File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 97061ms, 87.35% of 111122ms total Dropped 1186 nodes (cum <= 555.61ms) flat flat% sum% cum cum% 0 0% 0% 110740ms 99.66% __libc_start_call_main 0 0% 0% 110740ms 99.66% __libc_start_main_impl 0 0% 0% 110740ms 99.66% _start 0 0% 0% 110716ms 99.63% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 110716ms 99.63% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 110716ms 99.63% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 110716ms 99.63% main 0 0% 0% 110672ms 99.60% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 110672ms 99.60% CxxTest::TestRunner::runTest (inline) 0 0% 0% 110672ms 99.60% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0027% 0.0027% 110664ms 99.59% AbstractCellBasedSimulation::Solve 30ms 0.027% 0.03% 57638ms 51.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 16ms 0.014% 0.044% 54220ms 48.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 171ms 0.15% 0.2% 52653ms 47.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 348ms 0.31% 0.51% 40578ms 36.52% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.51% 39659ms 35.69% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0009% 0.51% 24637ms 22.17% VertexBasedCellPopulation::Update 0 0% 0.51% 24496ms 22.04% MutableVertexMesh::ReMesh 14606ms 13.14% 13.66% 23183ms 20.86% Cylindrical2dVertexMesh::GetVectorFromAtoB 81ms 0.073% 13.73% 17664ms 15.90% Cell::ReadyToDivide 53ms 0.048% 13.78% 16297ms 14.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 381ms 0.34% 14.12% 14423ms 12.98% NagaiHondaForce::GetAdhesionParameter 150ms 0.13% 14.26% 14102ms 12.69% SimpleWntCellCycleModel::UpdateCellCyclePhase 513ms 0.46% 14.72% 14047ms 12.64% boost::numeric::ublas::c_vector::c_vector (partial-inline) 103ms 0.093% 14.81% 13765ms 12.39% CellPropertyCollection::GetPropertiesType (inline) 288ms 0.26% 15.07% 12467ms 11.22% boost::numeric::ublas::vector_assign (inline) 134ms 0.12% 15.19% 11933ms 10.74% MutableVertexMesh::CheckForIntersections 3613ms 3.25% 18.44% 11774ms 10.60% __dynamic_cast 38ms 0.034% 18.48% 11621ms 10.46% AbstractCellProperty::IsSubType (inline) 65ms 0.058% 18.53% 11473ms 10.32% VertexBasedCellPopulation::GetDampingConstant 74ms 0.067% 18.60% 10797ms 9.72% AbstractTargetAreaModifier::UpdateTargetAreas 55ms 0.049% 18.65% 10701ms 9.63% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 35ms 0.031% 18.68% 10171ms 9.15% AbstractCellBasedSimulation::DoCellBirth 1450ms 1.30% 19.99% 10051ms 9.05% std::__new_allocator::allocate (inline) 479ms 0.43% 20.42% 9591ms 8.63% VertexMesh::GetNextEdgeGradientOfElementAtNode 2818ms 2.54% 22.95% 9514ms 8.56% boost::numeric::ublas::indexing_vector_assign 0 0% 22.95% 9506ms 8.55% std::allocator_traits::allocate (inline) 0 0% 22.95% 9452ms 8.51% std::_Rb_tree::_M_create_node (inline) 1336ms 1.20% 24.16% 8952ms 8.06% std::_Rb_tree::_M_erase 21ms 0.019% 24.18% 8816ms 7.93% VertexBasedCellPopulation::GetLocationOfCellCentre 854ms 0.77% 24.94% 8769ms 7.89% VertexMesh::ElementIncludesPoint 0 0% 24.94% 8708ms 7.84% std::_Rb_tree::_M_get_node (inline) 742ms 0.67% 25.61% 8688ms 7.82% operator new 96ms 0.086% 25.70% 8644ms 7.78% Cell::GetMutationState 0 0% 25.70% 8320ms 7.49% std::_Rb_tree::_Alloc_node::operator() (inline) 472ms 0.42% 26.12% 8263ms 7.44% VertexMesh::GetCentroidOfElement 15ms 0.013% 26.14% 8215ms 7.39% MutableVertexMesh::RemoveDeletedNodesAndElements 267ms 0.24% 26.38% 8042ms 7.24% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.38% 8040ms 7.24% std::_Rb_tree::_M_drop_node (inline) 499ms 0.45% 26.83% 7856ms 7.07% std::map::operator[] (partial-inline) 236ms 0.21% 27.04% 7830ms 7.05% std::__new_allocator::deallocate (inline) 0 0% 27.04% 7824ms 7.04% std::allocator_traits::deallocate (inline) 2910ms 2.62% 29.66% 7753ms 6.98% __GI___libc_malloc 0 0% 29.66% 7737ms 6.96% std::_Rb_tree::_M_put_node (inline) 0 0% 29.66% 7618ms 6.86% std::set::~set (inline) 1491ms 1.34% 31.00% 7469ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2347ms 2.11% 33.11% 7305ms 6.57% __GI___libc_free 154ms 0.14% 33.25% 7226ms 6.50% std::_Rb_tree::_Rb_tree (partial-inline) 739ms 0.67% 33.91% 6805ms 6.12% std::_Rb_tree::_M_copy (inline) 22ms 0.02% 33.93% 6692ms 6.02% std::set::set (inline) 6670ms 6.00% 39.94% 6670ms 6.00% __strcmp_avx2 122ms 0.11% 40.05% 6367ms 5.73% SimpleWntCellCycleModel::GetWntLevel 2594ms 2.33% 42.38% 6315ms 5.68% std::_Rb_tree::_M_lower_bound (inline) 6216ms 5.59% 47.97% 6216ms 5.59% boost::numeric::ublas::c_vector::operator() 186ms 0.17% 48.14% 6180ms 5.56% WntConcentration::GetWntLevel 843ms 0.76% 48.90% 5804ms 5.22% std::_Rb_tree::_M_clone_node (inline) 18ms 0.016% 48.92% 5632ms 5.07% MutableVertexMesh::RemoveDeletedNodes 2801ms 2.52% 51.44% 5583ms 5.02% __cxxabiv1::__si_class_type_info::__do_dyncast 35ms 0.031% 51.47% 5425ms 4.88% EdgeHelper::RemoveDeletedEdges 1983ms 1.78% 53.25% 5348ms 4.81% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.25% 5250ms 4.72% std::set::insert (inline) 0 0% 53.25% 5135ms 4.62% std::_Rb_tree::lower_bound (inline) 0 0% 53.25% 5135ms 4.62% std::map::lower_bound (inline) 41ms 0.037% 53.29% 5081ms 4.57% EdgeHelper::UpdateEdgesMapKey 220ms 0.2% 53.49% 5012ms 4.51% MutableElement::ResetIndex 4509ms 4.06% 57.55% 4932ms 4.44% _int_free 1ms 0.0009% 57.55% 4838ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 153ms 0.14% 57.68% 4610ms 4.15% AbstractCellPopulation::GetCellUsingLocationIndex 493ms 0.44% 58.13% 4376ms 3.94% std::_Rb_tree::_M_insert_ (inline) 126ms 0.11% 58.24% 4332ms 3.90% std::set_intersection (inline) 240ms 0.22% 58.46% 4206ms 3.79% std::__set_intersection 52ms 0.047% 58.50% 3921ms 3.53% AbstractCellProperty::IsType (inline) 37ms 0.033% 58.54% 3920ms 3.53% Cell::GetCellProliferativeType 3915ms 3.52% 62.06% 3915ms 3.52% boost::numeric::ublas::same_impl_ex 12ms 0.011% 62.07% 3558ms 3.20% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1047ms 0.94% 63.01% 3305ms 2.97% AbstractElement::GetNodeLocation 62ms 0.056% 63.07% 3301ms 2.97% std::_Rb_tree::erase 2218ms 2.00% 65.07% 3277ms 2.95% _int_malloc 0 0% 65.07% 3189ms 2.87% std::insert_iterator::operator= (inline) 48ms 0.043% 65.11% 3180ms 2.86% Cell::SetCellProliferativeType 3162ms 2.85% 67.95% 3162ms 2.85% std::_Rb_tree::_S_right (inline) 29ms 0.026% 67.98% 2905ms 2.61% CellPropertyCollection::HasProperty 772ms 0.69% 68.67% 2820ms 2.54% AbstractCellProperty::IsSame 0 0% 68.67% 2816ms 2.53% Cell::HasCellProperty (inline) 4ms 0.0036% 68.68% 2765ms 2.49% std::_Rb_tree::_M_insert_unique_ (inline) 240ms 0.22% 68.89% 2749ms 2.47% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 68.89% 2700ms 2.43% boost::numeric::ublas::c_vector::operator-= (inline) 282ms 0.25% 69.15% 2695ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 641ms 0.58% 69.73% 2619ms 2.36% boost::numeric::ublas::vector_binary::size (inline) 0 0% 69.73% 2571ms 2.31% boost::numeric::ublas::c_vector::assign (inline) 28ms 0.025% 69.75% 2548ms 2.29% Cell::GetCellData 0 0% 69.75% 2520ms 2.27% AbstractCellPopulation::WriteResultsToFiles 3ms 0.0027% 69.75% 2485ms 2.24% std::_Rb_tree::_M_insert_unique 5ms 0.0045% 69.76% 2248ms 2.02% AbstractCellPopulation::Iterator::operator++ (inline) 93ms 0.084% 69.84% 2239ms 2.01% VertexMesh::GetVolumeOfElement 171ms 0.15% 70.00% 2227ms 2.00% AbstractCellPopulation::Iterator::IsRealCell (inline) 1460ms 1.31% 71.31% 2191ms 1.97% std::_Rb_tree::equal_range (inline) 46ms 0.041% 71.35% 2180ms 1.96% std::_Rb_tree::_M_emplace_hint_unique 2150ms 1.93% 73.29% 2150ms 1.93% std::_Rb_tree_increment 59ms 0.053% 73.34% 2123ms 1.91% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 73.34% 2117ms 1.91% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.34% 2117ms 1.91% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 471ms 0.42% 73.76% 2048ms 1.84% std::type_info::operator== (inline) 0 0% 73.76% 2044ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0009% 73.76% 2033ms 1.83% VertexBasedCellPopulation::WriteCellVtkResultsToFile 0 0% 73.76% 1844ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 71ms 0.064% 73.83% 1827ms 1.64% MutableVertexMesh::CheckForSwapsFromShortEdges 32ms 0.029% 73.86% 1732ms 1.56% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 46ms 0.041% 73.90% 1577ms 1.42% Node::RemoveElement 36ms 0.032% 73.93% 1563ms 1.41% VertexMesh::GetSurfaceAreaOfElement 41ms 0.037% 73.97% 1546ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 13ms 0.012% 73.98% 1536ms 1.38% std::set::erase (inline) 92ms 0.083% 74.06% 1530ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 139ms 0.13% 74.19% 1426ms 1.28% CellPropertyCollection::AddProperty 3ms 0.0027% 74.19% 1410ms 1.27% OffLatticeSimulation::ApplyBoundaries 72ms 0.065% 74.26% 1397ms 1.26% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.26% 1385ms 1.25% tcache_get (inline) 1385ms 1.25% 75.50% 1385ms 1.25% tcache_get_n (inline) 0 0% 75.50% 1364ms 1.23% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.50% 1358ms 1.22% boost::numeric::ublas::norm_2 (inline) 589ms 0.53% 76.03% 1342ms 1.21% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 74ms 0.067% 76.10% 1324ms 1.19% std::less::operator() (inline) 1250ms 1.12% 77.22% 1250ms 1.12% [libchaste_cell_based.so] 1015ms 0.91% 78.14% 1250ms 1.12% std::operator< (inline) 7ms 0.0063% 78.14% 1240ms 1.12% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 67ms 0.06% 78.20% 1240ms 1.12% std::_Rb_tree::_M_erase_aux (partial-inline) 20ms 0.018% 78.22% 1218ms 1.10% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 93ms 0.084% 78.30% 1188ms 1.07% std::_Rb_tree::find (inline) 0 0% 78.30% 1181ms 1.06% std::_Rb_tree::clear (inline) 0 0% 78.30% 1162ms 1.05% std::map::clear (inline) 0 0% 78.30% 1132ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 19ms 0.017% 78.32% 1126ms 1.01% CellPropertyRegistry::Get 0 0% 78.32% 1121ms 1.01% boost::numeric::ublas::c_vector::assign_temporary (inline) 24ms 0.022% 78.34% 1121ms 1.01% boost::numeric::ublas::c_vector::swap (inline) 1101ms 0.99% 79.33% 1101ms 0.99% std::_Rb_tree_insert_and_rebalance 81ms 0.073% 79.41% 1097ms 0.99% std::swap_ranges (inline) 18ms 0.016% 79.42% 1069ms 0.96% boost::numeric::ublas::detail::expression_type_check (inline) 213ms 0.19% 79.62% 1042ms 0.94% boost::numeric::ublas::detail::equals 1034ms 0.93% 80.55% 1034ms 0.93% Node::rGetLocation 1017ms 0.92% 81.46% 1017ms 0.92% std::swap (inline) 0 0% 81.46% 1016ms 0.91% std::iter_swap (inline) 0 0% 81.46% 996ms 0.9% std::map::find (inline) 116ms 0.1% 81.57% 977ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.57% 977ms 0.88% boost::shared_ptr::~shared_ptr (inline) 896ms 0.81% 82.37% 896ms 0.81% std::vector::size (inline) 0 0% 82.37% 856ms 0.77% VertexMeshWriter::MakeVtkMesh 834ms 0.75% 83.12% 834ms 0.75% [libchaste_mesh.so] 775ms 0.7% 83.82% 822ms 0.74% boost::detail::sp_counted_base::release 431ms 0.39% 84.21% 806ms 0.73% Edge::GetMapIndex 90ms 0.081% 84.29% 803ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0009% 84.29% 796ms 0.72% std::_Vector_base::_M_allocate (inline) 244ms 0.22% 84.51% 791ms 0.71% std::__new_allocator::construct (inline) 0 0% 84.51% 791ms 0.71% std::allocator_traits::construct (inline) 438ms 0.39% 84.90% 783ms 0.7% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 84.90% 760ms 0.68% boost::numeric::ublas::norm_inf (inline) 388ms 0.35% 85.25% 760ms 0.68% boost::numeric::ublas::vector_norm_inf::apply (inline) 20ms 0.018% 85.27% 752ms 0.68% MutableElement::RegisterWithEdges (inline) 23ms 0.021% 85.29% 750ms 0.67% AbstractNumericalMethod::DetectStepSizeExceptions 26ms 0.023% 85.31% 748ms 0.67% Edge::AddElement 0 0% 85.31% 745ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.31% 744ms 0.67% std::_Rb_tree::_M_construct_node (inline) 131ms 0.12% 85.43% 733ms 0.66% MutableElement::GetNodeLocalIndex 126ms 0.11% 85.55% 727ms 0.65% VertexBasedCellPopulation::CheckForStepSizeException 171ms 0.15% 85.70% 717ms 0.65% boost::shared_ptr::shared_ptr (inline) 0 0% 85.70% 705ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 8ms 0.0072% 85.71% 681ms 0.61% std::vector::_M_default_append (inline) 0 0% 85.71% 670ms 0.6% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 85.73% 670ms 0.6% std::_Rb_tree::_M_insert_node (inline) 644ms 0.58% 86.31% 644ms 0.58% [libstdc++.so.6.0.33] 642ms 0.58% 86.88% 642ms 0.58% Node::GetIndex 0 0% 86.88% 628ms 0.57% vtkPolygon::New 1ms 0.0009% 86.89% 628ms 0.57% vtkPolygon::vtkPolygon 27ms 0.024% 86.91% 613ms 0.55% MutableElement::RegisterWithNodes (inline) 420ms 0.38% 87.29% 596ms 0.54% malloc_consolidate 31ms 0.028% 87.32% 595ms 0.54% Node::AddElement 3ms 0.0027% 87.32% 594ms 0.53% VertexElementMap::VertexElementMap 0 0% 87.32% 591ms 0.53% std::vector::resize (inline) 31ms 0.028% 87.35% 576ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.35% 576ms 0.52% boost::numeric::ublas::vector::vector (inline) 0 0% 87.35% 564ms 0.51% std::map::map (inline)