File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94738ms, 88.04% of 107607ms total Dropped 1068 nodes (cum <= 538.03ms) flat flat% sum% cum cum% 0 0% 0% 107199ms 99.62% __libc_start_call_main 0 0% 0% 107199ms 99.62% __libc_start_main_impl 0 0% 0% 107199ms 99.62% _start 0 0% 0% 107181ms 99.60% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 107181ms 99.60% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 107181ms 99.60% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 107181ms 99.60% main 0 0% 0% 107145ms 99.57% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 107145ms 99.57% CxxTest::TestRunner::runTest (inline) 0 0% 0% 107145ms 99.57% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 1ms 0.00093% 0.00093% 107138ms 99.56% AbstractCellBasedSimulation::Solve 19ms 0.018% 0.019% 55680ms 51.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 24ms 0.022% 0.041% 52511ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 115ms 0.11% 0.15% 51467ms 47.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 437ms 0.41% 0.55% 40008ms 37.18% NagaiHondaForce::AddForceContribution 1ms 0.00093% 0.55% 38743ms 36.00% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0019% 0.56% 23990ms 22.29% VertexBasedCellPopulation::Update 1ms 0.00093% 0.56% 23864ms 22.18% MutableVertexMesh::ReMesh 14415ms 13.40% 13.95% 22996ms 21.37% Cylindrical2dVertexMesh::GetVectorFromAtoB 85ms 0.079% 14.03% 17270ms 16.05% Cell::ReadyToDivide 90ms 0.084% 14.12% 16073ms 14.94% AbstractPhaseBasedCellCycleModel::ReadyToDivide 310ms 0.29% 14.40% 14884ms 13.83% NagaiHondaForce::GetAdhesionParameter 426ms 0.4% 14.80% 14623ms 13.59% boost::numeric::ublas::c_vector::c_vector (partial-inline) 148ms 0.14% 14.94% 13670ms 12.70% SimpleWntCellCycleModel::UpdateCellCyclePhase 110ms 0.1% 15.04% 13315ms 12.37% CellPropertyCollection::GetPropertiesType (inline) 383ms 0.36% 15.40% 13062ms 12.14% boost::numeric::ublas::vector_assign (inline) 146ms 0.14% 15.53% 12103ms 11.25% MutableVertexMesh::CheckForIntersections 3110ms 2.89% 18.42% 11086ms 10.30% __dynamic_cast 104ms 0.097% 18.52% 11013ms 10.23% AbstractCellProperty::IsSubType (inline) 66ms 0.061% 18.58% 10945ms 10.17% VertexBasedCellPopulation::GetDampingConstant 74ms 0.069% 18.65% 10290ms 9.56% AbstractTargetAreaModifier::UpdateTargetAreas 70ms 0.065% 18.71% 10193ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 13ms 0.012% 18.73% 10129ms 9.41% AbstractCellBasedSimulation::DoCellBirth 1238ms 1.15% 19.88% 9818ms 9.12% std::__new_allocator::allocate (inline) 2703ms 2.51% 22.39% 9783ms 9.09% boost::numeric::ublas::indexing_vector_assign 1348ms 1.25% 23.64% 9342ms 8.68% std::_Rb_tree::_M_erase 0 0% 23.64% 9192ms 8.54% std::allocator_traits::allocate (inline) 0 0% 23.64% 9162ms 8.51% std::_Rb_tree::_M_create_node (inline) 345ms 0.32% 23.96% 8961ms 8.33% VertexMesh::GetNextEdgeGradientOfElementAtNode 839ms 0.78% 24.74% 8947ms 8.31% VertexMesh::ElementIncludesPoint 31ms 0.029% 24.77% 8707ms 8.09% VertexBasedCellPopulation::GetLocationOfCellCentre 807ms 0.75% 25.52% 8672ms 8.06% operator new 0 0% 25.52% 8544ms 7.94% std::_Rb_tree::_M_get_node (inline) 205ms 0.19% 25.71% 8487ms 7.89% std::_Rb_tree::~_Rb_tree (inline) 89ms 0.083% 25.79% 8421ms 7.83% Cell::GetMutationState 471ms 0.44% 26.23% 8291ms 7.70% VertexMesh::GetCentroidOfElement 0 0% 26.23% 8286ms 7.70% std::_Rb_tree::_M_drop_node (inline) 241ms 0.22% 26.45% 8052ms 7.48% std::__new_allocator::deallocate (inline) 0 0% 26.45% 8049ms 7.48% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.45% 8035ms 7.47% std::set::~set (inline) 0 0% 26.45% 8025ms 7.46% std::allocator_traits::deallocate (inline) 0 0% 26.45% 7948ms 7.39% std::_Rb_tree::_M_put_node (inline) 3114ms 2.89% 29.35% 7858ms 7.30% __GI___libc_free 3028ms 2.81% 32.16% 7675ms 7.13% __GI___libc_malloc 11ms 0.01% 32.17% 7384ms 6.86% MutableVertexMesh::RemoveDeletedNodesAndElements 500ms 0.46% 32.64% 7234ms 6.72% std::map::operator[] (partial-inline) 1254ms 1.17% 33.80% 7160ms 6.65% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 130ms 0.12% 33.92% 6660ms 6.19% std::_Rb_tree::_Rb_tree (partial-inline) 6412ms 5.96% 39.88% 6412ms 5.96% boost::numeric::ublas::c_vector::operator() 662ms 0.62% 40.50% 6318ms 5.87% std::_Rb_tree::_M_copy (inline) 6300ms 5.85% 46.35% 6300ms 5.85% __strcmp_avx2 126ms 0.12% 46.47% 6281ms 5.84% SimpleWntCellCycleModel::GetWntLevel 16ms 0.015% 46.48% 6255ms 5.81% std::set::set (inline) 114ms 0.11% 46.59% 6047ms 5.62% WntConcentration::GetWntLevel 2438ms 2.27% 48.86% 5641ms 5.24% std::_Rb_tree::_M_lower_bound (inline) 2810ms 2.61% 51.47% 5495ms 5.11% __cxxabiv1::__si_class_type_info::__do_dyncast 765ms 0.71% 52.18% 5334ms 4.96% std::_Rb_tree::_M_clone_node (inline) 0 0% 52.18% 5321ms 4.94% std::set::insert (inline) 33ms 0.031% 52.21% 5301ms 4.93% MutableVertexMesh::RemoveDeletedNodes 36ms 0.033% 52.24% 5138ms 4.77% EdgeHelper::RemoveDeletedEdges 1513ms 1.41% 53.65% 4893ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 36ms 0.033% 53.68% 4874ms 4.53% EdgeHelper::UpdateEdgesMapKey 4423ms 4.11% 57.79% 4744ms 4.41% _int_free 51ms 0.047% 57.84% 4663ms 4.33% std::set_intersection (inline) 293ms 0.27% 58.11% 4612ms 4.29% std::__set_intersection 2ms 0.0019% 58.11% 4609ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 192ms 0.18% 58.29% 4575ms 4.25% MutableElement::ResetIndex 0 0% 58.29% 4562ms 4.24% std::_Rb_tree::lower_bound (inline) 0 0% 58.29% 4562ms 4.24% std::map::lower_bound (inline) 471ms 0.44% 58.73% 4515ms 4.20% std::_Rb_tree::_M_insert_ (inline) 4024ms 3.74% 62.47% 4024ms 3.74% boost::numeric::ublas::same_impl_ex 45ms 0.042% 62.51% 4009ms 3.73% Cell::GetCellProliferativeType 102ms 0.095% 62.61% 3969ms 3.69% AbstractCellPopulation::GetCellUsingLocationIndex 59ms 0.055% 62.66% 3686ms 3.43% AbstractCellProperty::IsType (inline) 9ms 0.0084% 62.67% 3535ms 3.29% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 62.67% 3332ms 3.10% std::insert_iterator::operator= (inline) 59ms 0.055% 62.72% 3153ms 2.93% Cell::SetCellProliferativeType 740ms 0.69% 63.41% 3140ms 2.92% AbstractElement::GetNodeLocation 2215ms 2.06% 65.47% 3067ms 2.85% _int_malloc 8ms 0.0074% 65.48% 2938ms 2.73% std::_Rb_tree::_M_insert_unique_ (inline) 37ms 0.034% 65.51% 2904ms 2.70% std::_Rb_tree::erase 630ms 0.59% 66.10% 2834ms 2.63% boost::numeric::ublas::vector_binary::size (inline) 468ms 0.43% 66.53% 2797ms 2.60% std::_Rb_tree_const_iterator::operator++ (inline) 2635ms 2.45% 68.98% 2635ms 2.45% std::_Rb_tree::_S_right (inline) 705ms 0.66% 69.64% 2623ms 2.44% AbstractCellProperty::IsSame 43ms 0.04% 69.68% 2554ms 2.37% CellPropertyCollection::HasProperty 0 0% 69.68% 2467ms 2.29% Cell::HasCellProperty (inline) 0 0% 69.68% 2451ms 2.28% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.68% 2449ms 2.28% boost::numeric::ublas::c_vector::operator-= (inline) 219ms 0.2% 69.88% 2428ms 2.26% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 69.88% 2403ms 2.23% AbstractCellPopulation::WriteResultsToFiles 1ms 0.00093% 69.88% 2383ms 2.21% std::_Rb_tree::_M_insert_unique (inline) 32ms 0.03% 69.91% 2301ms 2.14% Cell::GetCellData 119ms 0.11% 70.02% 2276ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 88ms 0.082% 70.10% 2239ms 2.08% VertexMesh::GetVolumeOfElement 4ms 0.0037% 70.11% 2224ms 2.07% AbstractCellPopulation::Iterator::operator++ (inline) 202ms 0.19% 70.29% 2206ms 2.05% AbstractCellPopulation::Iterator::IsRealCell (inline) 2142ms 1.99% 72.28% 2142ms 1.99% std::_Rb_tree_increment 52ms 0.048% 72.33% 2125ms 1.97% std::_Rb_tree::_M_emplace_hint_unique 0 0% 72.33% 1969ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1363ms 1.27% 73.60% 1966ms 1.83% std::_Rb_tree::equal_range (inline) 0 0% 73.60% 1960ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 422ms 0.39% 73.99% 1918ms 1.78% std::type_info::operator== (inline) 1ms 0.00093% 73.99% 1853ms 1.72% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.99% 1853ms 1.72% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 90ms 0.084% 74.08% 1811ms 1.68% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.08% 1769ms 1.64% VertexMeshWriter::WriteVtkUsingMesh 31ms 0.029% 74.10% 1705ms 1.58% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 24ms 0.022% 74.13% 1668ms 1.55% VertexMesh::GetSurfaceAreaOfElement 119ms 0.11% 74.24% 1564ms 1.45% boost::numeric::ublas::vector_reference::operator() (inline) 44ms 0.041% 74.28% 1544ms 1.43% Node::RemoveElement 24ms 0.022% 74.30% 1515ms 1.41% std::set::erase (inline) 29ms 0.027% 74.33% 1500ms 1.39% AbstractCellPopulation::GetLocationIndexUsingCell 87ms 0.081% 74.41% 1479ms 1.37% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.41% 1469ms 1.37% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.41% 1398ms 1.30% tcache_get (inline) 1398ms 1.30% 75.71% 1398ms 1.30% tcache_get_n (inline) 145ms 0.13% 75.84% 1379ms 1.28% CellPropertyCollection::AddProperty 2ms 0.0019% 75.84% 1305ms 1.21% OffLatticeSimulation::ApplyBoundaries 0 0% 75.84% 1163ms 1.08% boost::numeric::ublas::norm_2 (inline) 69ms 0.064% 75.91% 1163ms 1.08% std::less::operator() (inline) 512ms 0.48% 76.38% 1156ms 1.07% boost::numeric::ublas::vector_norm_2::apply 1136ms 1.06% 77.44% 1136ms 1.06% std::_Rb_tree_insert_and_rebalance 0 0% 77.44% 1113ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 23ms 0.021% 77.46% 1098ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 869ms 0.81% 78.27% 1094ms 1.02% std::operator< (inline) 1092ms 1.01% 79.28% 1092ms 1.01% Node::rGetLocation 77ms 0.072% 79.36% 1083ms 1.01% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 79.36% 1068ms 0.99% std::_Rb_tree::clear (inline) 17ms 0.016% 79.37% 1062ms 0.99% CellPropertyRegistry::Get 1059ms 0.98% 80.36% 1059ms 0.98% [libchaste_cell_based.so] 90ms 0.084% 80.44% 1054ms 0.98% std::_Rb_tree::find (inline) 0 0% 80.44% 1054ms 0.98% std::map::clear (inline) 8ms 0.0074% 80.45% 1020ms 0.95% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 144ms 0.13% 80.58% 1012ms 0.94% boost::detail::shared_count::~shared_count (inline) 0 0% 80.58% 1012ms 0.94% boost::shared_ptr::~shared_ptr (inline) 941ms 0.87% 81.45% 941ms 0.87% [libchaste_mesh.so] 926ms 0.86% 82.32% 926ms 0.86% std::vector::size (inline) 31ms 0.029% 82.34% 904ms 0.84% boost::numeric::ublas::detail::expression_type_check (inline) 356ms 0.33% 82.67% 878ms 0.82% Edge::GetMapIndex 0 0% 82.67% 871ms 0.81% std::map::find (inline) 140ms 0.13% 82.81% 859ms 0.8% boost::numeric::ublas::detail::equals 0 0% 82.81% 856ms 0.8% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0065% 82.81% 856ms 0.8% boost::numeric::ublas::c_vector::swap (inline) 1ms 0.00093% 82.81% 851ms 0.79% VertexMeshWriter::MakeVtkMesh 76ms 0.071% 82.88% 849ms 0.79% std::swap_ranges (inline) 115ms 0.11% 82.99% 844ms 0.78% MutableElement::GetNodeLocalIndex 840ms 0.78% 83.77% 844ms 0.78% boost::detail::sp_counted_base::release 144ms 0.13% 83.90% 816ms 0.76% boost::shared_ptr::shared_ptr (inline) 774ms 0.72% 84.62% 774ms 0.72% std::swap (inline) 0 0% 84.62% 773ms 0.72% std::iter_swap (inline) 22ms 0.02% 84.64% 757ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.64% 753ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 35ms 0.033% 84.68% 747ms 0.69% Edge::AddElement 436ms 0.41% 85.08% 733ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 114ms 0.11% 85.19% 722ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 721ms 0.67% 85.86% 721ms 0.67% Node::GetIndex 0 0% 85.86% 690ms 0.64% boost::numeric::ublas::norm_inf (inline) 342ms 0.32% 86.18% 690ms 0.64% boost::numeric::ublas::vector_norm_inf::apply (inline) 637ms 0.59% 86.77% 672ms 0.62% boost::detail::shared_count::shared_count (inline) 87ms 0.081% 86.85% 672ms 0.62% std::__new_allocator::construct (inline) 0 0% 86.85% 672ms 0.62% std::allocator_traits::construct (inline) 0 0% 86.85% 669ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 28ms 0.026% 86.87% 669ms 0.62% std::_Rb_tree::_M_insert_node (inline) 36ms 0.033% 86.91% 662ms 0.62% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.91% 662ms 0.62% boost::numeric::ublas::vector::vector (inline) 1ms 0.00093% 86.91% 647ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 86.91% 619ms 0.58% vtkPolygon::New 0 0% 86.91% 618ms 0.57% std::_Rb_tree::_M_construct_node (inline) 3ms 0.0028% 86.91% 618ms 0.57% vtkPolygon::vtkPolygon 578ms 0.54% 87.45% 578ms 0.54% operator delete 30ms 0.028% 87.48% 576ms 0.54% MutableElement::RegisterWithNodes (inline) 570ms 0.53% 88.01% 570ms 0.53% [libstdc++.so.6.0.33] 30ms 0.028% 88.03% 548ms 0.51% Node::AddElement 7ms 0.0065% 88.04% 542ms 0.5% std::vector::_M_default_append (inline)