File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96115ms, 88.58% of 108509ms total Dropped 1090 nodes (cum <= 542.54ms) flat flat% sum% cum cum% 0 0% 0% 108073ms 99.60% __libc_start_call_main 0 0% 0% 108073ms 99.60% __libc_start_main_impl 0 0% 0% 108073ms 99.60% _start 0 0% 0% 108052ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108052ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108052ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108052ms 99.58% main 0 0% 0% 108014ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108014ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108014ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108005ms 99.54% AbstractCellBasedSimulation::Solve 14ms 0.013% 0.016% 56016ms 51.62% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.036% 52949ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 145ms 0.13% 0.17% 51446ms 47.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.32% 0.49% 39614ms 36.51% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.49% 38844ms 35.80% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.49% 23954ms 22.08% VertexBasedCellPopulation::Update 0 0% 0.49% 23844ms 21.97% MutableVertexMesh::ReMesh 14377ms 13.25% 13.74% 22759ms 20.97% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.088% 13.83% 17735ms 16.34% Cell::ReadyToDivide 92ms 0.085% 13.91% 16450ms 15.16% AbstractPhaseBasedCellCycleModel::ReadyToDivide 362ms 0.33% 14.25% 14599ms 13.45% NagaiHondaForce::GetAdhesionParameter 429ms 0.4% 14.64% 14345ms 13.22% boost::numeric::ublas::c_vector::c_vector (partial-inline) 120ms 0.11% 14.75% 14030ms 12.93% SimpleWntCellCycleModel::UpdateCellCyclePhase 147ms 0.14% 14.89% 14001ms 12.90% CellPropertyCollection::GetPropertiesType (inline) 410ms 0.38% 15.27% 12828ms 11.82% boost::numeric::ublas::vector_assign (inline) 129ms 0.12% 15.38% 12050ms 11.11% MutableVertexMesh::CheckForIntersections 3345ms 3.08% 18.47% 11620ms 10.71% __dynamic_cast 70ms 0.065% 18.53% 11528ms 10.62% AbstractCellProperty::IsSubType (inline) 80ms 0.074% 18.61% 11331ms 10.44% VertexBasedCellPopulation::GetDampingConstant 72ms 0.066% 18.67% 10682ms 9.84% AbstractTargetAreaModifier::UpdateTargetAreas 62ms 0.057% 18.73% 10588ms 9.76% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 32ms 0.029% 18.76% 10350ms 9.54% AbstractCellBasedSimulation::DoCellBirth 1302ms 1.20% 19.96% 9918ms 9.14% std::__new_allocator::allocate (inline) 2808ms 2.59% 22.55% 9565ms 8.81% boost::numeric::ublas::indexing_vector_assign 0 0% 22.55% 9386ms 8.65% std::_Rb_tree::_M_create_node (inline) 0 0% 22.55% 9358ms 8.62% std::allocator_traits::allocate (inline) 1313ms 1.21% 23.76% 9036ms 8.33% std::_Rb_tree::_M_erase 796ms 0.73% 24.49% 8962ms 8.26% VertexMesh::ElementIncludesPoint 79ms 0.073% 24.56% 8884ms 8.19% Cell::GetMutationState 16ms 0.015% 24.58% 8762ms 8.07% VertexBasedCellPopulation::GetLocationOfCellCentre 846ms 0.78% 25.36% 8753ms 8.07% operator new 0 0% 25.36% 8744ms 8.06% std::_Rb_tree::_M_get_node (inline) 335ms 0.31% 25.67% 8743ms 8.06% VertexMesh::GetNextEdgeGradientOfElementAtNode 495ms 0.46% 26.12% 8359ms 7.70% VertexMesh::GetCentroidOfElement 0 0% 26.12% 8253ms 7.61% std::_Rb_tree::_Alloc_node::operator() (inline) 212ms 0.2% 26.32% 8226ms 7.58% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.32% 8097ms 7.46% std::_Rb_tree::_M_drop_node (inline) 226ms 0.21% 26.53% 7881ms 7.26% std::__new_allocator::deallocate (inline) 0 0% 26.53% 7849ms 7.23% std::allocator_traits::deallocate (inline) 0 0% 26.53% 7794ms 7.18% std::set::~set (inline) 3009ms 2.77% 29.30% 7784ms 7.17% __GI___libc_free 0 0% 29.30% 7768ms 7.16% std::_Rb_tree::_M_put_node (inline) 3154ms 2.91% 32.21% 7723ms 7.12% __GI___libc_malloc 12ms 0.011% 32.22% 7351ms 6.77% MutableVertexMesh::RemoveDeletedNodesAndElements 462ms 0.43% 32.64% 7149ms 6.59% std::map::operator[] (partial-inline) 1425ms 1.31% 33.96% 7055ms 6.50% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 183ms 0.17% 34.12% 6862ms 6.32% std::_Rb_tree::_Rb_tree (partial-inline) 6637ms 6.12% 40.24% 6637ms 6.12% __strcmp_avx2 645ms 0.59% 40.84% 6450ms 5.94% std::_Rb_tree::_M_copy (inline) 12ms 0.011% 40.85% 6396ms 5.89% std::set::set (inline) 103ms 0.095% 40.94% 6383ms 5.88% SimpleWntCellCycleModel::GetWntLevel 138ms 0.13% 41.07% 6185ms 5.70% WntConcentration::GetWntLevel 6070ms 5.59% 46.66% 6070ms 5.59% boost::numeric::ublas::c_vector::operator() 2784ms 2.57% 49.23% 5730ms 5.28% __cxxabiv1::__si_class_type_info::__do_dyncast 2384ms 2.20% 51.43% 5597ms 5.16% std::_Rb_tree::_M_lower_bound (inline) 735ms 0.68% 52.10% 5523ms 5.09% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.10% 5458ms 5.03% std::set::insert (inline) 27ms 0.025% 52.13% 5256ms 4.84% MutableVertexMesh::RemoveDeletedNodes 30ms 0.028% 52.16% 5083ms 4.68% EdgeHelper::RemoveDeletedEdges 48ms 0.044% 52.20% 4837ms 4.46% EdgeHelper::UpdateEdgesMapKey 4440ms 4.09% 56.29% 4775ms 4.40% _int_free 1498ms 1.38% 57.67% 4758ms 4.38% boost::numeric::ublas::c_vector::operator[] (inline) 204ms 0.19% 57.86% 4614ms 4.25% MutableElement::ResetIndex 590ms 0.54% 58.40% 4569ms 4.21% std::_Rb_tree::_M_insert_ (inline) 0 0% 58.40% 4550ms 4.19% std::_Rb_tree::lower_bound (inline) 0 0% 58.40% 4550ms 4.19% std::map::lower_bound (inline) 0 0% 58.40% 4532ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 64ms 0.059% 58.46% 4440ms 4.09% std::set_intersection (inline) 275ms 0.25% 58.72% 4376ms 4.03% std::__set_intersection 48ms 0.044% 58.76% 4030ms 3.71% Cell::GetCellProliferativeType 119ms 0.11% 58.87% 4008ms 3.69% AbstractCellPopulation::GetCellUsingLocationIndex 3903ms 3.60% 62.47% 3903ms 3.60% boost::numeric::ublas::same_impl_ex 61ms 0.056% 62.52% 3826ms 3.53% AbstractCellProperty::IsType (inline) 11ms 0.01% 62.53% 3499ms 3.22% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 831ms 0.77% 63.30% 3298ms 3.04% AbstractElement::GetNodeLocation 42ms 0.039% 63.34% 3190ms 2.94% Cell::SetCellProliferativeType 0 0% 63.34% 3166ms 2.92% std::insert_iterator::operator= (inline) 2048ms 1.89% 65.23% 2985ms 2.75% _int_malloc 35ms 0.032% 65.26% 2879ms 2.65% std::_Rb_tree::erase 781ms 0.72% 65.98% 2803ms 2.58% AbstractCellProperty::IsSame 6ms 0.0055% 65.98% 2796ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 627ms 0.58% 66.56% 2776ms 2.56% boost::numeric::ublas::vector_binary::size (inline) 2691ms 2.48% 69.04% 2691ms 2.48% std::_Rb_tree::_S_right (inline) 399ms 0.37% 69.41% 2676ms 2.47% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.41% 2662ms 2.45% std::_Rb_tree::_M_insert_unique 41ms 0.038% 69.45% 2626ms 2.42% CellPropertyCollection::HasProperty 0 0% 69.45% 2538ms 2.34% Cell::HasCellProperty (inline) 247ms 0.23% 69.67% 2515ms 2.32% VertexMesh::GetAreaGradientOfElementAtNode 59ms 0.054% 69.73% 2512ms 2.32% Cell::GetCellData 0 0% 69.73% 2437ms 2.25% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.73% 2436ms 2.24% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.73% 2429ms 2.24% boost::numeric::ublas::c_vector::operator-= (inline) 96ms 0.088% 69.82% 2308ms 2.13% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 112ms 0.1% 69.92% 2307ms 2.13% VertexMesh::GetVolumeOfElement 3ms 0.0028% 69.92% 2132ms 1.96% AbstractCellPopulation::Iterator::operator++ (inline) 229ms 0.21% 70.13% 2127ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 39ms 0.036% 70.17% 2099ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 2094ms 1.93% 72.10% 2094ms 1.93% std::_Rb_tree_increment 485ms 0.45% 72.55% 2022ms 1.86% std::type_info::operator== (inline) 0 0% 72.55% 1990ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 72.55% 1980ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1305ms 1.20% 73.75% 1931ms 1.78% std::_Rb_tree::equal_range (inline) 3ms 0.0028% 73.75% 1886ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.75% 1886ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 80ms 0.074% 73.83% 1874ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.83% 1764ms 1.63% VertexMeshWriter::WriteVtkUsingMesh 27ms 0.025% 73.85% 1663ms 1.53% VertexMesh::GetSurfaceAreaOfElement 20ms 0.018% 73.87% 1631ms 1.50% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 159ms 0.15% 74.02% 1607ms 1.48% CellPropertyCollection::AddProperty 38ms 0.035% 74.05% 1503ms 1.39% Node::RemoveElement 14ms 0.013% 74.06% 1472ms 1.36% std::set::erase (inline) 74ms 0.068% 74.13% 1436ms 1.32% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 128ms 0.12% 74.25% 1423ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 13ms 0.012% 74.26% 1410ms 1.30% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 74.26% 1384ms 1.28% tcache_get (inline) 1384ms 1.28% 75.54% 1384ms 1.28% tcache_get_n (inline) 0 0% 75.54% 1345ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 1210ms 1.12% 76.65% 1210ms 1.12% Node::rGetLocation 0 0% 76.65% 1199ms 1.10% boost::numeric::ublas::norm_2 (inline) 515ms 0.47% 77.13% 1185ms 1.09% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 61ms 0.056% 77.18% 1177ms 1.08% std::less::operator() (inline) 0 0% 77.18% 1154ms 1.06% OffLatticeSimulation::ApplyBoundaries 19ms 0.018% 77.20% 1144ms 1.05% CellPropertyRegistry::Get 0 0% 77.20% 1133ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 87ms 0.08% 77.28% 1132ms 1.04% std::_Rb_tree::_M_erase_aux (partial-inline) 929ms 0.86% 78.14% 1116ms 1.03% std::operator< (inline) 1080ms 1% 79.13% 1080ms 1% [libchaste_cell_based.so] 1051ms 0.97% 80.10% 1051ms 0.97% std::vector::size (inline) 1046ms 0.96% 81.06% 1046ms 0.96% std::_Rb_tree_insert_and_rebalance 100ms 0.092% 81.16% 1033ms 0.95% std::_Rb_tree::find (inline) 0 0% 81.16% 1025ms 0.94% std::_Rb_tree::clear (inline) 0 0% 81.16% 1010ms 0.93% std::map::clear (inline) 6ms 0.0055% 81.16% 983ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 121ms 0.11% 81.27% 977ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 81.27% 977ms 0.9% boost::shared_ptr::~shared_ptr (inline) 974ms 0.9% 82.17% 974ms 0.9% [libchaste_mesh.so] 16ms 0.015% 82.19% 961ms 0.89% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 21ms 0.019% 82.21% 937ms 0.86% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 82.21% 911ms 0.84% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0028% 82.21% 911ms 0.84% boost::numeric::ublas::c_vector::swap (inline) 79ms 0.073% 82.28% 908ms 0.84% std::swap_ranges (inline) 174ms 0.16% 82.44% 903ms 0.83% boost::numeric::ublas::detail::equals 366ms 0.34% 82.78% 901ms 0.83% Edge::GetMapIndex 2ms 0.0018% 82.78% 867ms 0.8% VertexMeshWriter::MakeVtkMesh 0 0% 82.78% 849ms 0.78% std::map::find (inline) 831ms 0.77% 83.55% 834ms 0.77% boost::detail::sp_counted_base::release 830ms 0.76% 84.31% 830ms 0.76% std::swap (inline) 0 0% 84.31% 829ms 0.76% std::iter_swap (inline) 92ms 0.085% 84.40% 811ms 0.75% MutableElement::GetNodeLocalIndex 112ms 0.1% 84.50% 808ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 136ms 0.13% 84.62% 787ms 0.73% boost::shared_ptr::shared_ptr (inline) 447ms 0.41% 85.04% 764ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 18ms 0.017% 85.05% 751ms 0.69% MutableElement::RegisterWithEdges (inline) 26ms 0.024% 85.08% 748ms 0.69% Edge::AddElement 15ms 0.014% 85.09% 732ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 730ms 0.67% 85.76% 730ms 0.67% Node::GetIndex 114ms 0.11% 85.87% 717ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 0 0% 85.87% 716ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.87% 687ms 0.63% boost::numeric::ublas::norm_inf (inline) 362ms 0.33% 86.20% 687ms 0.63% boost::numeric::ublas::vector_norm_inf::apply (inline) 130ms 0.12% 86.32% 687ms 0.63% std::__new_allocator::construct (inline) 0 0% 86.32% 687ms 0.63% std::allocator_traits::construct (inline) 623ms 0.57% 86.90% 651ms 0.6% boost::detail::shared_count::shared_count (inline) 0 0% 86.90% 642ms 0.59% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.90% 637ms 0.59% vtkPolygon::New 3ms 0.0028% 86.90% 636ms 0.59% vtkPolygon::vtkPolygon 30ms 0.028% 86.93% 626ms 0.58% MutableElement::RegisterWithNodes (inline) 0 0% 86.93% 622ms 0.57% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.027% 86.95% 622ms 0.57% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.95% 610ms 0.56% std::_Vector_base::_M_allocate (inline) 602ms 0.55% 87.51% 602ms 0.55% [libstdc++.so.6.0.33] 33ms 0.03% 87.54% 592ms 0.55% Node::AddElement 0 0% 87.54% 582ms 0.54% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 21ms 0.019% 87.56% 581ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.56% 581ms 0.54% boost::numeric::ublas::vector::vector (inline) 553ms 0.51% 88.07% 553ms 0.51% operator delete 553ms 0.51% 88.58% 553ms 0.51% tcache_put (inline)