File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96001ms, 87.77% of 109378ms total Dropped 1145 nodes (cum <= 546.89ms) flat flat% sum% cum cum% 0 0% 0% 109044ms 99.69% __libc_start_call_main 0 0% 0% 109044ms 99.69% __libc_start_main_impl 0 0% 0% 109044ms 99.69% _start 0 0% 0% 109020ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109020ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109020ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109020ms 99.67% main 0 0% 0% 108978ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108978ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108978ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00091% 0.00091% 108970ms 99.63% AbstractCellBasedSimulation::Solve 23ms 0.021% 0.022% 56864ms 51.99% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.034% 53565ms 48.97% ForwardEulerNumericalMethod::UpdateAllNodePositions 156ms 0.14% 0.18% 52096ms 47.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 409ms 0.37% 0.55% 40345ms 36.89% NagaiHondaForce::AddForceContribution 0 0% 0.55% 38739ms 35.42% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.55% 23805ms 21.76% VertexBasedCellPopulation::Update 1ms 0.00091% 0.55% 23655ms 21.63% MutableVertexMesh::ReMesh 14698ms 13.44% 13.99% 23535ms 21.52% Cylindrical2dVertexMesh::GetVectorFromAtoB 100ms 0.091% 14.08% 17889ms 16.36% Cell::ReadyToDivide 78ms 0.071% 14.16% 16526ms 15.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 354ms 0.32% 14.48% 14397ms 13.16% NagaiHondaForce::GetAdhesionParameter 146ms 0.13% 14.61% 14113ms 12.90% SimpleWntCellCycleModel::UpdateCellCyclePhase 158ms 0.14% 14.76% 14101ms 12.89% CellPropertyCollection::GetPropertiesType (inline) 509ms 0.47% 15.22% 14048ms 12.84% boost::numeric::ublas::c_vector::c_vector (partial-inline) 282ms 0.26% 15.48% 12537ms 11.46% boost::numeric::ublas::vector_assign (inline) 3344ms 3.06% 18.54% 12060ms 11.03% __dynamic_cast 42ms 0.038% 18.58% 11935ms 10.91% AbstractCellProperty::IsSubType (inline) 154ms 0.14% 18.72% 11757ms 10.75% MutableVertexMesh::CheckForIntersections 80ms 0.073% 18.79% 11156ms 10.20% VertexBasedCellPopulation::GetDampingConstant 56ms 0.051% 18.84% 10842ms 9.91% AbstractTargetAreaModifier::UpdateTargetAreas 28ms 0.026% 18.87% 10756ms 9.83% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 35ms 0.032% 18.90% 10311ms 9.43% AbstractCellBasedSimulation::DoCellBirth 1272ms 1.16% 20.06% 9802ms 8.96% std::__new_allocator::allocate (inline) 2822ms 2.58% 22.64% 9726ms 8.89% boost::numeric::ublas::indexing_vector_assign 366ms 0.33% 22.98% 9593ms 8.77% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.98% 9310ms 8.51% std::_Rb_tree::_M_create_node (inline) 0 0% 22.98% 9306ms 8.51% std::allocator_traits::allocate (inline) 1233ms 1.13% 24.10% 8857ms 8.10% std::_Rb_tree::_M_erase 836ms 0.76% 24.87% 8638ms 7.90% VertexMesh::ElementIncludesPoint 29ms 0.027% 24.89% 8607ms 7.87% VertexBasedCellPopulation::GetLocationOfCellCentre 717ms 0.66% 25.55% 8607ms 7.87% operator new 0 0% 25.55% 8592ms 7.86% std::_Rb_tree::_M_get_node (inline) 68ms 0.062% 25.61% 8558ms 7.82% Cell::GetMutationState 473ms 0.43% 26.04% 8208ms 7.50% VertexMesh::GetCentroidOfElement 0 0% 26.04% 8196ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 235ms 0.21% 26.26% 8058ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.26% 7981ms 7.30% std::_Rb_tree::_M_drop_node (inline) 255ms 0.23% 26.49% 7763ms 7.10% std::__new_allocator::deallocate (inline) 0 0% 26.49% 7752ms 7.09% std::allocator_traits::deallocate (inline) 14ms 0.013% 26.51% 7690ms 7.03% MutableVertexMesh::RemoveDeletedNodesAndElements 2992ms 2.74% 29.24% 7688ms 7.03% __GI___libc_malloc 0 0% 29.24% 7674ms 7.02% std::_Rb_tree::_M_put_node (inline) 0 0% 29.24% 7627ms 6.97% std::set::~set (inline) 1384ms 1.27% 30.51% 7489ms 6.85% AbstractMesh::GetDistanceBetweenNodes 489ms 0.45% 30.95% 7367ms 6.74% std::map::operator[] (partial-inline) 2278ms 2.08% 33.04% 7231ms 6.61% __GI___libc_free 195ms 0.18% 33.21% 6991ms 6.39% std::_Rb_tree::_Rb_tree (partial-inline) 6953ms 6.36% 39.57% 6953ms 6.36% __strcmp_avx2 716ms 0.65% 40.23% 6544ms 5.98% std::_Rb_tree::_M_copy (inline) 19ms 0.017% 40.24% 6525ms 5.97% std::set::set (inline) 6314ms 5.77% 46.02% 6314ms 5.77% boost::numeric::ublas::c_vector::operator() 119ms 0.11% 46.12% 6222ms 5.69% SimpleWntCellCycleModel::GetWntLevel 2983ms 2.73% 48.85% 6052ms 5.53% __cxxabiv1::__si_class_type_info::__do_dyncast 145ms 0.13% 48.98% 6020ms 5.50% WntConcentration::GetWntLevel 2438ms 2.23% 51.21% 5695ms 5.21% std::_Rb_tree::_M_lower_bound (inline) 794ms 0.73% 51.94% 5579ms 5.10% std::_Rb_tree::_M_clone_node (inline) 1997ms 1.83% 53.76% 5378ms 4.92% boost::numeric::ublas::c_vector::operator[] (inline) 26ms 0.024% 53.79% 5282ms 4.83% MutableVertexMesh::RemoveDeletedNodes 0 0% 53.79% 5255ms 4.80% std::set::insert (inline) 27ms 0.025% 53.81% 5102ms 4.66% EdgeHelper::RemoveDeletedEdges 4513ms 4.13% 57.94% 4938ms 4.51% _int_free 31ms 0.028% 57.97% 4787ms 4.38% EdgeHelper::UpdateEdgesMapKey 0 0% 57.97% 4650ms 4.25% std::_Rb_tree::lower_bound (inline) 0 0% 57.97% 4650ms 4.25% std::map::lower_bound (inline) 191ms 0.17% 58.14% 4649ms 4.25% MutableElement::ResetIndex 0 0% 58.14% 4614ms 4.22% AbstractCellBasedSimulation::DoCellRemoval (inline) 485ms 0.44% 58.59% 4407ms 4.03% std::_Rb_tree::_M_insert_ (inline) 146ms 0.13% 58.72% 4354ms 3.98% std::set_intersection (inline) 155ms 0.14% 58.86% 4281ms 3.91% AbstractCellPopulation::GetCellUsingLocationIndex 42ms 0.038% 58.90% 4221ms 3.86% Cell::GetCellProliferativeType 250ms 0.23% 59.13% 4208ms 3.85% std::__set_intersection 3964ms 3.62% 62.75% 3964ms 3.62% boost::numeric::ublas::same_impl_ex 67ms 0.061% 62.81% 3888ms 3.55% AbstractCellProperty::IsType (inline) 14ms 0.013% 62.83% 3438ms 3.14% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.83% 3220ms 2.94% std::insert_iterator::operator= (inline) 52ms 0.048% 62.87% 3200ms 2.93% Cell::SetCellProliferativeType 2207ms 2.02% 64.89% 3158ms 2.89% _int_malloc 914ms 0.84% 65.73% 3007ms 2.75% AbstractElement::GetNodeLocation 60ms 0.055% 65.78% 2931ms 2.68% std::_Rb_tree::erase 294ms 0.27% 66.05% 2929ms 2.68% VertexMesh::GetAreaGradientOfElementAtNode 38ms 0.035% 66.09% 2831ms 2.59% CellPropertyCollection::HasProperty 740ms 0.68% 66.76% 2825ms 2.58% AbstractCellProperty::IsSame 16ms 0.015% 66.78% 2800ms 2.56% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 66.78% 2740ms 2.51% Cell::HasCellProperty (inline) 2688ms 2.46% 69.23% 2688ms 2.46% std::_Rb_tree::_S_right (inline) 0 0% 69.23% 2671ms 2.44% boost::numeric::ublas::c_vector::operator-= (inline) 663ms 0.61% 69.84% 2647ms 2.42% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.84% 2622ms 2.40% boost::numeric::ublas::c_vector::assign (inline) 34ms 0.031% 69.87% 2573ms 2.35% Cell::GetCellData 252ms 0.23% 70.10% 2545ms 2.33% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 70.10% 2489ms 2.28% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0018% 70.10% 2455ms 2.24% std::_Rb_tree::_M_insert_unique 76ms 0.069% 70.17% 2359ms 2.16% VertexMesh::GetVolumeOfElement 31ms 0.028% 70.20% 2319ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 33ms 0.03% 70.23% 2180ms 1.99% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.0027% 70.23% 2129ms 1.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.23% 2129ms 1.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.0046% 70.24% 2103ms 1.92% AbstractCellPopulation::Iterator::operator++ (inline) 153ms 0.14% 70.38% 2096ms 1.92% AbstractCellPopulation::Iterator::IsRealCell (inline) 539ms 0.49% 70.87% 2085ms 1.91% std::type_info::operator== (inline) 1ms 0.00091% 70.87% 2032ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 70.87% 2022ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2017ms 1.84% 72.72% 2017ms 1.84% std::_Rb_tree_increment 1273ms 1.16% 73.88% 1896ms 1.73% std::_Rb_tree::equal_range (inline) 71ms 0.065% 73.95% 1892ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.95% 1822ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 19ms 0.017% 73.96% 1668ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 31ms 0.028% 73.99% 1542ms 1.41% VertexMesh::GetSurfaceAreaOfElement 35ms 0.032% 74.02% 1497ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 69ms 0.063% 74.09% 1475ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 45ms 0.041% 74.13% 1459ms 1.33% Node::RemoveElement 9ms 0.0082% 74.14% 1419ms 1.30% std::set::erase (inline) 0 0% 74.14% 1399ms 1.28% boost::numeric::ublas::norm_2 (inline) 116ms 0.11% 74.24% 1379ms 1.26% CellPropertyCollection::AddProperty 619ms 0.57% 74.81% 1379ms 1.26% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 67ms 0.061% 74.87% 1378ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 1362ms 1.25% 76.11% 1362ms 1.25% [libchaste_cell_based.so] 2ms 0.0018% 76.12% 1344ms 1.23% tcache_get (inline) 1342ms 1.23% 77.34% 1342ms 1.23% tcache_get_n (inline) 0 0% 77.34% 1341ms 1.23% OffLatticeSimulation::ApplyBoundaries 0 0% 77.34% 1334ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 59ms 0.054% 77.40% 1239ms 1.13% std::less::operator() (inline) 25ms 0.023% 77.42% 1191ms 1.09% CellPropertyRegistry::Get 948ms 0.87% 78.29% 1180ms 1.08% std::operator< (inline) 25ms 0.023% 78.31% 1136ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 78ms 0.071% 78.38% 1131ms 1.03% std::_Rb_tree::_M_erase_aux (partial-inline) 10ms 0.0091% 78.39% 1127ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 78.39% 1114ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1098ms 1.00% 79.39% 1098ms 1.00% std::_Rb_tree_insert_and_rebalance 0 0% 79.39% 1096ms 1.00% boost::numeric::ublas::c_vector::assign_temporary (inline) 12ms 0.011% 79.40% 1096ms 1.00% boost::numeric::ublas::c_vector::swap (inline) 65ms 0.059% 79.46% 1084ms 0.99% std::swap_ranges (inline) 98ms 0.09% 79.55% 1071ms 0.98% std::_Rb_tree::find (inline) 0 0% 79.55% 1037ms 0.95% std::_Rb_tree::clear (inline) 116ms 0.11% 79.66% 1027ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 79.66% 1027ms 0.94% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.66% 1019ms 0.93% std::iter_swap (inline) 1019ms 0.93% 80.59% 1019ms 0.93% std::swap (inline) 0 0% 80.59% 1017ms 0.93% std::map::clear (inline) 10ms 0.0091% 80.60% 986ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 179ms 0.16% 80.76% 963ms 0.88% boost::numeric::ublas::detail::equals 927ms 0.85% 81.61% 927ms 0.85% Node::rGetLocation 0 0% 81.61% 900ms 0.82% std::map::find (inline) 847ms 0.77% 82.39% 873ms 0.8% boost::detail::sp_counted_base::release 0 0% 82.39% 856ms 0.78% VertexMeshWriter::MakeVtkMesh 108ms 0.099% 82.48% 816ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 805ms 0.74% 83.22% 805ms 0.74% std::vector::size (inline) 449ms 0.41% 83.63% 785ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 228ms 0.21% 83.84% 779ms 0.71% std::__new_allocator::construct (inline) 0 0% 83.84% 779ms 0.71% std::allocator_traits::construct (inline) 20ms 0.018% 83.86% 770ms 0.7% MutableElement::RegisterWithEdges (inline) 22ms 0.02% 83.88% 764ms 0.7% Edge::AddElement 749ms 0.68% 84.56% 749ms 0.68% [libchaste_mesh.so] 423ms 0.39% 84.95% 735ms 0.67% Edge::GetMapIndex 0 0% 84.95% 730ms 0.67% boost::numeric::ublas::norm_inf (inline) 356ms 0.33% 85.27% 730ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 175ms 0.16% 85.43% 729ms 0.67% boost::shared_ptr::shared_ptr (inline) 0 0% 85.43% 718ms 0.66% std::_Rb_tree::_M_construct_node (inline) 2ms 0.0018% 85.44% 714ms 0.65% std::_Vector_base::_M_allocate (inline) 0 0% 85.44% 707ms 0.65% CellPropertyCollection::~CellPropertyCollection (inline) 22ms 0.02% 85.46% 704ms 0.64% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 85.46% 701ms 0.64% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 700ms 0.64% 86.10% 700ms 0.64% [libstdc++.so.6.0.33] 109ms 0.1% 86.20% 682ms 0.62% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 86.20% 670ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 11ms 0.01% 86.21% 670ms 0.61% std::_Rb_tree::_M_insert_node (inline) 34ms 0.031% 86.24% 617ms 0.56% MutableElement::RegisterWithNodes (inline) 133ms 0.12% 86.36% 615ms 0.56% MutableElement::GetNodeLocalIndex 0 0% 86.36% 610ms 0.56% vtkPolygon::New 0 0% 86.36% 610ms 0.56% vtkPolygon::vtkPolygon 13ms 0.012% 86.37% 599ms 0.55% std::vector::_M_default_append (inline) 36ms 0.033% 86.40% 586ms 0.54% Node::AddElement 584ms 0.53% 86.94% 584ms 0.53% Node::GetIndex 513ms 0.47% 87.41% 554ms 0.51% boost::detail::shared_count::shared_count (inline) 397ms 0.36% 87.77% 552ms 0.5% malloc_consolidate