File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96543ms, 88.75% of 108782ms total Dropped 1121 nodes (cum <= 543.91ms) flat flat% sum% cum cum% 0 0% 0% 108303ms 99.56% __libc_start_call_main 0 0% 0% 108303ms 99.56% __libc_start_main_impl 0 0% 0% 108303ms 99.56% _start 0 0% 0% 108281ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108281ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108281ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108281ms 99.54% main 0 0% 0% 108240ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108240ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108240ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108232ms 99.49% AbstractCellBasedSimulation::Solve 27ms 0.025% 0.028% 56297ms 51.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 13ms 0.012% 0.04% 53115ms 48.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 122ms 0.11% 0.15% 51547ms 47.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 354ms 0.33% 0.48% 39652ms 36.45% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.48% 39040ms 35.89% AbstractCellBasedSimulation::UpdateCellPopulation 5ms 0.0046% 0.48% 24180ms 22.23% VertexBasedCellPopulation::Update 2ms 0.0018% 0.48% 24044ms 22.10% MutableVertexMesh::ReMesh 14510ms 13.34% 13.82% 22987ms 21.13% Cylindrical2dVertexMesh::GetVectorFromAtoB 96ms 0.088% 13.91% 17314ms 15.92% Cell::ReadyToDivide 94ms 0.086% 14.00% 16092ms 14.79% AbstractPhaseBasedCellCycleModel::ReadyToDivide 376ms 0.35% 14.34% 14727ms 13.54% NagaiHondaForce::GetAdhesionParameter 438ms 0.4% 14.75% 14043ms 12.91% boost::numeric::ublas::c_vector::c_vector (partial-inline) 102ms 0.094% 14.84% 13748ms 12.64% SimpleWntCellCycleModel::UpdateCellCyclePhase 140ms 0.13% 14.97% 13709ms 12.60% CellPropertyCollection::GetPropertiesType (inline) 370ms 0.34% 15.31% 12482ms 11.47% boost::numeric::ublas::vector_assign (inline) 135ms 0.12% 15.43% 12045ms 11.07% MutableVertexMesh::CheckForIntersections 78ms 0.072% 15.50% 11415ms 10.49% VertexBasedCellPopulation::GetDampingConstant 3487ms 3.21% 18.71% 11365ms 10.45% __dynamic_cast 67ms 0.062% 18.77% 11252ms 10.34% AbstractCellProperty::IsSubType (inline) 67ms 0.062% 18.83% 10453ms 9.61% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.055% 18.89% 10359ms 9.52% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 21ms 0.019% 18.91% 10159ms 9.34% AbstractCellBasedSimulation::DoCellBirth 1270ms 1.17% 20.08% 10121ms 9.30% std::__new_allocator::allocate (inline) 0 0% 20.08% 9583ms 8.81% std::allocator_traits::allocate (inline) 0 0% 20.08% 9549ms 8.78% std::_Rb_tree::_M_create_node (inline) 2604ms 2.39% 22.47% 9334ms 8.58% boost::numeric::ublas::indexing_vector_assign 1371ms 1.26% 23.73% 9153ms 8.41% std::_Rb_tree::_M_erase 846ms 0.78% 24.51% 9007ms 8.28% operator new 810ms 0.74% 25.25% 8935ms 8.21% VertexMesh::ElementIncludesPoint 0 0% 25.25% 8921ms 8.20% std::_Rb_tree::_M_get_node (inline) 329ms 0.3% 25.55% 8843ms 8.13% VertexMesh::GetNextEdgeGradientOfElementAtNode 28ms 0.026% 25.58% 8760ms 8.05% VertexBasedCellPopulation::GetLocationOfCellCentre 75ms 0.069% 25.65% 8685ms 7.98% Cell::GetMutationState 0 0% 25.65% 8405ms 7.73% std::_Rb_tree::_Alloc_node::operator() (inline) 249ms 0.23% 25.88% 8403ms 7.72% std::_Rb_tree::~_Rb_tree (inline) 501ms 0.46% 26.34% 8249ms 7.58% VertexMesh::GetCentroidOfElement 0 0% 26.34% 8190ms 7.53% std::_Rb_tree::_M_drop_node (inline) 3169ms 2.91% 29.25% 7981ms 7.34% __GI___libc_malloc 235ms 0.22% 29.47% 7939ms 7.30% std::__new_allocator::deallocate (inline) 0 0% 29.47% 7927ms 7.29% std::set::~set (inline) 0 0% 29.47% 7915ms 7.28% std::allocator_traits::deallocate (inline) 0 0% 29.47% 7842ms 7.21% std::_Rb_tree::_M_put_node (inline) 3015ms 2.77% 32.24% 7769ms 7.14% __GI___libc_free 25ms 0.023% 32.26% 7592ms 6.98% MutableVertexMesh::RemoveDeletedNodesAndElements 483ms 0.44% 32.71% 7536ms 6.93% std::map::operator[] (partial-inline) 1412ms 1.30% 34.00% 7136ms 6.56% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 135ms 0.12% 34.13% 6835ms 6.28% std::_Rb_tree::_Rb_tree (partial-inline) 626ms 0.58% 34.70% 6503ms 5.98% std::_Rb_tree::_M_copy (inline) 17ms 0.016% 34.72% 6414ms 5.90% std::set::set (inline) 6309ms 5.80% 40.52% 6309ms 5.80% __strcmp_avx2 82ms 0.075% 40.59% 6252ms 5.75% SimpleWntCellCycleModel::GetWntLevel 6204ms 5.70% 46.30% 6204ms 5.70% boost::numeric::ublas::c_vector::operator() 112ms 0.1% 46.40% 6070ms 5.58% WntConcentration::GetWntLevel 2487ms 2.29% 48.69% 5971ms 5.49% std::_Rb_tree::_M_lower_bound (inline) 771ms 0.71% 49.40% 5601ms 5.15% std::_Rb_tree::_M_clone_node (inline) 0 0% 49.40% 5453ms 5.01% std::set::insert (inline) 2680ms 2.46% 51.86% 5428ms 4.99% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.019% 51.88% 5308ms 4.88% MutableVertexMesh::RemoveDeletedNodes 42ms 0.039% 51.92% 5145ms 4.73% EdgeHelper::RemoveDeletedEdges 1528ms 1.40% 53.32% 4958ms 4.56% boost::numeric::ublas::c_vector::operator[] (inline) 32ms 0.029% 53.35% 4870ms 4.48% EdgeHelper::UpdateEdgesMapKey 0 0% 53.35% 4847ms 4.46% std::_Rb_tree::lower_bound (inline) 0 0% 53.35% 4847ms 4.46% std::map::lower_bound (inline) 197ms 0.18% 53.53% 4747ms 4.36% MutableElement::ResetIndex 4426ms 4.07% 57.60% 4744ms 4.36% _int_free 0 0% 57.60% 4692ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 530ms 0.49% 58.09% 4611ms 4.24% std::_Rb_tree::_M_insert_ (inline) 43ms 0.04% 58.13% 4395ms 4.04% std::set_intersection (inline) 254ms 0.23% 58.36% 4352ms 4.00% std::__set_intersection 93ms 0.085% 58.45% 4187ms 3.85% AbstractCellPopulation::GetCellUsingLocationIndex 3973ms 3.65% 62.10% 3973ms 3.65% boost::numeric::ublas::same_impl_ex 51ms 0.047% 62.15% 3866ms 3.55% Cell::GetCellProliferativeType 78ms 0.072% 62.22% 3859ms 3.55% AbstractCellProperty::IsType (inline) 3ms 0.0028% 62.22% 3592ms 3.30% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 813ms 0.75% 62.97% 3217ms 2.96% AbstractElement::GetNodeLocation 0 0% 62.97% 3185ms 2.93% std::insert_iterator::operator= (inline) 2269ms 2.09% 65.05% 3183ms 2.93% _int_malloc 34ms 0.031% 65.08% 3070ms 2.82% Cell::SetCellProliferativeType 3010ms 2.77% 67.85% 3010ms 2.77% std::_Rb_tree::_S_right (inline) 45ms 0.041% 67.89% 2972ms 2.73% std::_Rb_tree::erase 5ms 0.0046% 67.90% 2807ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 641ms 0.59% 68.49% 2785ms 2.56% boost::numeric::ublas::vector_binary::size (inline) 825ms 0.76% 69.24% 2779ms 2.55% AbstractCellProperty::IsSame 47ms 0.043% 69.29% 2702ms 2.48% CellPropertyCollection::HasProperty 430ms 0.4% 69.68% 2691ms 2.47% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00092% 69.68% 2646ms 2.43% std::_Rb_tree::_M_insert_unique 0 0% 69.68% 2595ms 2.39% Cell::HasCellProperty (inline) 242ms 0.22% 69.91% 2558ms 2.35% VertexMesh::GetAreaGradientOfElementAtNode 25ms 0.023% 69.93% 2521ms 2.32% Cell::GetCellData 0 0% 69.93% 2418ms 2.22% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.93% 2368ms 2.18% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.93% 2367ms 2.18% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.93% 2251ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 229ms 0.21% 70.14% 2242ms 2.06% AbstractCellPopulation::Iterator::IsRealCell (inline) 138ms 0.13% 70.27% 2230ms 2.05% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 89ms 0.082% 70.35% 2180ms 2.00% VertexMesh::GetVolumeOfElement 29ms 0.027% 70.38% 2143ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 2082ms 1.91% 72.29% 2082ms 1.91% std::_Rb_tree_increment 1368ms 1.26% 73.55% 2042ms 1.88% std::_Rb_tree::equal_range (inline) 1ms 0.00092% 73.55% 1967ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 468ms 0.43% 73.98% 1954ms 1.80% std::type_info::operator== (inline) 3ms 0.0028% 73.98% 1953ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0028% 73.98% 1864ms 1.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.98% 1864ms 1.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 72ms 0.066% 74.05% 1860ms 1.71% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.05% 1765ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 22ms 0.02% 74.07% 1731ms 1.59% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 25ms 0.023% 74.09% 1665ms 1.53% VertexMesh::GetSurfaceAreaOfElement 37ms 0.034% 74.13% 1607ms 1.48% Node::RemoveElement 22ms 0.02% 74.15% 1581ms 1.45% std::set::erase (inline) 151ms 0.14% 74.29% 1548ms 1.42% CellPropertyCollection::AddProperty 22ms 0.02% 74.31% 1525ms 1.40% AbstractCellPopulation::GetLocationIndexUsingCell 93ms 0.085% 74.39% 1512ms 1.39% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.39% 1464ms 1.35% tcache_get (inline) 1464ms 1.35% 75.74% 1464ms 1.35% tcache_get_n (inline) 122ms 0.11% 75.85% 1438ms 1.32% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 75.85% 1371ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 75.85% 1274ms 1.17% OffLatticeSimulation::ApplyBoundaries 45ms 0.041% 75.89% 1227ms 1.13% CellPropertyRegistry::Get 1221ms 1.12% 77.01% 1221ms 1.12% Node::rGetLocation 0 0% 77.01% 1170ms 1.08% boost::numeric::ublas::norm_2 (inline) 470ms 0.43% 77.45% 1163ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 51ms 0.047% 77.49% 1162ms 1.07% std::less::operator() (inline) 1145ms 1.05% 78.55% 1145ms 1.05% [libchaste_cell_based.so] 0 0% 78.55% 1144ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 922ms 0.85% 79.39% 1111ms 1.02% std::operator< (inline) 95ms 0.087% 79.48% 1108ms 1.02% std::_Rb_tree::find (inline) 1100ms 1.01% 80.49% 1100ms 1.01% std::_Rb_tree_insert_and_rebalance 71ms 0.065% 80.56% 1090ms 1.00% std::_Rb_tree::_M_erase_aux (partial-inline) 10ms 0.0092% 80.57% 1070ms 0.98% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 164ms 0.15% 80.72% 1061ms 0.98% boost::detail::shared_count::~shared_count (inline) 0 0% 80.72% 1061ms 0.98% boost::shared_ptr::~shared_ptr (inline) 9ms 0.0083% 80.73% 1035ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.73% 1002ms 0.92% std::_Rb_tree::clear (inline) 0 0% 80.73% 987ms 0.91% std::map::clear (inline) 975ms 0.9% 81.62% 975ms 0.9% std::vector::size (inline) 14ms 0.013% 81.63% 930ms 0.85% boost::numeric::ublas::detail::expression_type_check (inline) 381ms 0.35% 81.99% 921ms 0.85% Edge::GetMapIndex 171ms 0.16% 82.14% 905ms 0.83% boost::numeric::ublas::detail::equals 902ms 0.83% 82.97% 902ms 0.83% [libchaste_mesh.so] 0 0% 82.97% 883ms 0.81% boost::numeric::ublas::c_vector::assign_temporary (inline) 9ms 0.0083% 82.98% 883ms 0.81% boost::numeric::ublas::c_vector::swap (inline) 0 0% 82.98% 881ms 0.81% std::map::find (inline) 76ms 0.07% 83.05% 874ms 0.8% std::swap_ranges (inline) 862ms 0.79% 83.84% 870ms 0.8% boost::detail::sp_counted_base::release 2ms 0.0018% 83.84% 844ms 0.78% VertexMeshWriter::MakeVtkMesh 113ms 0.1% 83.95% 833ms 0.77% MutableElement::GetNodeLocalIndex 21ms 0.019% 83.97% 812ms 0.75% MutableElement::RegisterWithEdges (inline) 34ms 0.031% 84.00% 799ms 0.73% Edge::AddElement 0 0% 84.00% 798ms 0.73% std::iter_swap (inline) 798ms 0.73% 84.73% 798ms 0.73% std::swap (inline) 768ms 0.71% 85.44% 768ms 0.71% Node::GetIndex 90ms 0.083% 85.52% 767ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.52% 753ms 0.69% CellPropertyCollection::~CellPropertyCollection (inline) 17ms 0.016% 85.54% 741ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 124ms 0.11% 85.65% 740ms 0.68% boost::shared_ptr::shared_ptr (inline) 119ms 0.11% 85.76% 724ms 0.67% VertexBasedCellPopulation::CheckForStepSizeException 407ms 0.37% 86.13% 721ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 101ms 0.093% 86.23% 696ms 0.64% std::__new_allocator::construct (inline) 0 0% 86.23% 696ms 0.64% std::allocator_traits::construct (inline) 0 0% 86.23% 694ms 0.64% boost::numeric::ublas::norm_inf (inline) 347ms 0.32% 86.55% 694ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.55% 664ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.56% 664ms 0.61% std::_Rb_tree::_M_insert_node (inline) 1ms 0.00092% 86.56% 658ms 0.6% std::_Vector_base::_M_allocate (inline) 33ms 0.03% 86.60% 648ms 0.6% MutableElement::RegisterWithNodes (inline) 0 0% 86.60% 628ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 86.60% 625ms 0.57% vtkPolygon::New 1ms 0.00092% 86.60% 625ms 0.57% vtkPolygon::vtkPolygon 573ms 0.53% 87.12% 616ms 0.57% boost::detail::shared_count::shared_count (inline) 35ms 0.032% 87.16% 611ms 0.56% Node::AddElement 573ms 0.53% 87.68% 573ms 0.53% [libstdc++.so.6.0.33] 30ms 0.028% 87.71% 568ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.71% 568ms 0.52% boost::numeric::ublas::vector::vector (inline) 0 0% 87.71% 563ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 10ms 0.0092% 87.72% 563ms 0.52% std::vector::_M_default_append (inline) 562ms 0.52% 88.24% 562ms 0.52% operator delete 559ms 0.51% 88.75% 559ms 0.51% boost::shared_ptr::operator-> (inline)