File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 104471ms, 89.00% of 117389ms total Dropped 1061 nodes (cum <= 586.95ms) flat flat% sum% cum cum% 0 0% 0% 117140ms 99.79% __libc_start_call_main 0 0% 0% 117140ms 99.79% __libc_start_main_impl 0 0% 0% 117140ms 99.79% _start 0 0% 0% 117123ms 99.77% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 117123ms 99.77% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 117123ms 99.77% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 117123ms 99.77% main 0 0% 0% 117091ms 99.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 117091ms 99.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 117090ms 99.75% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0034% 0.0034% 117082ms 99.74% AbstractCellBasedSimulation::Solve 13ms 0.011% 0.014% 62187ms 52.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 21ms 0.018% 0.032% 58156ms 49.54% ForwardEulerNumericalMethod::UpdateAllNodePositions 96ms 0.082% 0.11% 57201ms 48.73% AbstractNumericalMethod::ComputeForcesIncludingDamping 685ms 0.58% 0.7% 45392ms 38.67% NagaiHondaForce::AddForceContribution 1ms 0.00085% 0.7% 40101ms 34.16% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0034% 0.7% 23669ms 20.16% VertexBasedCellPopulation::Update 1ms 0.00085% 0.7% 23527ms 20.04% MutableVertexMesh::ReMesh 95ms 0.081% 0.78% 20256ms 17.26% Cell::ReadyToDivide 10077ms 8.58% 9.37% 20082ms 17.11% Cylindrical2dVertexMesh::GetVectorFromAtoB 43ms 0.037% 9.40% 19161ms 16.32% AbstractPhaseBasedCellCycleModel::ReadyToDivide 389ms 0.33% 9.74% 17848ms 15.20% boost::numeric::ublas::c_vector::c_vector (partial-inline) 89ms 0.076% 9.81% 17389ms 14.81% NagaiHondaForce::GetAdhesionParameter 121ms 0.1% 9.91% 16325ms 13.91% SimpleWntCellCycleModel::UpdateCellCyclePhase 512ms 0.44% 10.35% 15878ms 13.53% boost::numeric::ublas::vector_assign (inline) 1220ms 1.04% 11.39% 15120ms 12.88% std::__new_allocator::allocate (inline) 65ms 0.055% 11.45% 14412ms 12.28% CellPropertyCollection::GetPropertiesType (inline) 0 0% 11.45% 14372ms 12.24% std::allocator_traits::allocate (inline) 0 0% 11.45% 14034ms 11.96% std::_Rb_tree::_M_create_node (inline) 893ms 0.76% 12.21% 13783ms 11.74% operator new 0 0% 12.21% 13570ms 11.56% std::_Rb_tree::_M_get_node (inline) 4272ms 3.64% 15.85% 12277ms 10.46% __GI___libc_malloc 46ms 0.039% 15.88% 12200ms 10.39% AbstractTargetAreaModifier::UpdateTargetAreas 58ms 0.049% 15.93% 12120ms 10.32% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 0 0% 15.93% 12086ms 10.30% std::_Rb_tree::_Alloc_node::operator() (inline) 109ms 0.093% 16.03% 11793ms 10.05% AbstractCellProperty::IsSubType (inline) 3637ms 3.10% 19.13% 11775ms 10.03% __dynamic_cast 9ms 0.0077% 19.13% 11728ms 9.99% AbstractCellBasedSimulation::DoCellBirth 2772ms 2.36% 21.49% 11499ms 9.80% boost::numeric::ublas::indexing_vector_assign 76ms 0.065% 21.56% 11344ms 9.66% VertexBasedCellPopulation::GetDampingConstant 177ms 0.15% 21.71% 10570ms 9.00% MutableVertexMesh::CheckForIntersections 519ms 0.44% 22.15% 9834ms 8.38% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 22.15% 9802ms 8.35% std::_Rb_tree::_M_drop_node (inline) 1161ms 0.99% 23.14% 9767ms 8.32% std::_Rb_tree::_M_erase 64ms 0.055% 23.20% 9266ms 7.89% VertexBasedCellPopulation::GetLocationOfCellCentre 357ms 0.3% 23.50% 9050ms 7.71% std::_Rb_tree::~_Rb_tree (inline) 230ms 0.2% 23.70% 9007ms 7.67% std::__new_allocator::deallocate (inline) 0 0% 23.70% 9005ms 7.67% std::allocator_traits::deallocate (inline) 0 0% 23.70% 8927ms 7.60% std::_Rb_tree::_M_put_node (inline) 61ms 0.052% 23.75% 8909ms 7.59% Cell::GetMutationState 2312ms 1.97% 25.72% 8904ms 7.59% __GI___libc_free 816ms 0.7% 26.41% 8879ms 7.56% VertexMesh::GetCentroidOfElement 19ms 0.016% 26.43% 8841ms 7.53% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 26.43% 8651ms 7.37% std::set::~set (inline) 622ms 0.53% 26.96% 8581ms 7.31% std::map::operator[] (partial-inline) 120ms 0.1% 27.06% 8539ms 7.27% std::_Rb_tree::_Rb_tree (partial-inline) 719ms 0.61% 27.67% 8260ms 7.04% std::_Rb_tree::_M_copy (inline) 0 0% 27.67% 8114ms 6.91% std::set::insert (inline) 595ms 0.51% 28.18% 7889ms 6.72% VertexMesh::ElementIncludesPoint 10ms 0.0085% 28.19% 7695ms 6.56% std::set::set (inline) 7535ms 6.42% 34.61% 7535ms 6.42% boost::numeric::ublas::c_vector::operator() 1035ms 0.88% 35.49% 7287ms 6.21% std::_Rb_tree::_M_clone_node (inline) 917ms 0.78% 36.27% 7258ms 6.18% std::_Rb_tree::_M_insert_ (inline) 192ms 0.16% 36.43% 7209ms 6.14% SimpleWntCellCycleModel::GetWntLevel 172ms 0.15% 36.58% 6866ms 5.85% WntConcentration::GetWntLevel 5642ms 4.81% 41.39% 6321ms 5.38% _int_free 34ms 0.029% 41.42% 6201ms 5.28% std::set_intersection (inline) 208ms 0.18% 41.59% 6167ms 5.25% std::__set_intersection 955ms 0.81% 42.41% 6163ms 5.25% AbstractMesh::GetDistanceBetweenNodes 6139ms 5.23% 47.64% 6139ms 5.23% __strcmp_evex 27ms 0.023% 47.66% 5805ms 4.95% MutableVertexMesh::RemoveDeletedNodes 2202ms 1.88% 49.53% 5797ms 4.94% std::_Rb_tree::_M_lower_bound (inline) 4500ms 3.83% 53.37% 5731ms 4.88% _int_malloc 91ms 0.078% 53.45% 5641ms 4.81% EdgeHelper::RemoveDeletedEdges 235ms 0.2% 53.65% 5547ms 4.73% MutableElement::ResetIndex 968ms 0.82% 54.47% 5412ms 4.61% boost::numeric::ublas::c_vector::operator[] (inline) 23ms 0.02% 54.49% 5329ms 4.54% EdgeHelper::UpdateEdgesMapKey 2502ms 2.13% 56.62% 5188ms 4.42% __cxxabiv1::__si_class_type_info::__do_dyncast 5026ms 4.28% 60.90% 5026ms 4.28% boost::numeric::ublas::same_impl_ex 0 0% 60.90% 4990ms 4.25% std::insert_iterator::operator= (inline) 28ms 0.024% 60.93% 4928ms 4.20% Cell::GetCellProliferativeType 0 0% 60.93% 4875ms 4.15% std::_Rb_tree::lower_bound (inline) 0 0% 60.93% 4875ms 4.15% std::map::lower_bound (inline) 0 0% 60.93% 4747ms 4.04% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.00085% 60.93% 4682ms 3.99% AbstractCellBasedSimulation::DoCellRemoval (inline) 99ms 0.084% 61.01% 4654ms 3.96% AbstractCellPopulation::GetCellUsingLocationIndex 115ms 0.098% 61.11% 3914ms 3.33% Cell::SetCellProliferativeType 172ms 0.15% 61.26% 3862ms 3.29% AbstractCellProperty::IsType (inline) 872ms 0.74% 62.00% 3746ms 3.19% AbstractElement::GetNodeLocation 935ms 0.8% 62.80% 3562ms 3.03% boost::numeric::ublas::vector_binary::size (inline) 39ms 0.033% 62.83% 3526ms 3.00% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 3452ms 2.94% 65.77% 3452ms 2.94% [libchaste_cell_based.so] 71ms 0.06% 65.83% 3423ms 2.92% std::_Rb_tree::erase 2ms 0.0017% 65.83% 3367ms 2.87% std::_Rb_tree::_M_insert_unique 0 0% 65.83% 3243ms 2.76% boost::numeric::ublas::c_vector::assign (inline) 3058ms 2.61% 68.44% 3058ms 2.61% std::_Rb_tree::_S_right (inline) 43ms 0.037% 68.47% 3016ms 2.57% std::_Rb_tree::_M_emplace_hint_unique 361ms 0.31% 68.78% 2857ms 2.43% std::_Rb_tree_const_iterator::operator++ (inline) 365ms 0.31% 69.09% 2843ms 2.42% VertexMesh::GetAreaGradientOfElementAtNode 84ms 0.072% 69.16% 2760ms 2.35% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 159ms 0.14% 69.30% 2716ms 2.31% boost::detail::shared_count::~shared_count (inline) 0 0% 69.30% 2716ms 2.31% boost::shared_ptr::~shared_ptr (inline) 224ms 0.19% 69.49% 2678ms 2.28% AbstractCellPopulation::Iterator::IsRealCell (inline) 5ms 0.0043% 69.49% 2669ms 2.27% AbstractCellPopulation::Iterator::operator++ (inline) 14ms 0.012% 69.51% 2597ms 2.21% Cell::GetCellData 0 0% 69.51% 2561ms 2.18% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.51% 2529ms 2.15% boost::numeric::ublas::c_vector::operator-= (inline) 667ms 0.57% 70.07% 2509ms 2.14% AbstractCellProperty::IsSame 2460ms 2.10% 72.17% 2498ms 2.13% boost::detail::sp_counted_base::release 2483ms 2.12% 74.28% 2483ms 2.12% [libchaste_mesh.so] 32ms 0.027% 74.31% 2432ms 2.07% CellPropertyCollection::HasProperty 0 0% 74.31% 2350ms 2.00% Cell::HasCellProperty (inline) 0 0% 74.31% 2129ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0017% 74.31% 2117ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 137ms 0.12% 74.43% 2112ms 1.80% VertexMesh::GetVolumeOfElement 30ms 0.026% 74.46% 2072ms 1.77% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.46% 1969ms 1.68% tcache_get (inline) 1969ms 1.68% 76.13% 1969ms 1.68% tcache_get_n (inline) 0 0% 76.13% 1948ms 1.66% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.13% 1923ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 145ms 0.12% 76.26% 1890ms 1.61% CellPropertyCollection::AddProperty 457ms 0.39% 76.65% 1842ms 1.57% std::type_info::operator== (inline) 1110ms 0.95% 77.59% 1829ms 1.56% std::_Rb_tree::equal_range (inline) 225ms 0.19% 77.78% 1819ms 1.55% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 93ms 0.079% 77.86% 1813ms 1.54% std::_Rb_tree::_M_erase_aux (partial-inline) 1792ms 1.53% 79.39% 1792ms 1.53% std::_Rb_tree_increment 13ms 0.011% 79.40% 1755ms 1.50% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 79.40% 1755ms 1.50% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 117ms 0.1% 79.50% 1752ms 1.49% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 79.50% 1716ms 1.46% boost::numeric::ublas::vector_binary::operator() (inline) 83ms 0.071% 79.57% 1577ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 71ms 0.06% 79.63% 1521ms 1.30% MutableVertexMesh::CheckForSwapsFromShortEdges 84ms 0.072% 79.70% 1470ms 1.25% VertexMesh::GetSurfaceAreaOfElement 1454ms 1.24% 80.94% 1454ms 1.24% [libstdc++.so.6.0.33] 1ms 0.00085% 80.94% 1442ms 1.23% OffLatticeSimulation::ApplyBoundaries 33ms 0.028% 80.97% 1439ms 1.23% Node::RemoveElement 6ms 0.0051% 80.98% 1406ms 1.20% std::set::erase (inline) 35ms 0.03% 81.01% 1291ms 1.10% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 62ms 0.053% 81.06% 1281ms 1.09% CellPropertyRegistry::Get 1235ms 1.05% 82.11% 1235ms 1.05% Node::rGetLocation 35ms 0.03% 82.14% 1166ms 0.99% boost::numeric::ublas::detail::expression_type_check (inline) 22ms 0.019% 82.16% 1162ms 0.99% MutableElement::RegisterWithEdges (inline) 23ms 0.02% 82.18% 1155ms 0.98% Edge::AddElement 11ms 0.0094% 82.19% 1123ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 238ms 0.2% 82.39% 1093ms 0.93% boost::numeric::ublas::detail::equals 0 0% 82.39% 1079ms 0.92% std::_Rb_tree::clear (inline) 0 0% 82.39% 1052ms 0.9% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.39% 1052ms 0.9% std::map::clear (inline) 1019ms 0.87% 83.26% 1019ms 0.87% std::_Rb_tree_insert_and_rebalance 3ms 0.0026% 83.26% 982ms 0.84% VertexMeshWriter::MakeVtkMesh 102ms 0.087% 83.35% 969ms 0.83% std::_Rb_tree::find (inline) 0 0% 83.35% 930ms 0.79% boost::numeric::ublas::norm_2 (inline) 540ms 0.46% 83.81% 914ms 0.78% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 83.81% 899ms 0.77% std::map::map (inline) 374ms 0.32% 84.13% 898ms 0.76% boost::numeric::ublas::vector_norm_2::apply 0 0% 84.13% 880ms 0.75% std::__new_allocator::destroy (inline) 0 0% 84.13% 880ms 0.75% std::allocator_traits::destroy (inline) 53ms 0.045% 84.17% 879ms 0.75% std::less::operator() (inline) 0 0% 84.17% 877ms 0.75% std::_Rb_tree::_M_destroy_node (inline) 79ms 0.067% 84.24% 848ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 624ms 0.53% 84.77% 826ms 0.7% std::operator< (inline) 0 0% 84.77% 825ms 0.7% boost::numeric::ublas::norm_inf (inline) 433ms 0.37% 85.14% 825ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 1ms 0.00085% 85.14% 796ms 0.68% std::_Vector_base::_M_allocate (inline) 47ms 0.04% 85.18% 795ms 0.68% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 85.18% 795ms 0.68% boost::numeric::ublas::vector::vector (inline) 0 0% 85.18% 789ms 0.67% std::map::find (inline) 785ms 0.67% 85.85% 785ms 0.67% tcache_put (inline) 0 0% 85.85% 756ms 0.64% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0077% 85.86% 756ms 0.64% boost::numeric::ublas::c_vector::swap (inline) 88ms 0.075% 85.93% 747ms 0.64% std::swap_ranges (inline) 563ms 0.48% 86.41% 746ms 0.64% CellPropertyCollection::GetProperty 99ms 0.084% 86.50% 709ms 0.6% MutableElement::GetNodeLocalIndex 703ms 0.6% 87.09% 703ms 0.6% std::vector::size (inline) 0 0% 87.09% 681ms 0.58% vtkPolygon::New 0 0% 87.09% 680ms 0.58% vtkPolygon::vtkPolygon 0 0% 87.09% 659ms 0.56% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.017% 87.11% 659ms 0.56% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.11% 659ms 0.56% std::iter_swap (inline) 659ms 0.56% 87.67% 659ms 0.56% std::swap (inline) 23ms 0.02% 87.69% 656ms 0.56% MutableElement::RegisterWithNodes (inline) 642ms 0.55% 88.24% 642ms 0.55% Node::GetIndex 5ms 0.0043% 88.24% 642ms 0.55% std::vector::_M_default_append (inline) 322ms 0.27% 88.52% 634ms 0.54% Edge::GetMapIndex 34ms 0.029% 88.55% 629ms 0.54% Node::AddElement 527ms 0.45% 89.00% 617ms 0.53% malloc_consolidate