File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95875ms, 87.79% of 109214ms total Dropped 1104 nodes (cum <= 546.07ms) flat flat% sum% cum cum% 0 0% 0% 108857ms 99.67% __libc_start_call_main 0 0% 0% 108857ms 99.67% __libc_start_main_impl 0 0% 0% 108857ms 99.67% _start 0 0% 0% 108836ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108836ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108836ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108836ms 99.65% main 0 0% 0% 108797ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108797ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108797ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0037% 0.0037% 108789ms 99.61% AbstractCellBasedSimulation::Solve 21ms 0.019% 0.023% 56377ms 51.62% OffLatticeSimulation::UpdateCellLocationsAndTopology 12ms 0.011% 0.034% 53014ms 48.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 142ms 0.13% 0.16% 51932ms 47.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 295ms 0.27% 0.43% 39358ms 36.04% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.44% 39016ms 35.72% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00092% 0.44% 23967ms 21.94% VertexBasedCellPopulation::Update 0 0% 0.44% 23852ms 21.84% MutableVertexMesh::ReMesh 14498ms 13.27% 13.71% 23225ms 21.27% Cylindrical2dVertexMesh::GetVectorFromAtoB 78ms 0.071% 13.78% 18119ms 16.59% Cell::ReadyToDivide 63ms 0.058% 13.84% 16862ms 15.44% AbstractPhaseBasedCellCycleModel::ReadyToDivide 103ms 0.094% 13.94% 14785ms 13.54% CellPropertyCollection::GetPropertiesType (inline) 136ms 0.12% 14.06% 14493ms 13.27% SimpleWntCellCycleModel::UpdateCellCyclePhase 361ms 0.33% 14.39% 14222ms 13.02% NagaiHondaForce::GetAdhesionParameter 448ms 0.41% 14.80% 13701ms 12.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3547ms 3.25% 18.05% 13080ms 11.98% __dynamic_cast 52ms 0.048% 18.10% 12929ms 11.84% AbstractCellProperty::IsSubType (inline) 384ms 0.35% 18.45% 12281ms 11.24% boost::numeric::ublas::vector_assign (inline) 78ms 0.071% 18.52% 12025ms 11.01% VertexBasedCellPopulation::GetDampingConstant 148ms 0.14% 18.66% 11848ms 10.85% MutableVertexMesh::CheckForIntersections 74ms 0.068% 18.72% 10862ms 9.95% AbstractTargetAreaModifier::UpdateTargetAreas 34ms 0.031% 18.75% 10779ms 9.87% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 30ms 0.027% 18.78% 10459ms 9.58% AbstractCellBasedSimulation::DoCellBirth 1374ms 1.26% 20.04% 9956ms 9.12% std::__new_allocator::allocate (inline) 77ms 0.071% 20.11% 9444ms 8.65% Cell::GetMutationState 0 0% 20.11% 9428ms 8.63% std::allocator_traits::allocate (inline) 0 0% 20.11% 9381ms 8.59% std::_Rb_tree::_M_create_node (inline) 375ms 0.34% 20.45% 9374ms 8.58% VertexMesh::GetNextEdgeGradientOfElementAtNode 2942ms 2.69% 23.15% 9304ms 8.52% boost::numeric::ublas::indexing_vector_assign 26ms 0.024% 23.17% 8866ms 8.12% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 23.17% 8717ms 7.98% std::_Rb_tree::_M_get_node (inline) 740ms 0.68% 23.85% 8633ms 7.90% operator new 801ms 0.73% 24.58% 8622ms 7.89% VertexMesh::ElementIncludesPoint 1218ms 1.12% 25.70% 8611ms 7.88% std::_Rb_tree::_M_erase 449ms 0.41% 26.11% 8370ms 7.66% VertexMesh::GetCentroidOfElement 0 0% 26.11% 8162ms 7.47% std::_Rb_tree::_Alloc_node::operator() (inline) 494ms 0.45% 26.56% 7916ms 7.25% std::map::operator[] (partial-inline) 373ms 0.34% 26.90% 7897ms 7.23% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.90% 7785ms 7.13% std::_Rb_tree::_M_drop_node (inline) 10ms 0.0092% 26.91% 7743ms 7.09% MutableVertexMesh::RemoveDeletedNodesAndElements 2830ms 2.59% 29.50% 7687ms 7.04% __GI___libc_malloc 234ms 0.21% 29.72% 7577ms 6.94% std::__new_allocator::deallocate (inline) 0 0% 29.72% 7572ms 6.93% std::allocator_traits::deallocate (inline) 0 0% 29.72% 7506ms 6.87% std::_Rb_tree::_M_put_node (inline) 0 0% 29.72% 7503ms 6.87% std::set::~set (inline) 7499ms 6.87% 36.58% 7499ms 6.87% __strcmp_avx2 1288ms 1.18% 37.76% 7249ms 6.64% AbstractMesh::GetDistanceBetweenNodes 146ms 0.13% 37.90% 7114ms 6.51% std::_Rb_tree::_Rb_tree (partial-inline) 2250ms 2.06% 39.96% 7073ms 6.48% __GI___libc_free 782ms 0.72% 40.67% 6725ms 6.16% std::_Rb_tree::_M_copy (inline) 27ms 0.025% 40.70% 6634ms 6.07% std::set::set (inline) 3265ms 2.99% 43.69% 6595ms 6.04% __cxxabiv1::__si_class_type_info::__do_dyncast 131ms 0.12% 43.81% 6429ms 5.89% SimpleWntCellCycleModel::GetWntLevel 172ms 0.16% 43.96% 6239ms 5.71% WntConcentration::GetWntLevel 2569ms 2.35% 46.32% 6181ms 5.66% std::_Rb_tree::_M_lower_bound (inline) 5965ms 5.46% 51.78% 5965ms 5.46% boost::numeric::ublas::c_vector::operator() 772ms 0.71% 52.49% 5713ms 5.23% std::_Rb_tree::_M_clone_node (inline) 17ms 0.016% 52.50% 5472ms 5.01% MutableVertexMesh::RemoveDeletedNodes 1972ms 1.81% 54.31% 5316ms 4.87% boost::numeric::ublas::c_vector::operator[] (inline) 41ms 0.038% 54.34% 5301ms 4.85% EdgeHelper::RemoveDeletedEdges 0 0% 54.34% 5127ms 4.69% std::_Rb_tree::lower_bound (inline) 0 0% 54.34% 5127ms 4.69% std::map::lower_bound (inline) 0 0% 54.34% 5068ms 4.64% std::set::insert (inline) 43ms 0.039% 54.38% 4980ms 4.56% EdgeHelper::UpdateEdgesMapKey 4344ms 3.98% 58.36% 4808ms 4.40% _int_free 196ms 0.18% 58.54% 4661ms 4.27% MutableElement::ResetIndex 2ms 0.0018% 58.54% 4581ms 4.19% AbstractCellBasedSimulation::DoCellRemoval (inline) 147ms 0.13% 58.68% 4472ms 4.09% AbstractCellPopulation::GetCellUsingLocationIndex 493ms 0.45% 59.13% 4247ms 3.89% std::_Rb_tree::_M_insert_ (inline) 128ms 0.12% 59.25% 4182ms 3.83% std::set_intersection (inline) 45ms 0.041% 59.29% 4181ms 3.83% Cell::GetCellProliferativeType 225ms 0.21% 59.49% 4054ms 3.71% std::__set_intersection 3799ms 3.48% 62.97% 3799ms 3.48% boost::numeric::ublas::same_impl_ex 46ms 0.042% 63.01% 3720ms 3.41% AbstractCellProperty::IsType (inline) 14ms 0.013% 63.03% 3485ms 3.19% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 74ms 0.068% 63.09% 3393ms 3.11% Cell::SetCellProliferativeType 2313ms 2.12% 65.21% 3259ms 2.98% _int_malloc 0 0% 65.21% 3124ms 2.86% std::insert_iterator::operator= (inline) 842ms 0.77% 65.98% 3043ms 2.79% AbstractElement::GetNodeLocation 65ms 0.06% 66.04% 2953ms 2.70% std::_Rb_tree::erase 2951ms 2.70% 68.74% 2951ms 2.70% std::_Rb_tree::_S_right (inline) 5ms 0.0046% 68.75% 2725ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 22ms 0.02% 68.77% 2692ms 2.46% CellPropertyCollection::HasProperty 620ms 0.57% 69.34% 2675ms 2.45% AbstractCellProperty::IsSame 0 0% 69.34% 2599ms 2.38% Cell::HasCellProperty (inline) 0 0% 69.34% 2570ms 2.35% boost::numeric::ublas::c_vector::assign (inline) 606ms 0.55% 69.89% 2559ms 2.34% boost::numeric::ublas::vector_binary::size (inline) 202ms 0.18% 70.08% 2540ms 2.33% VertexMesh::GetAreaGradientOfElementAtNode 28ms 0.026% 70.10% 2502ms 2.29% Cell::GetCellData 0 0% 70.10% 2485ms 2.28% AbstractCellPopulation::WriteResultsToFiles 241ms 0.22% 70.32% 2472ms 2.26% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.32% 2369ms 2.17% boost::numeric::ublas::c_vector::operator-= (inline) 4ms 0.0037% 70.33% 2343ms 2.15% std::_Rb_tree::_M_insert_unique 90ms 0.082% 70.41% 2306ms 2.11% VertexMesh::GetVolumeOfElement 37ms 0.034% 70.44% 2295ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 40ms 0.037% 70.48% 2255ms 2.06% std::_Rb_tree::_M_emplace_hint_unique 161ms 0.15% 70.63% 2111ms 1.93% AbstractCellPopulation::Iterator::IsRealCell 2ms 0.0018% 70.63% 2104ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.0027% 70.63% 2075ms 1.90% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.63% 2075ms 1.90% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 597ms 0.55% 71.18% 2055ms 1.88% std::type_info::operator== (inline) 0 0% 71.18% 2024ms 1.85% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 71.18% 2012ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1993ms 1.82% 73.00% 1993ms 1.82% std::_Rb_tree_increment 1266ms 1.16% 74.16% 1881ms 1.72% std::_Rb_tree::equal_range (inline) 74ms 0.068% 74.23% 1811ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 74.23% 1808ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 18ms 0.016% 74.25% 1657ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 44ms 0.04% 74.29% 1518ms 1.39% VertexMesh::GetSurfaceAreaOfElement 42ms 0.038% 74.33% 1506ms 1.38% AbstractCellPopulation::GetLocationIndexUsingCell 55ms 0.05% 74.38% 1481ms 1.36% Node::RemoveElement 68ms 0.062% 74.44% 1477ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 20ms 0.018% 74.46% 1441ms 1.32% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.0073% 74.46% 1428ms 1.31% std::set::erase (inline) 1ms 0.00092% 74.47% 1414ms 1.29% tcache_get (inline) 1413ms 1.29% 75.76% 1413ms 1.29% tcache_get_n (inline) 3ms 0.0027% 75.76% 1382ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 75.76% 1349ms 1.24% boost::numeric::ublas::norm_2 (inline) 612ms 0.56% 76.32% 1333ms 1.22% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 170ms 0.16% 76.48% 1331ms 1.22% CellPropertyCollection::AddProperty 68ms 0.062% 76.54% 1331ms 1.22% std::less::operator() (inline) 1299ms 1.19% 77.73% 1299ms 1.19% [libchaste_cell_based.so] 0 0% 77.73% 1288ms 1.18% boost::numeric::ublas::vector_binary::operator() (inline) 1045ms 0.96% 78.69% 1263ms 1.16% std::operator< (inline) 0 0% 78.69% 1219ms 1.12% std::_Rb_tree::_Auto_node::_Auto_node (inline) 79ms 0.072% 78.76% 1216ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 29ms 0.027% 78.79% 1165ms 1.07% CellPropertyRegistry::Get 22ms 0.02% 78.81% 1165ms 1.07% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.81% 1105ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 14ms 0.013% 78.82% 1105ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 1091ms 1% 79.82% 1091ms 1% std::_Rb_tree_insert_and_rebalance 86ms 0.079% 79.90% 1091ms 1% std::swap_ranges (inline) 0 0% 79.90% 1089ms 1% std::_Rb_tree::clear (inline) 95ms 0.087% 79.98% 1088ms 1% std::_Rb_tree::find (inline) 0 0% 79.98% 1076ms 0.99% std::map::clear (inline) 5ms 0.0046% 79.99% 1052ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1018ms 0.93% 80.92% 1018ms 0.93% Node::rGetLocation 1006ms 0.92% 81.84% 1006ms 0.92% std::swap (inline) 0 0% 81.84% 1005ms 0.92% std::iter_swap (inline) 4ms 0.0037% 81.84% 968ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 173ms 0.16% 82.00% 955ms 0.87% boost::numeric::ublas::detail::equals 0 0% 82.00% 907ms 0.83% std::map::find (inline) 115ms 0.11% 82.11% 905ms 0.83% boost::detail::shared_count::~shared_count (inline) 0 0% 82.11% 905ms 0.83% boost::shared_ptr::~shared_ptr (inline) 0 0% 82.11% 869ms 0.8% VertexMeshWriter::MakeVtkMesh 852ms 0.78% 82.89% 852ms 0.78% std::vector::size (inline) 99ms 0.091% 82.98% 829ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 795ms 0.73% 83.71% 795ms 0.73% [libchaste_mesh.so] 0 0% 83.71% 770ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 730ms 0.67% 84.38% 759ms 0.69% boost::detail::sp_counted_base::release 20ms 0.018% 84.39% 749ms 0.69% MutableElement::RegisterWithEdges (inline) 405ms 0.37% 84.76% 745ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 405ms 0.37% 85.14% 735ms 0.67% Edge::GetMapIndex 17ms 0.016% 85.15% 729ms 0.67% Edge::AddElement 0 0% 85.15% 726ms 0.66% boost::numeric::ublas::norm_inf (inline) 385ms 0.35% 85.50% 726ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 228ms 0.21% 85.71% 723ms 0.66% std::__new_allocator::construct (inline) 0 0% 85.71% 723ms 0.66% std::allocator_traits::construct (inline) 0 0% 85.71% 719ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 2ms 0.0018% 85.71% 708ms 0.65% std::_Vector_base::_M_allocate (inline) 128ms 0.12% 85.83% 696ms 0.64% MutableElement::GetNodeLocalIndex 675ms 0.62% 86.45% 675ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.45% 664ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.45% 663ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 86.47% 663ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.47% 652ms 0.6% vtkPolygon::New 2ms 0.0018% 86.48% 652ms 0.6% vtkPolygon::vtkPolygon 172ms 0.16% 86.63% 648ms 0.59% boost::shared_ptr::shared_ptr (inline) 40ms 0.037% 86.67% 616ms 0.56% MutableElement::RegisterWithNodes (inline) 601ms 0.55% 87.22% 601ms 0.55% Node::GetIndex 6ms 0.0055% 87.23% 584ms 0.53% std::vector::_M_default_append (inline) 24ms 0.022% 87.25% 576ms 0.53% Node::AddElement 41ms 0.038% 87.29% 569ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.29% 569ms 0.52% boost::numeric::ublas::vector::vector (inline) 547ms 0.5% 87.79% 547ms 0.5% boost::shared_ptr::operator-> (inline)