File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95889ms, 87.92% of 109060ms total Dropped 1047 nodes (cum <= 545.30ms) flat flat% sum% cum cum% 0 0% 0% 108570ms 99.55% __libc_start_call_main 0 0% 0% 108570ms 99.55% __libc_start_main_impl 0 0% 0% 108570ms 99.55% _start 0 0% 0% 108551ms 99.53% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108551ms 99.53% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108551ms 99.53% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108551ms 99.53% main 0 0% 0% 108516ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108516ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108516ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 108509ms 99.49% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.016% 56743ms 52.03% OffLatticeSimulation::UpdateCellLocationsAndTopology 18ms 0.017% 0.032% 53495ms 49.05% ForwardEulerNumericalMethod::UpdateAllNodePositions 134ms 0.12% 0.15% 52436ms 48.08% AbstractNumericalMethod::ComputeForcesIncludingDamping 347ms 0.32% 0.47% 40496ms 37.13% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.47% 38959ms 35.72% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.47% 24129ms 22.12% VertexBasedCellPopulation::Update 1ms 0.00092% 0.47% 24012ms 22.02% MutableVertexMesh::ReMesh 14404ms 13.21% 13.68% 22798ms 20.90% Cylindrical2dVertexMesh::GetVectorFromAtoB 72ms 0.066% 13.75% 17332ms 15.89% Cell::ReadyToDivide 93ms 0.085% 13.83% 16152ms 14.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 353ms 0.32% 14.16% 15665ms 14.36% NagaiHondaForce::GetAdhesionParameter 400ms 0.37% 14.52% 14370ms 13.18% boost::numeric::ublas::c_vector::c_vector (partial-inline) 151ms 0.14% 14.66% 13724ms 12.58% CellPropertyCollection::GetPropertiesType (inline) 125ms 0.11% 14.78% 13687ms 12.55% SimpleWntCellCycleModel::UpdateCellCyclePhase 390ms 0.36% 15.13% 12890ms 11.82% boost::numeric::ublas::vector_assign (inline) 147ms 0.13% 15.27% 12139ms 11.13% MutableVertexMesh::CheckForIntersections 3338ms 3.06% 18.33% 11430ms 10.48% __dynamic_cast 127ms 0.12% 18.45% 11428ms 10.48% VertexBasedCellPopulation::GetDampingConstant 83ms 0.076% 18.52% 11321ms 10.38% AbstractCellProperty::IsSubType (inline) 1209ms 1.11% 19.63% 10502ms 9.63% std::__new_allocator::allocate (inline) 89ms 0.082% 19.71% 10446ms 9.58% AbstractTargetAreaModifier::UpdateTargetAreas 51ms 0.047% 19.76% 10334ms 9.48% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 37ms 0.034% 19.79% 10141ms 9.30% AbstractCellBasedSimulation::DoCellBirth 0 0% 19.79% 9953ms 9.13% std::allocator_traits::allocate (inline) 0 0% 19.79% 9864ms 9.04% std::_Rb_tree::_M_create_node (inline) 2652ms 2.43% 22.23% 9566ms 8.77% boost::numeric::ublas::indexing_vector_assign 1366ms 1.25% 23.48% 9532ms 8.74% std::_Rb_tree::_M_erase 856ms 0.78% 24.26% 9424ms 8.64% operator new 0 0% 24.26% 9273ms 8.50% std::_Rb_tree::_M_get_node (inline) 796ms 0.73% 24.99% 8991ms 8.24% VertexMesh::ElementIncludesPoint 80ms 0.073% 25.07% 8723ms 8.00% Cell::GetMutationState 253ms 0.23% 25.30% 8722ms 8.00% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.30% 8715ms 7.99% std::_Rb_tree::_Alloc_node::operator() (inline) 20ms 0.018% 25.32% 8702ms 7.98% VertexBasedCellPopulation::GetLocationOfCellCentre 327ms 0.3% 25.62% 8684ms 7.96% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.62% 8502ms 7.80% std::_Rb_tree::_M_drop_node (inline) 3681ms 3.38% 28.99% 8392ms 7.69% __GI___libc_malloc 494ms 0.45% 29.44% 8295ms 7.61% VertexMesh::GetCentroidOfElement 247ms 0.23% 29.67% 8287ms 7.60% std::__new_allocator::deallocate (inline) 0 0% 29.67% 8255ms 7.57% std::allocator_traits::deallocate (inline) 0 0% 29.67% 8240ms 7.56% std::set::~set (inline) 0 0% 29.67% 8198ms 7.52% std::_Rb_tree::_M_put_node (inline) 3025ms 2.77% 32.44% 8072ms 7.40% __GI___libc_free 14ms 0.013% 32.46% 7532ms 6.91% MutableVertexMesh::RemoveDeletedNodesAndElements 478ms 0.44% 32.90% 7406ms 6.79% std::map::operator[] (partial-inline) 161ms 0.15% 33.04% 7237ms 6.64% std::_Rb_tree::_Rb_tree (partial-inline) 1297ms 1.19% 34.23% 6958ms 6.38% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 674ms 0.62% 34.85% 6857ms 6.29% std::_Rb_tree::_M_copy (inline) 20ms 0.018% 34.87% 6838ms 6.27% std::set::set (inline) 6502ms 5.96% 40.83% 6502ms 5.96% __strcmp_avx2 6225ms 5.71% 46.54% 6225ms 5.71% boost::numeric::ublas::c_vector::operator() 93ms 0.085% 46.62% 6186ms 5.67% SimpleWntCellCycleModel::GetWntLevel 110ms 0.1% 46.72% 6043ms 5.54% WntConcentration::GetWntLevel 746ms 0.68% 47.41% 5920ms 5.43% std::_Rb_tree::_M_clone_node (inline) 2442ms 2.24% 49.65% 5796ms 5.31% std::_Rb_tree::_M_lower_bound (inline) 2671ms 2.45% 52.10% 5452ms 5.00% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 52.10% 5404ms 4.96% std::set::insert (inline) 31ms 0.028% 52.13% 5394ms 4.95% MutableVertexMesh::RemoveDeletedNodes 35ms 0.032% 52.16% 5214ms 4.78% EdgeHelper::RemoveDeletedEdges 4702ms 4.31% 56.47% 5037ms 4.62% _int_free 27ms 0.025% 56.49% 4950ms 4.54% EdgeHelper::UpdateEdgesMapKey 1490ms 1.37% 57.86% 4820ms 4.42% boost::numeric::ublas::c_vector::operator[] (inline) 198ms 0.18% 58.04% 4687ms 4.30% MutableElement::ResetIndex 0 0% 58.04% 4685ms 4.30% std::_Rb_tree::lower_bound (inline) 0 0% 58.04% 4685ms 4.30% std::map::lower_bound (inline) 1ms 0.00092% 58.04% 4678ms 4.29% AbstractCellBasedSimulation::DoCellRemoval (inline) 519ms 0.48% 58.52% 4597ms 4.22% std::_Rb_tree::_M_insert_ (inline) 61ms 0.056% 58.57% 4573ms 4.19% std::set_intersection (inline) 291ms 0.27% 58.84% 4512ms 4.14% std::__set_intersection 118ms 0.11% 58.95% 4121ms 3.78% AbstractCellPopulation::GetCellUsingLocationIndex 42ms 0.039% 58.99% 4023ms 3.69% Cell::GetCellProliferativeType 3952ms 3.62% 62.61% 3952ms 3.62% boost::numeric::ublas::same_impl_ex 65ms 0.06% 62.67% 3862ms 3.54% AbstractCellProperty::IsType (inline) 8ms 0.0073% 62.68% 3538ms 3.24% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.68% 3330ms 3.05% std::insert_iterator::operator= (inline) 805ms 0.74% 63.42% 3231ms 2.96% AbstractElement::GetNodeLocation 63ms 0.058% 63.47% 3124ms 2.86% Cell::SetCellProliferativeType 2157ms 1.98% 65.45% 3026ms 2.77% _int_malloc 33ms 0.03% 65.48% 2969ms 2.72% std::_Rb_tree::erase 6ms 0.0055% 65.49% 2901ms 2.66% std::_Rb_tree::_M_insert_unique_ (inline) 2877ms 2.64% 68.13% 2877ms 2.64% std::_Rb_tree::_S_right (inline) 653ms 0.6% 68.72% 2843ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 446ms 0.41% 69.13% 2807ms 2.57% std::_Rb_tree_const_iterator::operator++ (inline) 748ms 0.69% 69.82% 2783ms 2.55% AbstractCellProperty::IsSame 43ms 0.039% 69.86% 2677ms 2.45% CellPropertyCollection::HasProperty 0 0% 69.86% 2582ms 2.37% Cell::HasCellProperty (inline) 1ms 0.00092% 69.86% 2503ms 2.30% std::_Rb_tree::_M_insert_unique 244ms 0.22% 70.08% 2496ms 2.29% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.08% 2477ms 2.27% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 70.08% 2464ms 2.26% boost::numeric::ublas::c_vector::assign (inline) 33ms 0.03% 70.11% 2429ms 2.23% Cell::GetCellData 111ms 0.1% 70.22% 2362ms 2.17% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 70.22% 2338ms 2.14% AbstractCellPopulation::WriteResultsToFiles 11ms 0.01% 70.23% 2233ms 2.05% AbstractCellPopulation::Iterator::operator++ (inline) 95ms 0.087% 70.31% 2226ms 2.04% VertexMesh::GetVolumeOfElement 35ms 0.032% 70.34% 2205ms 2.02% std::_Rb_tree::_M_emplace_hint_unique 222ms 0.2% 70.55% 2201ms 2.02% AbstractCellPopulation::Iterator::IsRealCell 2189ms 2.01% 72.56% 2189ms 2.01% std::_Rb_tree_increment 1380ms 1.27% 73.82% 2055ms 1.88% std::_Rb_tree::equal_range (inline) 498ms 0.46% 74.28% 2035ms 1.87% std::type_info::operator== (inline) 0 0% 74.28% 1918ms 1.76% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 74.28% 1910ms 1.75% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1ms 0.00092% 74.28% 1902ms 1.74% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.28% 1902ms 1.74% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 72ms 0.066% 74.35% 1736ms 1.59% MutableVertexMesh::CheckForSwapsFromShortEdges 1ms 0.00092% 74.35% 1723ms 1.58% VertexMeshWriter::WriteVtkUsingMesh 36ms 0.033% 74.38% 1711ms 1.57% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 49ms 0.045% 74.42% 1591ms 1.46% Node::RemoveElement 21ms 0.019% 74.44% 1582ms 1.45% VertexMesh::GetSurfaceAreaOfElement 17ms 0.016% 74.46% 1551ms 1.42% std::set::erase (inline) 142ms 0.13% 74.59% 1500ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 16ms 0.015% 74.60% 1494ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 170ms 0.16% 74.76% 1494ms 1.37% CellPropertyCollection::AddProperty 0 0% 74.76% 1491ms 1.37% tcache_get (inline) 1491ms 1.37% 76.13% 1491ms 1.37% tcache_get_n (inline) 86ms 0.079% 76.21% 1471ms 1.35% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 76.21% 1377ms 1.26% boost::numeric::ublas::vector_binary::operator() (inline) 1ms 0.00092% 76.21% 1376ms 1.26% OffLatticeSimulation::ApplyBoundaries 0 0% 76.21% 1173ms 1.08% boost::numeric::ublas::norm_2 (inline) 541ms 0.5% 76.70% 1164ms 1.07% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.70% 1149ms 1.05% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1147ms 1.05% 77.75% 1147ms 1.05% Node::rGetLocation 60ms 0.055% 77.81% 1136ms 1.04% std::less::operator() (inline) 1127ms 1.03% 78.84% 1127ms 1.03% std::_Rb_tree_insert_and_rebalance 22ms 0.02% 78.86% 1117ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 5ms 0.0046% 78.87% 1087ms 1% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 890ms 0.82% 79.68% 1076ms 0.99% std::operator< (inline) 100ms 0.092% 79.78% 1075ms 0.99% std::_Rb_tree::_M_erase_aux (partial-inline) 93ms 0.085% 79.86% 1070ms 0.98% std::_Rb_tree::find (inline) 1063ms 0.97% 80.84% 1063ms 0.97% [libchaste_cell_based.so] 0 0% 80.84% 1063ms 0.97% std::_Rb_tree::clear (inline) 0 0% 80.84% 1049ms 0.96% std::map::clear (inline) 17ms 0.016% 80.85% 1021ms 0.94% CellPropertyRegistry::Get 1016ms 0.93% 81.78% 1016ms 0.93% std::vector::size (inline) 157ms 0.14% 81.93% 994ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 81.93% 994ms 0.91% boost::shared_ptr::~shared_ptr (inline) 25ms 0.023% 81.95% 993ms 0.91% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 81.95% 963ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0092% 81.96% 963ms 0.88% boost::numeric::ublas::c_vector::swap 190ms 0.17% 82.13% 958ms 0.88% boost::numeric::ublas::detail::equals 80ms 0.073% 82.21% 953ms 0.87% std::swap_ranges (inline) 914ms 0.84% 83.04% 914ms 0.84% [libchaste_mesh.so] 364ms 0.33% 83.38% 886ms 0.81% Edge::GetMapIndex 1ms 0.00092% 83.38% 879ms 0.81% std::map::find (inline) 0 0% 83.38% 873ms 0.8% std::iter_swap (inline) 873ms 0.8% 84.18% 873ms 0.8% std::swap (inline) 1ms 0.00092% 84.18% 846ms 0.78% VertexMeshWriter::MakeVtkMesh 115ms 0.11% 84.29% 838ms 0.77% MutableElement::GetNodeLocalIndex 810ms 0.74% 85.03% 814ms 0.75% boost::detail::sp_counted_base::release 116ms 0.11% 85.13% 781ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.13% 767ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 22ms 0.02% 85.15% 764ms 0.7% MutableElement::RegisterWithEdges (inline) 25ms 0.023% 85.18% 758ms 0.7% Edge::AddElement 411ms 0.38% 85.55% 742ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 146ms 0.13% 85.69% 739ms 0.68% boost::shared_ptr::shared_ptr (inline) 0 0% 85.69% 729ms 0.67% boost::numeric::ublas::norm_inf (inline) 348ms 0.32% 86.01% 729ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 86.01% 696ms 0.64% std::_Rb_tree::_Auto_node::_M_insert (inline) 29ms 0.027% 86.03% 696ms 0.64% std::_Rb_tree::_M_insert_node (inline) 695ms 0.64% 86.67% 695ms 0.64% Node::GetIndex 1ms 0.00092% 86.67% 680ms 0.62% std::_Vector_base::_M_allocate (inline) 84ms 0.077% 86.75% 647ms 0.59% std::__new_allocator::construct (inline) 0 0% 86.75% 647ms 0.59% std::allocator_traits::construct (inline) 627ms 0.57% 87.32% 627ms 0.57% operator delete 1ms 0.00092% 87.33% 617ms 0.57% vtkPolygon::New 0 0% 87.33% 616ms 0.56% vtkPolygon::vtkPolygon 26ms 0.024% 87.35% 597ms 0.55% MutableElement::RegisterWithNodes (inline) 560ms 0.51% 87.86% 593ms 0.54% boost::detail::shared_count::shared_count (inline) 0 0% 87.86% 591ms 0.54% std::_Rb_tree::_M_construct_node (inline) 32ms 0.029% 87.89% 570ms 0.52% Node::AddElement 21ms 0.019% 87.91% 570ms 0.52% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.91% 570ms 0.52% boost::numeric::ublas::vector::vector (inline) 13ms 0.012% 87.92% 550ms 0.5% std::vector::_M_default_append (inline) 0 0% 87.92% 546ms 0.5% boost::numeric::ublas::scalar_traits::type_sqrt (inline)