File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95435ms, 87.14% of 109514ms total Dropped 1130 nodes (cum <= 547.57ms) flat flat% sum% cum cum% 0 0% 0% 109189ms 99.70% __libc_start_call_main 0 0% 0% 109189ms 99.70% __libc_start_main_impl 0 0% 0% 109189ms 99.70% _start 0 0% 0% 109169ms 99.68% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109169ms 99.68% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109169ms 99.68% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109169ms 99.68% main 0 0% 0% 109128ms 99.65% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109128ms 99.65% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109128ms 99.65% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 109120ms 99.64% AbstractCellBasedSimulation::Solve 17ms 0.016% 0.017% 56538ms 51.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.03% 53180ms 48.56% ForwardEulerNumericalMethod::UpdateAllNodePositions 129ms 0.12% 0.15% 52055ms 47.53% AbstractNumericalMethod::ComputeForcesIncludingDamping 340ms 0.31% 0.46% 39830ms 36.37% NagaiHondaForce::AddForceContribution 3ms 0.0027% 0.46% 39367ms 35.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.46% 24270ms 22.16% VertexBasedCellPopulation::Update 0 0% 0.46% 24121ms 22.03% MutableVertexMesh::ReMesh 14659ms 13.39% 13.85% 23195ms 21.18% Cylindrical2dVertexMesh::GetVectorFromAtoB 80ms 0.073% 13.92% 17751ms 16.21% Cell::ReadyToDivide 43ms 0.039% 13.96% 16527ms 15.09% AbstractPhaseBasedCellCycleModel::ReadyToDivide 337ms 0.31% 14.27% 14481ms 13.22% NagaiHondaForce::GetAdhesionParameter 160ms 0.15% 14.41% 14145ms 12.92% SimpleWntCellCycleModel::UpdateCellCyclePhase 97ms 0.089% 14.50% 14006ms 12.79% CellPropertyCollection::GetPropertiesType (inline) 491ms 0.45% 14.95% 13510ms 12.34% boost::numeric::ublas::c_vector::c_vector (partial-inline) 3525ms 3.22% 18.17% 12003ms 10.96% __dynamic_cast 319ms 0.29% 18.46% 12002ms 10.96% boost::numeric::ublas::vector_assign (inline) 147ms 0.13% 18.59% 11907ms 10.87% MutableVertexMesh::CheckForIntersections 55ms 0.05% 18.64% 11880ms 10.85% AbstractCellProperty::IsSubType (inline) 100ms 0.091% 18.74% 11642ms 10.63% VertexBasedCellPopulation::GetDampingConstant 67ms 0.061% 18.80% 10654ms 9.73% AbstractTargetAreaModifier::UpdateTargetAreas 40ms 0.037% 18.83% 10573ms 9.65% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 22ms 0.02% 18.85% 10438ms 9.53% AbstractCellBasedSimulation::DoCellBirth 1481ms 1.35% 20.21% 10239ms 9.35% std::__new_allocator::allocate (inline) 0 0% 20.21% 9654ms 8.82% std::_Rb_tree::_M_create_node (inline) 0 0% 20.21% 9629ms 8.79% std::allocator_traits::allocate (inline) 378ms 0.35% 20.55% 9337ms 8.53% VertexMesh::GetNextEdgeGradientOfElementAtNode 2863ms 2.61% 23.17% 9063ms 8.28% boost::numeric::ublas::indexing_vector_assign 0 0% 23.17% 8919ms 8.14% std::_Rb_tree::_M_get_node (inline) 819ms 0.75% 23.91% 8801ms 8.04% operator new 107ms 0.098% 24.01% 8773ms 8.01% Cell::GetMutationState 20ms 0.018% 24.03% 8753ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 820ms 0.75% 24.78% 8706ms 7.95% VertexMesh::ElementIncludesPoint 1264ms 1.15% 25.93% 8703ms 7.95% std::_Rb_tree::_M_erase 0 0% 25.93% 8517ms 7.78% std::_Rb_tree::_Alloc_node::operator() (inline) 440ms 0.4% 26.33% 8323ms 7.60% VertexMesh::GetCentroidOfElement 412ms 0.38% 26.71% 8008ms 7.31% std::_Rb_tree::~_Rb_tree (inline) 21ms 0.019% 26.73% 7955ms 7.26% MutableVertexMesh::RemoveDeletedNodesAndElements 454ms 0.41% 27.14% 7864ms 7.18% std::map::operator[] (partial-inline) 0 0% 27.14% 7780ms 7.10% std::_Rb_tree::_M_drop_node (inline) 3068ms 2.80% 29.95% 7771ms 7.10% __GI___libc_malloc 0 0% 29.95% 7600ms 6.94% std::set::~set (inline) 203ms 0.19% 30.13% 7590ms 6.93% std::__new_allocator::deallocate (inline) 0 0% 30.13% 7583ms 6.92% std::allocator_traits::deallocate (inline) 0 0% 30.13% 7514ms 6.86% std::_Rb_tree::_M_put_node (inline) 1524ms 1.39% 31.52% 7242ms 6.61% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 191ms 0.17% 31.70% 7236ms 6.61% std::_Rb_tree::_Rb_tree (partial-inline) 2335ms 2.13% 33.83% 7125ms 6.51% __GI___libc_free 682ms 0.62% 34.45% 6801ms 6.21% std::_Rb_tree::_M_copy (inline) 25ms 0.023% 34.47% 6751ms 6.16% std::set::set (inline) 6683ms 6.10% 40.58% 6683ms 6.10% __strcmp_avx2 2468ms 2.25% 42.83% 6387ms 5.83% std::_Rb_tree::_M_lower_bound (inline) 111ms 0.1% 42.93% 6288ms 5.74% SimpleWntCellCycleModel::GetWntLevel 185ms 0.17% 43.10% 6096ms 5.57% WntConcentration::GetWntLevel 6022ms 5.50% 48.60% 6022ms 5.50% boost::numeric::ublas::c_vector::operator() 834ms 0.76% 49.36% 5888ms 5.38% std::_Rb_tree::_M_clone_node (inline) 2925ms 2.67% 52.03% 5566ms 5.08% __cxxabiv1::__si_class_type_info::__do_dyncast 26ms 0.024% 52.06% 5449ms 4.98% MutableVertexMesh::RemoveDeletedNodes 0 0% 52.06% 5370ms 4.90% std::set::insert (inline) 1954ms 1.78% 53.84% 5300ms 4.84% boost::numeric::ublas::c_vector::operator[] (inline) 29ms 0.026% 53.87% 5247ms 4.79% EdgeHelper::RemoveDeletedEdges 0 0% 53.87% 5236ms 4.78% std::_Rb_tree::lower_bound (inline) 0 0% 53.87% 5236ms 4.78% std::map::lower_bound (inline) 44ms 0.04% 53.91% 4940ms 4.51% EdgeHelper::UpdateEdgesMapKey 211ms 0.19% 54.10% 4861ms 4.44% MutableElement::ResetIndex 4330ms 3.95% 58.05% 4770ms 4.36% _int_free 156ms 0.14% 58.20% 4698ms 4.29% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.00091% 58.20% 4636ms 4.23% AbstractCellBasedSimulation::DoCellRemoval (inline) 538ms 0.49% 58.69% 4546ms 4.15% std::_Rb_tree::_M_insert_ (inline) 124ms 0.11% 58.80% 4429ms 4.04% std::set_intersection (inline) 225ms 0.21% 59.01% 4305ms 3.93% std::__set_intersection 41ms 0.037% 59.04% 4082ms 3.73% Cell::GetCellProliferativeType 81ms 0.074% 59.12% 3698ms 3.38% AbstractCellProperty::IsType (inline) 3637ms 3.32% 62.44% 3637ms 3.32% boost::numeric::ublas::same_impl_ex 14ms 0.013% 62.45% 3571ms 3.26% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.45% 3359ms 3.07% std::insert_iterator::operator= (inline) 3233ms 2.95% 65.40% 3233ms 2.95% std::_Rb_tree::_S_right (inline) 51ms 0.047% 65.45% 3186ms 2.91% Cell::SetCellProliferativeType 2233ms 2.04% 67.49% 3167ms 2.89% _int_malloc 61ms 0.056% 67.54% 3147ms 2.87% std::_Rb_tree::erase 922ms 0.84% 68.39% 3092ms 2.82% AbstractElement::GetNodeLocation 7ms 0.0064% 68.39% 2893ms 2.64% std::_Rb_tree::_M_insert_unique_ (inline) 697ms 0.64% 69.03% 2653ms 2.42% AbstractCellProperty::IsSame 24ms 0.022% 69.05% 2631ms 2.40% Cell::GetCellData 67ms 0.061% 69.11% 2618ms 2.39% CellPropertyCollection::HasProperty 212ms 0.19% 69.31% 2611ms 2.38% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.31% 2526ms 2.31% AbstractCellPopulation::WriteResultsToFiles 246ms 0.22% 69.53% 2516ms 2.30% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.53% 2505ms 2.29% Cell::HasCellProperty (inline) 603ms 0.55% 70.08% 2490ms 2.27% boost::numeric::ublas::vector_binary::size (inline) 2ms 0.0018% 70.08% 2477ms 2.26% std::_Rb_tree::_M_insert_unique 0 0% 70.08% 2463ms 2.25% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.08% 2395ms 2.19% boost::numeric::ublas::c_vector::operator-= (inline) 54ms 0.049% 70.13% 2323ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 92ms 0.084% 70.22% 2319ms 2.12% VertexMesh::GetVolumeOfElement 6ms 0.0055% 70.22% 2299ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 164ms 0.15% 70.37% 2295ms 2.10% AbstractCellPopulation::Iterator::IsRealCell (inline) 40ms 0.037% 70.41% 2132ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 1439ms 1.31% 71.72% 2104ms 1.92% std::_Rb_tree::equal_range (inline) 0 0% 71.72% 2062ms 1.88% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0027% 71.73% 2049ms 1.87% VertexBasedCellPopulation::WriteCellVtkResultsToFile 3ms 0.0027% 71.73% 2047ms 1.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.73% 2047ms 1.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2029ms 1.85% 73.58% 2029ms 1.85% std::_Rb_tree_increment 522ms 0.48% 74.06% 1956ms 1.79% std::type_info::operator== (inline) 0 0% 74.06% 1858ms 1.70% VertexMeshWriter::WriteVtkUsingMesh 63ms 0.058% 74.11% 1831ms 1.67% MutableVertexMesh::CheckForSwapsFromShortEdges 28ms 0.026% 74.14% 1807ms 1.65% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 80ms 0.073% 74.21% 1587ms 1.45% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 42ms 0.038% 74.25% 1585ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 51ms 0.047% 74.30% 1566ms 1.43% Node::RemoveElement 31ms 0.028% 74.33% 1520ms 1.39% VertexMesh::GetSurfaceAreaOfElement 11ms 0.01% 74.34% 1518ms 1.39% std::set::erase (inline) 23ms 0.021% 74.36% 1516ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 133ms 0.12% 74.48% 1414ms 1.29% CellPropertyCollection::AddProperty 0 0% 74.48% 1396ms 1.27% OffLatticeSimulation::ApplyBoundaries 0 0% 74.48% 1351ms 1.23% tcache_get (inline) 1351ms 1.23% 75.71% 1351ms 1.23% tcache_get_n (inline) 61ms 0.056% 75.77% 1347ms 1.23% std::less::operator() (inline) 0 0% 75.77% 1321ms 1.21% boost::numeric::ublas::norm_2 (inline) 1311ms 1.20% 76.97% 1311ms 1.20% [libchaste_cell_based.so] 0 0% 76.97% 1310ms 1.20% boost::numeric::ublas::vector_binary::operator() (inline) 567ms 0.52% 77.48% 1307ms 1.19% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1068ms 0.98% 78.46% 1286ms 1.17% std::operator< (inline) 40ms 0.037% 78.49% 1216ms 1.11% CellPropertyRegistry::Get 21ms 0.019% 78.51% 1189ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 80ms 0.073% 78.59% 1171ms 1.07% std::_Rb_tree::_M_erase_aux (partial-inline) 78ms 0.071% 78.66% 1155ms 1.05% std::_Rb_tree::find (inline) 0 0% 78.66% 1137ms 1.04% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.66% 1109ms 1.01% std::_Rb_tree::clear (inline) 1096ms 1.00% 79.66% 1096ms 1.00% std::_Rb_tree_insert_and_rebalance 0 0% 79.66% 1090ms 1% std::map::clear (inline) 0 0% 79.66% 1075ms 0.98% boost::numeric::ublas::c_vector::assign_temporary (inline) 0 0% 79.66% 1075ms 0.98% boost::numeric::ublas::c_vector::swap (inline) 74ms 0.068% 79.73% 1075ms 0.98% std::swap_ranges (inline) 1044ms 0.95% 80.68% 1044ms 0.95% Node::rGetLocation 11ms 0.01% 80.69% 1034ms 0.94% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.69% 1001ms 0.91% std::iter_swap (inline) 1001ms 0.91% 81.60% 1001ms 0.91% std::swap (inline) 0 0% 81.60% 999ms 0.91% std::map::find (inline) 119ms 0.11% 81.71% 965ms 0.88% boost::detail::shared_count::~shared_count (inline) 0 0% 81.71% 965ms 0.88% boost::shared_ptr::~shared_ptr (inline) 7ms 0.0064% 81.72% 956ms 0.87% boost::numeric::ublas::detail::expression_type_check (inline) 159ms 0.15% 81.86% 939ms 0.86% boost::numeric::ublas::detail::equals 877ms 0.8% 82.67% 877ms 0.8% std::vector::size (inline) 1ms 0.00091% 82.67% 855ms 0.78% VertexMeshWriter::MakeVtkMesh 0 0% 82.67% 838ms 0.77% CellPropertyCollection::~CellPropertyCollection (inline) 253ms 0.23% 82.90% 798ms 0.73% std::__new_allocator::construct (inline) 0 0% 82.90% 798ms 0.73% std::allocator_traits::construct (inline) 413ms 0.38% 83.27% 795ms 0.73% Edge::GetMapIndex 770ms 0.7% 83.98% 791ms 0.72% boost::detail::sp_counted_base::release 93ms 0.085% 84.06% 785ms 0.72% boost::numeric::ublas::c_vector::operator= (inline) 776ms 0.71% 84.77% 776ms 0.71% [libchaste_mesh.so] 438ms 0.4% 85.17% 745ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 147ms 0.13% 85.31% 743ms 0.68% MutableElement::GetNodeLocalIndex 13ms 0.012% 85.32% 740ms 0.68% MutableElement::RegisterWithEdges (inline) 0 0% 85.32% 735ms 0.67% std::_Rb_tree::_M_construct_node (inline) 25ms 0.023% 85.34% 733ms 0.67% Edge::AddElement 0 0% 85.34% 727ms 0.66% boost::numeric::ublas::norm_inf (inline) 385ms 0.35% 85.69% 727ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 2ms 0.0018% 85.69% 707ms 0.65% std::_Vector_base::_M_allocate (inline) 150ms 0.14% 85.83% 696ms 0.64% boost::shared_ptr::shared_ptr (inline) 677ms 0.62% 86.45% 677ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.45% 675ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 38ms 0.035% 86.48% 647ms 0.59% MutableElement::RegisterWithNodes (inline) 646ms 0.59% 87.07% 646ms 0.59% Node::GetIndex 1ms 0.00091% 87.07% 643ms 0.59% vtkPolygon::New 1ms 0.00091% 87.07% 642ms 0.59% vtkPolygon::vtkPolygon 0 0% 87.07% 641ms 0.59% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 87.09% 641ms 0.59% std::_Rb_tree::_M_insert_node (inline) 15ms 0.014% 87.11% 625ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.11% 625ms 0.57% boost::numeric::ublas::vector::vector (inline) 35ms 0.032% 87.14% 607ms 0.55% Node::AddElement 6ms 0.0055% 87.14% 583ms 0.53% std::vector::_M_default_append (inline)