File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94989ms, 88.39% of 107468ms total Dropped 1046 nodes (cum <= 537.34ms) flat flat% sum% cum cum% 0 0% 0% 106975ms 99.54% __libc_start_call_main 0 0% 0% 106975ms 99.54% __libc_start_main_impl 0 0% 0% 106975ms 99.54% _start 0 0% 0% 106956ms 99.52% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 106956ms 99.52% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 106956ms 99.52% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 106956ms 99.52% main 0 0% 0% 106919ms 99.49% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 106919ms 99.49% CxxTest::TestRunner::runTest (inline) 0 0% 0% 106919ms 99.49% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 106912ms 99.48% AbstractCellBasedSimulation::Solve 9ms 0.0084% 0.0084% 55875ms 51.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 11ms 0.01% 0.019% 52791ms 49.12% ForwardEulerNumericalMethod::UpdateAllNodePositions 122ms 0.11% 0.13% 51753ms 48.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 424ms 0.39% 0.53% 40295ms 37.49% NagaiHondaForce::AddForceContribution 0 0% 0.53% 38437ms 35.77% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00093% 0.53% 23765ms 22.11% VertexBasedCellPopulation::Update 3ms 0.0028% 0.53% 23651ms 22.01% MutableVertexMesh::ReMesh 14569ms 13.56% 14.09% 23107ms 21.50% Cylindrical2dVertexMesh::GetVectorFromAtoB 75ms 0.07% 14.16% 17224ms 16.03% Cell::ReadyToDivide 94ms 0.087% 14.24% 16020ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 303ms 0.28% 14.53% 14717ms 13.69% NagaiHondaForce::GetAdhesionParameter 350ms 0.33% 14.85% 14326ms 13.33% boost::numeric::ublas::c_vector::c_vector (partial-inline) 121ms 0.11% 14.96% 13601ms 12.66% SimpleWntCellCycleModel::UpdateCellCyclePhase 89ms 0.083% 15.05% 13274ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 403ms 0.37% 15.42% 12854ms 11.96% boost::numeric::ublas::vector_assign (inline) 133ms 0.12% 15.55% 12051ms 11.21% MutableVertexMesh::CheckForIntersections 3221ms 3.00% 18.54% 11198ms 10.42% __dynamic_cast 88ms 0.082% 18.63% 11065ms 10.30% AbstractCellProperty::IsSubType (inline) 70ms 0.065% 18.69% 10955ms 10.19% VertexBasedCellPopulation::GetDampingConstant 67ms 0.062% 18.75% 10237ms 9.53% AbstractTargetAreaModifier::UpdateTargetAreas 49ms 0.046% 18.80% 10156ms 9.45% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 20ms 0.019% 18.82% 10059ms 9.36% AbstractCellBasedSimulation::DoCellBirth 1144ms 1.06% 19.88% 9615ms 8.95% std::__new_allocator::allocate (inline) 2544ms 2.37% 22.25% 9507ms 8.85% boost::numeric::ublas::indexing_vector_assign 1304ms 1.21% 23.46% 9270ms 8.63% std::_Rb_tree::_M_erase 0 0% 23.46% 9083ms 8.45% std::allocator_traits::allocate (inline) 0 0% 23.46% 9011ms 8.38% std::_Rb_tree::_M_create_node (inline) 781ms 0.73% 24.19% 8984ms 8.36% VertexMesh::ElementIncludesPoint 350ms 0.33% 24.51% 8949ms 8.33% VertexMesh::GetNextEdgeGradientOfElementAtNode 26ms 0.024% 24.54% 8649ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 785ms 0.73% 25.27% 8549ms 7.95% operator new 223ms 0.21% 25.48% 8499ms 7.91% std::_Rb_tree::~_Rb_tree (inline) 95ms 0.088% 25.56% 8486ms 7.90% Cell::GetMutationState 0 0% 25.56% 8422ms 7.84% std::_Rb_tree::_M_get_node (inline) 0 0% 25.56% 8264ms 7.69% std::_Rb_tree::_M_drop_node (inline) 446ms 0.42% 25.98% 8211ms 7.64% VertexMesh::GetCentroidOfElement 0 0% 25.98% 8063ms 7.50% std::set::~set (inline) 294ms 0.27% 26.25% 8013ms 7.46% std::__new_allocator::deallocate (inline) 0 0% 26.25% 7972ms 7.42% std::allocator_traits::deallocate (inline) 0 0% 26.25% 7925ms 7.37% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.25% 7911ms 7.36% std::_Rb_tree::_M_put_node (inline) 2990ms 2.78% 29.04% 7740ms 7.20% __GI___libc_free 3004ms 2.80% 31.83% 7570ms 7.04% __GI___libc_malloc 11ms 0.01% 31.84% 7271ms 6.77% MutableVertexMesh::RemoveDeletedNodesAndElements 1369ms 1.27% 33.11% 7219ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 514ms 0.48% 33.59% 7131ms 6.64% std::map::operator[] (partial-inline) 178ms 0.17% 33.76% 6451ms 6.00% std::_Rb_tree::_Rb_tree (partial-inline) 6195ms 5.76% 39.52% 6195ms 5.76% boost::numeric::ublas::c_vector::operator() 6171ms 5.74% 45.27% 6171ms 5.74% __strcmp_avx2 109ms 0.1% 45.37% 6167ms 5.74% SimpleWntCellCycleModel::GetWntLevel 646ms 0.6% 45.97% 6079ms 5.66% std::_Rb_tree::_M_copy (inline) 4ms 0.0037% 45.97% 6051ms 5.63% std::set::set (inline) 135ms 0.13% 46.10% 5955ms 5.54% WntConcentration::GetWntLevel 2777ms 2.58% 48.68% 5595ms 5.21% __cxxabiv1::__si_class_type_info::__do_dyncast 2390ms 2.22% 50.91% 5517ms 5.13% std::_Rb_tree::_M_lower_bound (inline) 0 0% 50.91% 5382ms 5.01% std::set::insert (inline) 25ms 0.023% 50.93% 5176ms 4.82% MutableVertexMesh::RemoveDeletedNodes 694ms 0.65% 51.57% 5147ms 4.79% std::_Rb_tree::_M_clone_node (inline) 36ms 0.033% 51.61% 4996ms 4.65% EdgeHelper::RemoveDeletedEdges 1548ms 1.44% 53.05% 4839ms 4.50% boost::numeric::ublas::c_vector::operator[] (inline) 4438ms 4.13% 57.18% 4744ms 4.41% _int_free 44ms 0.041% 57.22% 4692ms 4.37% EdgeHelper::UpdateEdgesMapKey 1ms 0.00093% 57.22% 4607ms 4.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 49ms 0.046% 57.27% 4598ms 4.28% std::set_intersection (inline) 262ms 0.24% 57.51% 4549ms 4.23% std::__set_intersection 193ms 0.18% 57.69% 4531ms 4.22% MutableElement::ResetIndex 530ms 0.49% 58.18% 4531ms 4.22% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.18% 4508ms 4.19% std::_Rb_tree::lower_bound (inline) 0 0% 58.18% 4508ms 4.19% std::map::lower_bound (inline) 4012ms 3.73% 61.92% 4012ms 3.73% boost::numeric::ublas::same_impl_ex 110ms 0.1% 62.02% 3977ms 3.70% AbstractCellPopulation::GetCellUsingLocationIndex 44ms 0.041% 62.06% 3967ms 3.69% Cell::GetCellProliferativeType 78ms 0.073% 62.13% 3684ms 3.43% AbstractCellProperty::IsType (inline) 7ms 0.0065% 62.14% 3554ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.14% 3269ms 3.04% std::insert_iterator::operator= (inline) 55ms 0.051% 62.19% 3109ms 2.89% Cell::SetCellProliferativeType 2138ms 1.99% 64.18% 3032ms 2.82% _int_malloc 853ms 0.79% 64.97% 2991ms 2.78% AbstractElement::GetNodeLocation 629ms 0.59% 65.56% 2914ms 2.71% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.00093% 65.56% 2902ms 2.70% std::_Rb_tree::_M_insert_unique_ (inline) 31ms 0.029% 65.59% 2795ms 2.60% std::_Rb_tree::erase 448ms 0.42% 66.00% 2726ms 2.54% std::_Rb_tree_const_iterator::operator++ (inline) 2633ms 2.45% 68.45% 2633ms 2.45% std::_Rb_tree::_S_right (inline) 833ms 0.78% 69.23% 2609ms 2.43% AbstractCellProperty::IsSame 69ms 0.064% 69.29% 2599ms 2.42% VertexMesh::GetVolumeOfElement 38ms 0.035% 69.33% 2505ms 2.33% CellPropertyCollection::HasProperty 0 0% 69.33% 2480ms 2.31% std::_Rb_tree::_M_insert_unique (inline) 239ms 0.22% 69.55% 2471ms 2.30% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.55% 2447ms 2.28% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.55% 2418ms 2.25% Cell::HasCellProperty (inline) 1ms 0.00093% 69.55% 2345ms 2.18% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.55% 2316ms 2.16% boost::numeric::ublas::c_vector::assign (inline) 122ms 0.11% 69.67% 2308ms 2.15% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 30ms 0.028% 69.69% 2292ms 2.13% Cell::GetCellData 4ms 0.0037% 69.70% 2111ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 2103ms 1.96% 71.65% 2103ms 1.96% std::_Rb_tree_increment 216ms 0.2% 71.85% 2086ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 32ms 0.03% 71.88% 2064ms 1.92% std::_Rb_tree::_M_emplace_hint_unique 0 0% 71.88% 1930ms 1.80% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0019% 71.89% 1918ms 1.78% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1259ms 1.17% 73.06% 1865ms 1.74% std::_Rb_tree::equal_range (inline) 1ms 0.00093% 73.06% 1840ms 1.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.06% 1840ms 1.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 53ms 0.049% 73.11% 1836ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 429ms 0.4% 73.51% 1776ms 1.65% std::type_info::operator== (inline) 0 0% 73.51% 1718ms 1.60% VertexMeshWriter::WriteVtkUsingMesh 17ms 0.016% 73.52% 1622ms 1.51% VertexMesh::GetSurfaceAreaOfElement 35ms 0.033% 73.56% 1606ms 1.49% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 141ms 0.13% 73.69% 1568ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 167ms 0.16% 73.84% 1464ms 1.36% CellPropertyCollection::AddProperty 0 0% 73.84% 1464ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 57ms 0.053% 73.90% 1454ms 1.35% Node::RemoveElement 34ms 0.032% 73.93% 1431ms 1.33% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.023% 73.95% 1411ms 1.31% std::set::erase (inline) 81ms 0.075% 74.03% 1405ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.03% 1364ms 1.27% tcache_get (inline) 1364ms 1.27% 75.29% 1364ms 1.27% tcache_get_n (inline) 105ms 0.098% 75.39% 1284ms 1.19% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 75.39% 1231ms 1.15% OffLatticeSimulation::ApplyBoundaries 0 0% 75.39% 1138ms 1.06% boost::numeric::ublas::norm_2 (inline) 72ms 0.067% 75.46% 1132ms 1.05% std::less::operator() (inline) 511ms 0.48% 75.94% 1131ms 1.05% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 84ms 0.078% 76.01% 1112ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 1112ms 1.03% 77.05% 1112ms 1.03% std::_Rb_tree_insert_and_rebalance 31ms 0.029% 77.08% 1100ms 1.02% CellPropertyRegistry::Get 1092ms 1.02% 78.09% 1092ms 1.02% [libchaste_cell_based.so] 0 0% 78.09% 1086ms 1.01% std::_Rb_tree::_Auto_node::_Auto_node (inline) 843ms 0.78% 78.88% 1060ms 0.99% std::operator< (inline) 21ms 0.02% 78.90% 1043ms 0.97% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 90ms 0.084% 78.98% 1016ms 0.95% std::_Rb_tree::find (inline) 1007ms 0.94% 79.92% 1007ms 0.94% Node::rGetLocation 1ms 0.00093% 79.92% 997ms 0.93% std::_Rb_tree::clear (inline) 6ms 0.0056% 79.92% 990ms 0.92% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 79.92% 982ms 0.91% std::map::clear (inline) 980ms 0.91% 80.84% 980ms 0.91% std::vector::size (inline) 155ms 0.14% 80.98% 975ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.98% 975ms 0.91% boost::shared_ptr::~shared_ptr (inline) 938ms 0.87% 81.85% 938ms 0.87% [libchaste_mesh.so] 20ms 0.019% 81.87% 911ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 111ms 0.1% 81.98% 903ms 0.84% MutableElement::GetNodeLocalIndex 393ms 0.37% 82.34% 894ms 0.83% Edge::GetMapIndex 135ms 0.13% 82.47% 881ms 0.82% boost::numeric::ublas::detail::equals 0 0% 82.47% 879ms 0.82% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 82.47% 879ms 0.82% boost::numeric::ublas::c_vector::swap (inline) 72ms 0.067% 82.54% 875ms 0.81% std::swap_ranges (inline) 3ms 0.0028% 82.54% 852ms 0.79% VertexMeshWriter::MakeVtkMesh 836ms 0.78% 83.32% 836ms 0.78% __memcpy_avx_unaligned_erms 0 0% 83.32% 831ms 0.77% std::map::find (inline) 0 0% 83.32% 803ms 0.75% std::iter_swap (inline) 803ms 0.75% 84.07% 803ms 0.75% std::swap (inline) 791ms 0.74% 84.80% 802ms 0.75% boost::detail::sp_counted_base::release 57ms 0.053% 84.85% 797ms 0.74% std::__copy_move::__copy_m (inline) 0 0% 84.85% 797ms 0.74% std::__copy_move_a (inline) 0 0% 84.85% 797ms 0.74% std::__copy_move_a1 (inline) 0 0% 84.85% 797ms 0.74% std::__copy_move_a2 (inline) 0 0% 84.85% 797ms 0.74% std::copy (inline) 148ms 0.14% 84.99% 788ms 0.73% boost::shared_ptr::shared_ptr (inline) 0 0% 84.99% 770ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 23ms 0.021% 85.01% 760ms 0.71% MutableElement::RegisterWithEdges (inline) 27ms 0.025% 85.04% 753ms 0.7% Edge::AddElement 459ms 0.43% 85.47% 746ms 0.69% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 725ms 0.67% 86.14% 725ms 0.67% Node::GetIndex 0 0% 86.14% 702ms 0.65% boost::numeric::ublas::norm_inf (inline) 337ms 0.31% 86.45% 702ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.45% 664ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.019% 86.47% 664ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.47% 660ms 0.61% std::_Vector_base::_M_allocate (inline) 85ms 0.079% 86.55% 644ms 0.6% std::__new_allocator::construct (inline) 0 0% 86.55% 644ms 0.6% std::allocator_traits::construct (inline) 604ms 0.56% 87.11% 640ms 0.6% boost::detail::shared_count::shared_count (inline) 632ms 0.59% 87.70% 632ms 0.59% [libstdc++.so.6.0.33] 629ms 0.59% 88.29% 629ms 0.59% operator delete 29ms 0.027% 88.31% 620ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 88.31% 603ms 0.56% vtkPolygon::New 4ms 0.0037% 88.32% 603ms 0.56% vtkPolygon::vtkPolygon 0 0% 88.32% 589ms 0.55% std::_Rb_tree::_M_construct_node (inline) 28ms 0.026% 88.34% 569ms 0.53% Node::AddElement 29ms 0.027% 88.37% 561ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.37% 561ms 0.52% boost::numeric::ublas::vector::vector (inline) 19ms 0.018% 88.39% 559ms 0.52% AbstractNumericalMethod::SafeNodePositionUpdate 0 0% 88.39% 541ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)