51% WntConcentration::GetWntLevel 5988ms 5.47% 48.36% 5988ms 5.47% boost::numeric::ublas::c_vector::operator() 767ms 0.7% 49.07% 5945ms 5.43% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.07% 5528ms 5.05% std::set::insert (inline) 2800ms 2.56% 51.62% 5470ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 30ms 0.027% 51.65% 5427ms 4.96% MutableVertexMesh::RemoveDeletedNodes 1934ms 1.77% 53.42% 5251ms 4.80% boost::numeric::ublas::c_vector::operator[] (inline) 24ms 0.022% 53.44% 5249ms 4.80% EdgeHelper::RemoveDeletedEdges 0 0% 53.44% 5025ms 4.59% std::_Rb_tree::lower_bound (inline) 0 0% 53.44% 5025ms 4.59% std::map::lower_bound (inline) 29ms 0.026% 53.47% 4934ms 4.51% EdgeHelper::UpdateEdgesMapKey 4526ms 4.14% 57.60% 4927ms 4.50% _int_free 1ms 0.00091% 57.60% 4778ms 4.37% AbstractCellBasedSimulation::DoCellRemoval (inline) 202ms 0.18% 57.79% 4726ms 4.32% MutableElement::ResetIndex 579ms 0.53% 58.32% 4669ms 4.27% std::_Rb_tree::_M_insert_ (inline) 122ms 0.11% 58.43% 4357ms 3.98% std::set_intersection (inline) 117ms 0.11% 58.54% 4323ms 3.95% AbstractCellPopulation::GetCellUsingLocationIndex 203ms 0.19% 58.72% 4235ms 3.87% std::__set_intersection 62ms 0.057% 58.78% 3927ms 3.59% AbstractCellProperty::IsType (inline) 41ms 0.037% 58.82% 3876ms 3.54% Cell::GetCellProliferativeType 3779ms 3.45% 62.27% 3779ms 3.45% boost::numeric::ublas::same_impl_ex 17ms 0.016% 62.28% 3682ms 3.36% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.28% 3279ms 3.00% std::insert_iterator::operator= (inline) 2299ms 2.10% 64.38% 3248ms 2.97% _int_malloc 38ms 0.035% 64.42% 3114ms 2.85% Cell::SetCellProliferativeType 917ms 0.84% 65.26% 3031ms 2.77% AbstractElement::GetNodeLocation 3007ms 2.75% 68.01% 3007ms 2.75% std::_Rb_tree::_S_right (inline) 67ms 0.061% 68.07% 2996ms 2.74% std::_Rb_tree::erase 10ms 0.0091% 68.08% 2869ms 2.62% std::_Rb_tree::_M_insert_unique_ (inline) 43ms 0.039% 68.11% 2811ms 2.57% CellPropertyCollection::HasProperty 770ms 0.7% 68.82% 2749ms 2.51% AbstractCellProperty::IsSame 679ms 0.62% 69.44% 2735ms 2.50% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.44% 2673ms 2.44% Cell::HasCellProperty (inline) 0 0% 69.44% 2659ms 2.43% std::_Rb_tree::_M_insert_unique 200ms 0.18% 69.62% 2642ms 2.41% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.62% 2610ms 2.38% boost::numeric::ublas::c_vector::operator-= (inline) 248ms 0.23% 69.85% 2534ms 2.32% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.85% 2492ms 2.28% AbstractCellPopulation::WriteResultsToFiles 37ms 0.034% 69.88% 2470ms 2.26% Cell::GetCellData 0 0% 69.88% 2441ms 2.23% boost::numeric::ublas::c_vector::assign (inline) 69ms 0.063% 69.94% 2342ms 2.14% VertexMesh::GetVolumeOfElement 195ms 0.18% 70.12% 2340ms 2.14% AbstractCellPopulation::Iterator::IsRealCell (inline) 7ms 0.0064% 70.13% 2333ms 2.13% AbstractCellPopulation::Iterator::operator++ (inline) 38ms 0.035% 70.16% 2208ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 36ms 0.033% 70.20% 2198ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.00091% 70.20% 2064ms 1.89% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.20% 2064ms 1.89% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 70.20% 2023ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 2022ms 1.85% 72.05% 2022ms 1.85% std::_Rb_tree_increment 1ms 0.00091% 72.05% 2016ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 445ms 0.41% 72.45% 1979ms 1.81% std::type_info::operator== (inline) 1288ms 1.18% 73.63% 1936ms 1.77% std::_Rb_tree::equal_range (inline) 71ms 0.065% 73.69% 1891ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 19ms 0.017% 73.71% 1826ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 73.71% 1825ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 151ms 0.14% 73.85% 1655ms 1.51% CellPropertyCollection::AddProperty 47ms 0.043% 73.89% 1653ms 1.51% AbstractCellPopulation::GetLocationIndexUsingCell 95ms 0.087% 73.98% 1643ms 1.50% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 52ms 0.048% 74.03% 1528ms 1.40% Node::RemoveElement 33ms 0.03% 74.06% 1523ms 1.39% VertexMesh::GetSurfaceAreaOfElement 9ms 0.0082% 74.07% 1478ms 1.35% std::set::erase (inline) 0 0% 74.07% 1459ms 1.33% tcache_get (inline) 1459ms 1.33% 75.40% 1459ms 1.33% tcache_get_n (inline) 0 0% 75.40% 1392ms 1.27% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 75.40% 1373ms 1.25% OffLatticeSimulation::ApplyBoundaries 1341ms 1.23% 76.63% 1341ms 1.23% [libchaste_cell_based.so] 0 0% 76.63% 1332ms 1.22% boost::numeric::ublas::norm_2 (inline) 69ms 0.063% 76.69% 1326ms 1.21% boost::numeric::ublas::vector_reference::operator() (inline) 605ms 0.55% 77.24% 1324ms 1.21% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 62ms 0.057% 77.30% 1305ms 1.19% std::less::operator() (inline) 1007ms 0.92% 78.22% 1243ms 1.14% std::operator< (inline) 26ms 0.024% 78.24% 1209ms 1.10% CellPropertyRegistry::Get 91ms 0.083% 78.33% 1198ms 1.09% std::_Rb_tree::find (inline) 17ms 0.016% 78.34% 1168ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 82ms 0.075% 78.42% 1166ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 1132ms 1.03% 79.45% 1132ms 1.03% std::_Rb_tree_insert_and_rebalance 0 0% 79.45% 1129ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 79.45% 1127ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 79.46% 1127ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 72ms 0.066% 79.52% 1120ms 1.02% std::swap_ranges (inline) 0 0% 79.52% 1094ms 1% std::_Rb_tree::clear (inline) 0 0% 79.52% 1076ms 0.98% std::map::clear (inline) 7ms 0.0064% 79.53% 1052ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1050ms 0.96% 80.49% 1050ms 0.96% std::swap (inline) 0 0% 80.49% 1048ms 0.96% std::iter_swap (inline) 131ms 0.12% 80.61% 1017ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 80.61% 1017ms 0.93% boost::shared_ptr::~shared_ptr (inline) 16ms 0.015% 80.62% 1000ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 80.62% 996ms 0.91% std::map::find (inline) 190ms 0.17% 80.80% 969ms 0.89% boost::numeric::ublas::detail::equals 957ms 0.87% 81.67% 957ms 0.87% Node::rGetLocation 232ms 0.21% 81.88% 888ms 0.81% std::__new_allocator::construct (inline) 0 0% 81.88% 888ms 0.81% std::allocator_traits::construct (inline) 86ms 0.079% 81.96% 876ms 0.8% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 81.96% 868ms 0.79% VertexMeshWriter::MakeVtkMesh 854ms 0.78% 82.74% 854ms 0.78% std::vector::size (inline) 0 0% 82.74% 836ms 0.76% std::_Rb_tree::_M_construct_node (inline) 806ms 0.74% 83.48% 832ms 0.76% boost::detail::sp_counted_base::release 195ms 0.18% 83.66% 803ms 0.73% boost::shared_ptr::shared_ptr (inline) 439ms 0.4% 84.06% 789ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 20ms 0.018% 84.08% 785ms 0.72% MutableElement::RegisterWithEdges (inline) 26ms 0.024% 84.10% 774ms 0.71% Edge::AddElement 770ms 0.7% 84.80% 770ms 0.7% [libchaste_mesh.so] 419ms 0.38% 85.19% 748ms 0.68% Edge::GetMapIndex 0 0% 85.19% 732ms 0.67% boost::numeric::ublas::norm_inf (inline) 369ms 0.34% 85.52% 732ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 85.52% 724ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 151ms 0.14% 85.66% 719ms 0.66% MutableElement::GetNodeLocalIndex 0 0% 85.66% 717ms 0.66% std::_Vector_base::_M_allocate (inline) 0 0% 85.66% 694ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 85.69% 694ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.69% 693ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 673ms 0.61% 86.30% 673ms 0.61% [libstdc++.so.6.0.33] 0 0% 86.30% 635ms 0.58% vtkPolygon::New 1ms 0.00091% 86.30% 635ms 0.58% vtkPolygon::vtkPolygon 31ms 0.028% 86.33% 631ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.33% 631ms 0.58% boost::numeric::ublas::vector::vector (inline) 630ms 0.58% 86.91% 630ms 0.58% Node::GetIndex 576ms 0.53% 87.43% 608ms 0.56% boost::detail::shared_count::shared_count (inline) 35ms 0.032% 87.46% 600ms 0.55% MutableElement::RegisterWithNodes (inline) 5ms 0.0046% 87.47% 590ms 0.54% std::vector::_M_default_append (inline) 35ms 0.032% 87.50% 565ms 0.52% Node::AddElement 557ms 0.51% 88.01% 557ms 0.51% boost::shared_ptr::operator-> (inline)