File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 86646ms, 87.92% of 98555ms total Dropped 1036 nodes (cum <= 492.77ms) flat flat% sum% cum cum% 0 0% 0% 98303ms 99.74% __libc_start_call_main 0 0% 0% 98303ms 99.74% __libc_start_main_impl 0 0% 0% 98303ms 99.74% _start 0 0% 0% 98285ms 99.73% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 98285ms 99.73% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 98285ms 99.73% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 98285ms 99.73% main 0 0% 0% 98250ms 99.69% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 98250ms 99.69% CxxTest::TestRunner::runTest (inline) 0 0% 0% 98250ms 99.69% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.001% 0.001% 98243ms 99.68% AbstractCellBasedSimulation::Solve 10ms 0.01% 0.011% 52244ms 53.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.015% 0.026% 48997ms 49.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 50ms 0.051% 0.077% 47992ms 48.70% AbstractNumericalMethod::ComputeForcesIncludingDamping 306ms 0.31% 0.39% 37512ms 38.06% NagaiHondaForce::AddForceContribution 1ms 0.001% 0.39% 33826ms 34.32% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.003% 0.39% 20085ms 20.38% VertexBasedCellPopulation::Update 0 0% 0.39% 19967ms 20.26% MutableVertexMesh::ReMesh 9021ms 9.15% 9.54% 17203ms 17.46% Cylindrical2dVertexMesh::GetVectorFromAtoB 102ms 0.1% 9.65% 16467ms 16.71% Cell::ReadyToDivide 29ms 0.029% 9.68% 15496ms 15.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 71ms 0.072% 9.75% 15323ms 15.55% NagaiHondaForce::GetAdhesionParameter 71ms 0.072% 9.82% 13218ms 13.41% SimpleWntCellCycleModel::UpdateCellCyclePhase 430ms 0.44% 10.26% 12918ms 13.11% boost::numeric::ublas::c_vector::c_vector (partial-inline) 76ms 0.077% 10.34% 12400ms 12.58% CellPropertyCollection::GetPropertiesType (inline) 541ms 0.55% 10.88% 12382ms 12.56% std::__new_allocator::allocate (inline) 0 0% 10.88% 11841ms 12.01% std::allocator_traits::allocate (inline) 854ms 0.87% 11.75% 11700ms 11.87% operator new 0 0% 11.75% 11628ms 11.80% std::_Rb_tree::_M_create_node (inline) 231ms 0.23% 11.99% 11505ms 11.67% boost::numeric::ublas::vector_assign (inline) 0 0% 11.99% 11299ms 11.46% std::_Rb_tree::_M_get_node (inline) 3636ms 3.69% 15.67% 10490ms 10.64% __GI___libc_malloc 91ms 0.092% 15.77% 10233ms 10.38% AbstractCellProperty::IsSubType (inline) 2727ms 2.77% 18.53% 10151ms 10.30% __dynamic_cast 153ms 0.16% 18.69% 10145ms 10.29% VertexBasedCellPopulation::GetDampingConstant 0 0% 18.69% 10013ms 10.16% std::_Rb_tree::_Alloc_node::operator() (inline) 50ms 0.051% 18.74% 9925ms 10.07% AbstractTargetAreaModifier::UpdateTargetAreas 55ms 0.056% 18.80% 9835ms 9.98% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 8ms 0.0081% 18.80% 9744ms 9.89% AbstractCellBasedSimulation::DoCellBirth 133ms 0.13% 18.94% 9223ms 9.36% MutableVertexMesh::CheckForIntersections 983ms 1% 19.94% 8638ms 8.76% std::_Rb_tree::_M_erase 0 0% 19.94% 8564ms 8.69% std::_Rb_tree::_M_drop_node (inline) 2421ms 2.46% 22.39% 8313ms 8.43% boost::numeric::ublas::indexing_vector_assign 310ms 0.31% 22.71% 8164ms 8.28% std::_Rb_tree::~_Rb_tree (inline) 63ms 0.064% 22.77% 7949ms 8.07% Cell::GetMutationState 0 0% 22.77% 7813ms 7.93% std::set::~set (inline) 100ms 0.1% 22.87% 7803ms 7.92% std::__new_allocator::deallocate (inline) 0 0% 22.87% 7785ms 7.90% std::allocator_traits::deallocate (inline) 396ms 0.4% 23.27% 7743ms 7.86% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 23.27% 7739ms 7.85% std::_Rb_tree::_M_put_node (inline) 1944ms 1.97% 25.25% 7525ms 7.64% __GI___libc_free 506ms 0.51% 25.76% 7491ms 7.60% std::map::operator[] (partial-inline) 47ms 0.048% 25.81% 7322ms 7.43% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.81% 7266ms 7.37% std::set::insert (inline) 524ms 0.53% 26.34% 6975ms 7.08% VertexMesh::GetCentroidOfElement 9ms 0.0091% 26.35% 6891ms 6.99% MutableVertexMesh::RemoveDeletedNodesAndElements 506ms 0.51% 26.86% 6802ms 6.90% VertexMesh::ElementIncludesPoint 799ms 0.81% 27.67% 6729ms 6.83% std::_Rb_tree::_M_insert_ (inline) 133ms 0.13% 27.81% 6305ms 6.40% std::_Rb_tree::_Rb_tree (partial-inline) 6249ms 6.34% 34.15% 6249ms 6.34% boost::numeric::ublas::c_vector::operator() 922ms 0.94% 35.08% 6187ms 6.28% AbstractMesh::GetDistanceBetweenNodes 82ms 0.083% 35.17% 6185ms 6.28% std::set_intersection (inline) 289ms 0.29% 35.46% 6103ms 6.19% std::__set_intersection 637ms 0.65% 36.11% 5968ms 6.06% std::_Rb_tree::_M_copy (inline) 10ms 0.01% 36.12% 5912ms 6.00% std::set::set (inline) 5668ms 5.75% 41.87% 5668ms 5.75% __strcmp_evex 159ms 0.16% 42.03% 5523ms 5.60% SimpleWntCellCycleModel::GetWntLevel 4790ms 4.86% 46.89% 5523ms 5.60% _int_free 120ms 0.12% 47.01% 5257ms 5.33% WntConcentration::GetWntLevel 622ms 0.63% 47.64% 5161ms 5.24% std::_Rb_tree::_M_clone_node (inline) 2416ms 2.45% 50.09% 5135ms 5.21% __cxxabiv1::__si_class_type_info::__do_dyncast 522ms 0.53% 50.62% 5045ms 5.12% boost::numeric::ublas::c_vector::operator[] (inline) 4202ms 4.26% 54.89% 5039ms 5.11% _int_malloc 25ms 0.025% 54.91% 5016ms 5.09% MutableVertexMesh::RemoveDeletedNodes 2153ms 2.18% 57.10% 4938ms 5.01% std::_Rb_tree::_M_lower_bound (inline) 67ms 0.068% 57.17% 4881ms 4.95% EdgeHelper::RemoveDeletedEdges 0 0% 57.17% 4700ms 4.77% std::insert_iterator::operator= (inline) 21ms 0.021% 57.19% 4635ms 4.70% EdgeHelper::UpdateEdgesMapKey 0 0% 57.19% 4416ms 4.48% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 57.19% 4310ms 4.37% std::_Rb_tree::lower_bound (inline) 0 0% 57.19% 4310ms 4.37% std::map::lower_bound (inline) 32ms 0.032% 57.22% 4261ms 4.32% Cell::GetCellProliferativeType 4154ms 4.21% 61.43% 4154ms 4.21% boost::numeric::ublas::same_impl_ex 98ms 0.099% 61.53% 4072ms 4.13% MutableElement::ResetIndex 1ms 0.001% 61.53% 3985ms 4.04% AbstractCellBasedSimulation::DoCellRemoval (inline) 52ms 0.053% 61.59% 3829ms 3.89% AbstractCellPopulation::GetCellUsingLocationIndex 3187ms 3.23% 64.82% 3187ms 3.23% [libchaste_cell_based.so] 185ms 0.19% 65.01% 3159ms 3.21% AbstractCellProperty::IsType (inline) 129ms 0.13% 65.14% 3155ms 3.20% Cell::SetCellProliferativeType 43ms 0.044% 65.18% 3125ms 3.17% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 65.18% 2850ms 2.89% std::_Rb_tree::_M_insert_unique 132ms 0.13% 65.32% 2794ms 2.83% boost::detail::shared_count::~shared_count (inline) 0 0% 65.32% 2794ms 2.83% boost::shared_ptr::~shared_ptr (inline) 728ms 0.74% 66.06% 2785ms 2.83% AbstractElement::GetNodeLocation 34ms 0.034% 66.09% 2626ms 2.66% std::_Rb_tree::_M_emplace_hint_unique 2595ms 2.63% 68.72% 2606ms 2.64% boost::detail::sp_counted_base::release 171ms 0.17% 68.90% 2537ms 2.57% AbstractCellPopulation::Iterator::IsRealCell (inline) 2ms 0.002% 68.90% 2529ms 2.57% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 68.90% 2527ms 2.56% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 68.90% 2427ms 2.46% boost::numeric::ublas::c_vector::assign (inline) 122ms 0.12% 69.02% 2398ms 2.43% boost::numeric::ublas::vector_binary::size (inline) 334ms 0.34% 69.36% 2310ms 2.34% std::_Rb_tree_const_iterator::operator++ (inline) 59ms 0.06% 69.42% 2292ms 2.33% std::_Rb_tree::erase 21ms 0.021% 69.44% 2290ms 2.32% Cell::GetCellData 49ms 0.05% 69.49% 2227ms 2.26% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 69.49% 2220ms 2.25% AbstractCellPopulation::WriteResultsToFiles 2196ms 2.23% 71.72% 2196ms 2.23% std::_Rb_tree::_S_right (inline) 2131ms 2.16% 73.88% 2131ms 2.16% [libchaste_mesh.so] 247ms 0.25% 74.13% 2111ms 2.14% VertexMesh::GetAreaGradientOfElementAtNode 46ms 0.047% 74.18% 2093ms 2.12% CellPropertyCollection::HasProperty 0 0% 74.18% 2029ms 2.06% Cell::HasCellProperty (inline) 390ms 0.4% 74.58% 1930ms 1.96% AbstractCellProperty::IsSame 22ms 0.022% 74.60% 1900ms 1.93% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.60% 1836ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.001% 74.60% 1824ms 1.85% VertexBasedCellPopulation::WriteCellVtkResultsToFile 102ms 0.1% 74.70% 1714ms 1.74% VertexMesh::GetVolumeOfElement 328ms 0.33% 75.04% 1697ms 1.72% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1ms 0.001% 75.04% 1661ms 1.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.04% 1661ms 1.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 75.04% 1643ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 132ms 0.13% 75.17% 1616ms 1.64% CellPropertyCollection::AddProperty 0 0% 75.17% 1615ms 1.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 62ms 0.063% 75.23% 1600ms 1.62% MutableVertexMesh::CheckForSwapsFromShortEdges 206ms 0.21% 75.44% 1540ms 1.56% std::type_info::operator== (inline) 60ms 0.061% 75.50% 1472ms 1.49% VertexMesh::GetSurfaceAreaOfElement 2ms 0.002% 75.51% 1433ms 1.45% tcache_get (inline) 1431ms 1.45% 76.96% 1431ms 1.45% tcache_get_n (inline) 44ms 0.045% 77.00% 1422ms 1.44% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.002% 77.00% 1390ms 1.41% OffLatticeSimulation::ApplyBoundaries 0 0% 77.00% 1386ms 1.41% boost::numeric::ublas::vector_binary::operator() (inline) 1375ms 1.40% 78.40% 1375ms 1.40% std::_Rb_tree_increment 0 0% 78.40% 1361ms 1.38% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0071% 78.41% 1361ms 1.38% boost::numeric::ublas::c_vector::swap (inline) 360ms 0.37% 78.77% 1354ms 1.37% std::swap_ranges (inline) 67ms 0.068% 78.84% 1340ms 1.36% std::_Rb_tree::_M_erase_aux (partial-inline) 49ms 0.05% 78.89% 1211ms 1.23% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 77ms 0.078% 78.97% 1180ms 1.20% boost::numeric::ublas::vector_reference::operator() (inline) 42ms 0.043% 79.01% 1114ms 1.13% CellPropertyRegistry::Get 46ms 0.047% 79.06% 1095ms 1.11% Node::RemoveElement 27ms 0.027% 79.08% 1072ms 1.09% boost::numeric::ublas::detail::expression_type_check (inline) 12ms 0.012% 79.10% 1060ms 1.08% MutableElement::RegisterWithEdges (inline) 2ms 0.002% 79.10% 1049ms 1.06% std::set::erase (inline) 48ms 0.049% 79.15% 1048ms 1.06% Edge::AddElement 642ms 0.65% 79.80% 1047ms 1.06% std::_Rb_tree::equal_range (inline) 1018ms 1.03% 80.83% 1018ms 1.03% [libstdc++.so.6.0.33] 161ms 0.16% 80.99% 1014ms 1.03% boost::numeric::ublas::detail::equals 0 0% 80.99% 994ms 1.01% std::iter_swap (inline) 994ms 1.01% 82.00% 994ms 1.01% std::swap (inline) 57ms 0.058% 82.06% 988ms 1.00% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 82.06% 960ms 0.97% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 82.06% 940ms 0.95% boost::numeric::ublas::norm_2 (inline) 667ms 0.68% 82.74% 932ms 0.95% CellPropertyCollection::GetProperty 491ms 0.5% 83.24% 910ms 0.92% boost::numeric::ublas::vector_norm_2::apply 909ms 0.92% 84.16% 909ms 0.92% std::_Rb_tree_insert_and_rebalance 0 0% 84.16% 864ms 0.88% VertexMeshWriter::MakeVtkMesh 834ms 0.85% 85.00% 834ms 0.85% Node::rGetLocation 0 0% 85.00% 834ms 0.85% std::__new_allocator::destroy (inline) 0 0% 85.00% 834ms 0.85% std::allocator_traits::destroy (inline) 8ms 0.0081% 85.01% 831ms 0.84% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 85.01% 830ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 811ms 0.82% 85.84% 811ms 0.82% tcache_put (inline) 0 0% 85.84% 793ms 0.8% std::_Rb_tree::clear (inline) 0 0% 85.84% 771ms 0.78% std::map::clear (inline) 0 0% 85.84% 728ms 0.74% boost::numeric::ublas::norm_inf (inline) 273ms 0.28% 86.11% 728ms 0.74% boost::numeric::ublas::vector_norm_inf::apply (inline) 48ms 0.049% 86.16% 718ms 0.73% std::less::operator() (inline) 100ms 0.1% 86.26% 710ms 0.72% std::_Rb_tree::find (inline) 345ms 0.35% 86.61% 709ms 0.72% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 509ms 0.52% 87.13% 670ms 0.68% std::operator< (inline) 0 0% 87.13% 636ms 0.65% std::_Rb_tree::_Auto_node::_M_insert (inline) 37ms 0.038% 87.17% 636ms 0.65% std::_Rb_tree::_M_insert_node (inline) 0 0% 87.17% 609ms 0.62% vtkPolygon::New 1ms 0.001% 87.17% 608ms 0.62% vtkPolygon::vtkPolygon 599ms 0.61% 87.78% 599ms 0.61% std::vector::size (inline) 0 0% 87.78% 587ms 0.6% std::map::find (inline) 12ms 0.012% 87.79% 553ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.79% 553ms 0.56% boost::numeric::ublas::vector::vector (inline) 65ms 0.066% 87.85% 550ms 0.56% MutableElement::GetNodeLocalIndex 1ms 0.001% 87.85% 540ms 0.55% std::_Vector_base::_M_allocate (inline) 12ms 0.012% 87.87% 534ms 0.54% MutableElement::RegisterWithNodes (inline) 49ms 0.05% 87.92% 505ms 0.51% Node::AddElement