File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96253ms, 88.67% of 108548ms total Dropped 1064 nodes (cum <= 542.74ms) flat flat% sum% cum cum% 0 0% 0% 108113ms 99.60% __libc_start_call_main 0 0% 0% 108113ms 99.60% __libc_start_main_impl 0 0% 0% 108113ms 99.60% _start 0 0% 0% 108094ms 99.58% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108094ms 99.58% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108094ms 99.58% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108094ms 99.58% main 0 0% 0% 108057ms 99.55% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108057ms 99.55% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108057ms 99.55% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 0 0% 0% 108050ms 99.54% AbstractCellBasedSimulation::Solve 13ms 0.012% 0.012% 55953ms 51.55% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.025% 52705ms 48.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 128ms 0.12% 0.14% 51662ms 47.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 415ms 0.38% 0.53% 40184ms 37.02% NagaiHondaForce::AddForceContribution 3ms 0.0028% 0.53% 39244ms 36.15% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.53% 24289ms 22.38% VertexBasedCellPopulation::Update 0 0% 0.53% 24170ms 22.27% MutableVertexMesh::ReMesh 14707ms 13.55% 14.08% 23265ms 21.43% Cylindrical2dVertexMesh::GetVectorFromAtoB 70ms 0.064% 14.14% 17439ms 16.07% Cell::ReadyToDivide 118ms 0.11% 14.25% 16374ms 15.08% AbstractPhaseBasedCellCycleModel::ReadyToDivide 357ms 0.33% 14.58% 14835ms 13.67% NagaiHondaForce::GetAdhesionParameter 441ms 0.41% 14.99% 14630ms 13.48% boost::numeric::ublas::c_vector::c_vector (partial-inline) 137ms 0.13% 15.11% 14022ms 12.92% SimpleWntCellCycleModel::UpdateCellCyclePhase 121ms 0.11% 15.22% 13411ms 12.35% CellPropertyCollection::GetPropertiesType (inline) 431ms 0.4% 15.62% 13037ms 12.01% boost::numeric::ublas::vector_assign (inline) 131ms 0.12% 15.74% 12122ms 11.17% MutableVertexMesh::CheckForIntersections 3225ms 2.97% 18.71% 11108ms 10.23% __dynamic_cast 91ms 0.084% 18.80% 11003ms 10.14% AbstractCellProperty::IsSubType (inline) 62ms 0.057% 18.85% 10963ms 10.10% VertexBasedCellPopulation::GetDampingConstant 90ms 0.083% 18.94% 10392ms 9.57% AbstractTargetAreaModifier::UpdateTargetAreas 18ms 0.017% 18.95% 10295ms 9.48% AbstractCellBasedSimulation::DoCellBirth 59ms 0.054% 19.01% 10277ms 9.47% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 1359ms 1.25% 20.26% 10140ms 9.34% std::__new_allocator::allocate (inline) 2730ms 2.52% 22.77% 9628ms 8.87% boost::numeric::ublas::indexing_vector_assign 0 0% 22.77% 9579ms 8.82% std::_Rb_tree::_M_create_node (inline) 0 0% 22.77% 9544ms 8.79% std::allocator_traits::allocate (inline) 1301ms 1.20% 23.97% 9434ms 8.69% std::_Rb_tree::_M_erase 798ms 0.74% 24.71% 9066ms 8.35% VertexMesh::ElementIncludesPoint 368ms 0.34% 25.05% 9064ms 8.35% VertexMesh::GetNextEdgeGradientOfElementAtNode 21ms 0.019% 25.07% 8983ms 8.28% VertexBasedCellPopulation::GetLocationOfCellCentre 0 0% 25.07% 8915ms 8.21% std::_Rb_tree::_M_get_node (inline) 831ms 0.77% 25.83% 8890ms 8.19% operator new 216ms 0.2% 26.03% 8597ms 7.92% std::_Rb_tree::~_Rb_tree (inline) 73ms 0.067% 26.10% 8549ms 7.88% Cell::GetMutationState 459ms 0.42% 26.52% 8533ms 7.86% VertexMesh::GetCentroidOfElement 0 0% 26.52% 8502ms 7.83% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.52% 8364ms 7.71% std::_Rb_tree::_Alloc_node::operator() (inline) 236ms 0.22% 26.74% 8282ms 7.63% std::__new_allocator::deallocate (inline) 0 0% 26.74% 8255ms 7.60% std::allocator_traits::deallocate (inline) 0 0% 26.74% 8193ms 7.55% std::_Rb_tree::_M_put_node (inline) 0 0% 26.74% 8152ms 7.51% std::set::~set (inline) 2854ms 2.63% 29.37% 8111ms 7.47% __GI___libc_free 3112ms 2.87% 32.23% 7871ms 7.25% __GI___libc_malloc 21ms 0.019% 32.25% 7597ms 7.00% MutableVertexMesh::RemoveDeletedNodesAndElements 1455ms 1.34% 33.59% 7389ms 6.81% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 461ms 0.42% 34.02% 7351ms 6.77% std::map::operator[] (partial-inline) 134ms 0.12% 34.14% 6876ms 6.33% std::_Rb_tree::_Rb_tree (partial-inline) 634ms 0.58% 34.73% 6519ms 6.01% std::_Rb_tree::_M_copy (inline) 100ms 0.092% 34.82% 6468ms 5.96% SimpleWntCellCycleModel::GetWntLevel 11ms 0.01% 34.83% 6406ms 5.90% std::set::set (inline) 6372ms 5.87% 40.70% 6372ms 5.87% boost::numeric::ublas::c_vector::operator() 160ms 0.15% 40.85% 6263ms 5.77% WntConcentration::GetWntLevel 6163ms 5.68% 46.52% 6163ms 5.68% __strcmp_avx2 2461ms 2.27% 48.79% 5724ms 5.27% std::_Rb_tree::_M_lower_bound (inline) 733ms 0.68% 49.47% 5587ms 5.15% std::_Rb_tree::_M_clone_node (inline) 2701ms 2.49% 51.95% 5399ms 4.97% __cxxabiv1::__si_class_type_info::__do_dyncast 38ms 0.035% 51.99% 5361ms 4.94% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.99% 5325ms 4.91% std::set::insert (inline) 4948ms 4.56% 56.55% 5246ms 4.83% _int_free 43ms 0.04% 56.59% 5206ms 4.80% EdgeHelper::RemoveDeletedEdges 39ms 0.036% 56.62% 4944ms 4.55% EdgeHelper::UpdateEdgesMapKey 1468ms 1.35% 57.98% 4859ms 4.48% boost::numeric::ublas::c_vector::operator[] (inline) 221ms 0.2% 58.18% 4711ms 4.34% MutableElement::ResetIndex 2ms 0.0018% 58.18% 4645ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 0 0% 58.18% 4594ms 4.23% std::_Rb_tree::lower_bound (inline) 0 0% 58.18% 4594ms 4.23% std::map::lower_bound (inline) 487ms 0.45% 58.63% 4526ms 4.17% std::_Rb_tree::_M_insert_ (inline) 55ms 0.051% 58.68% 4359ms 4.02% std::set_intersection (inline) 272ms 0.25% 58.93% 4304ms 3.97% std::__set_intersection 3991ms 3.68% 62.61% 3991ms 3.68% boost::numeric::ublas::same_impl_ex 54ms 0.05% 62.66% 3961ms 3.65% Cell::GetCellProliferativeType 101ms 0.093% 62.75% 3836ms 3.53% AbstractCellPopulation::GetCellUsingLocationIndex 70ms 0.064% 62.81% 3634ms 3.35% AbstractCellProperty::IsType (inline) 10ms 0.0092% 62.82% 3611ms 3.33% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 44ms 0.041% 62.86% 3197ms 2.95% Cell::SetCellProliferativeType 770ms 0.71% 63.57% 3151ms 2.90% AbstractElement::GetNodeLocation 0 0% 63.57% 3131ms 2.88% std::insert_iterator::operator= (inline) 2200ms 2.03% 65.60% 3085ms 2.84% _int_malloc 41ms 0.038% 65.64% 2950ms 2.72% std::_Rb_tree::erase 591ms 0.54% 66.18% 2833ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 5ms 0.0046% 66.19% 2813ms 2.59% std::_Rb_tree::_M_insert_unique_ (inline) 2760ms 2.54% 68.73% 2760ms 2.54% std::_Rb_tree::_S_right (inline) 461ms 0.42% 69.15% 2584ms 2.38% std::_Rb_tree_const_iterator::operator++ (inline) 749ms 0.69% 69.84% 2549ms 2.35% AbstractCellProperty::IsSame 1ms 0.00092% 69.85% 2512ms 2.31% std::_Rb_tree::_M_insert_unique 0 0% 69.85% 2498ms 2.30% boost::numeric::ublas::c_vector::operator-= (inline) 38ms 0.035% 69.88% 2496ms 2.30% CellPropertyCollection::HasProperty 271ms 0.25% 70.13% 2439ms 2.25% VertexMesh::GetAreaGradientOfElementAtNode 0 0% 70.13% 2430ms 2.24% AbstractCellPopulation::WriteResultsToFiles 0 0% 70.13% 2381ms 2.19% boost::numeric::ublas::c_vector::assign (inline) 0 0% 70.13% 2361ms 2.18% Cell::HasCellProperty (inline) 30ms 0.028% 70.16% 2315ms 2.13% Cell::GetCellData 77ms 0.071% 70.23% 2259ms 2.08% VertexMesh::GetVolumeOfElement 42ms 0.039% 70.27% 2252ms 2.07% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.0037% 70.27% 2217ms 2.04% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 0.092% 70.36% 2212ms 2.04% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 196ms 0.18% 70.54% 2199ms 2.03% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 70.54% 1996ms 1.84% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 70.54% 1981ms 1.82% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1307ms 1.20% 71.75% 1977ms 1.82% std::_Rb_tree::equal_range (inline) 1951ms 1.80% 73.55% 1951ms 1.80% std::_Rb_tree_increment 2ms 0.0018% 73.55% 1945ms 1.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 73.55% 1945ms 1.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 75ms 0.069% 73.62% 1909ms 1.76% MutableVertexMesh::CheckForSwapsFromShortEdges 429ms 0.4% 74.01% 1800ms 1.66% std::type_info::operator== (inline) 0 0% 74.01% 1787ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 37ms 0.034% 74.05% 1687ms 1.55% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 28ms 0.026% 74.07% 1623ms 1.50% VertexMesh::GetSurfaceAreaOfElement 135ms 0.12% 74.20% 1587ms 1.46% boost::numeric::ublas::vector_reference::operator() (inline) 27ms 0.025% 74.22% 1552ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 42ms 0.039% 74.26% 1514ms 1.39% Node::RemoveElement 0 0% 74.26% 1510ms 1.39% tcache_get (inline) 1510ms 1.39% 75.65% 1510ms 1.39% tcache_get_n (inline) 75ms 0.069% 75.72% 1499ms 1.38% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 26ms 0.024% 75.74% 1486ms 1.37% std::set::erase (inline) 0 0% 75.74% 1481ms 1.36% boost::numeric::ublas::vector_binary::operator() (inline) 152ms 0.14% 75.88% 1473ms 1.36% CellPropertyCollection::AddProperty 4ms 0.0037% 75.89% 1297ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 75.89% 1227ms 1.13% boost::numeric::ublas::norm_2 (inline) 524ms 0.48% 76.37% 1219ms 1.12% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 76.37% 1215ms 1.12% std::_Rb_tree::_Auto_node::_Auto_node (inline) 71ms 0.065% 76.44% 1190ms 1.10% std::less::operator() (inline) 1165ms 1.07% 77.51% 1165ms 1.07% Node::rGetLocation 62ms 0.057% 77.57% 1137ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 98ms 0.09% 77.66% 1120ms 1.03% std::_Rb_tree::find (inline) 891ms 0.82% 78.48% 1119ms 1.03% std::operator< (inline) 1116ms 1.03% 79.51% 1116ms 1.03% std::_Rb_tree_insert_and_rebalance 20ms 0.018% 79.52% 1097ms 1.01% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 29ms 0.027% 79.55% 1085ms 1% CellPropertyRegistry::Get 1061ms 0.98% 80.53% 1061ms 0.98% [libchaste_cell_based.so] 0 0% 80.53% 1057ms 0.97% std::_Rb_tree::clear (inline) 0 0% 80.53% 1042ms 0.96% std::map::clear (inline) 164ms 0.15% 80.68% 986ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 80.68% 986ms 0.91% boost::shared_ptr::~shared_ptr (inline) 7ms 0.0064% 80.69% 981ms 0.9% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 20ms 0.018% 80.70% 964ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 942ms 0.87% 81.57% 942ms 0.87% std::vector::size (inline) 0 0% 81.57% 937ms 0.86% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0037% 81.58% 937ms 0.86% boost::numeric::ublas::c_vector::swap (inline) 172ms 0.16% 81.73% 933ms 0.86% boost::numeric::ublas::detail::equals 83ms 0.076% 81.81% 933ms 0.86% std::swap_ranges (inline) 928ms 0.85% 82.67% 928ms 0.85% [libchaste_mesh.so] 0 0% 82.67% 897ms 0.83% std::map::find (inline) 370ms 0.34% 83.01% 870ms 0.8% Edge::GetMapIndex 851ms 0.78% 83.79% 851ms 0.78% std::swap (inline) 0 0% 83.79% 850ms 0.78% std::iter_swap (inline) 2ms 0.0018% 83.79% 845ms 0.78% VertexMeshWriter::MakeVtkMesh 107ms 0.099% 83.89% 835ms 0.77% MutableElement::GetNodeLocalIndex 797ms 0.73% 84.63% 802ms 0.74% boost::detail::sp_counted_base::release 135ms 0.12% 84.75% 800ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.017% 84.77% 774ms 0.71% MutableElement::RegisterWithEdges (inline) 39ms 0.036% 84.80% 769ms 0.71% Edge::AddElement 163ms 0.15% 84.95% 767ms 0.71% boost::shared_ptr::shared_ptr (inline) 0 0% 84.95% 735ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 427ms 0.39% 85.35% 726ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.35% 718ms 0.66% boost::numeric::ublas::norm_inf (inline) 339ms 0.31% 85.66% 718ms 0.66% boost::numeric::ublas::vector_norm_inf::apply (inline) 112ms 0.1% 85.76% 718ms 0.66% std::__new_allocator::construct (inline) 0 0% 85.76% 718ms 0.66% std::allocator_traits::construct (inline) 706ms 0.65% 86.41% 706ms 0.65% Node::GetIndex 0 0% 86.41% 672ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.43% 672ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.43% 664ms 0.61% std::_Rb_tree::_M_construct_node (inline) 32ms 0.029% 86.46% 637ms 0.59% MutableElement::RegisterWithNodes (inline) 1ms 0.00092% 86.46% 624ms 0.57% std::_Vector_base::_M_allocate (inline) 23ms 0.021% 86.48% 619ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.48% 619ms 0.57% boost::numeric::ublas::vector::vector (inline) 618ms 0.57% 87.05% 618ms 0.57% operator delete 32ms 0.029% 87.08% 607ms 0.56% Node::AddElement 0 0% 87.08% 607ms 0.56% vtkPolygon::New 1ms 0.00092% 87.08% 607ms 0.56% vtkPolygon::vtkPolygon 606ms 0.56% 87.64% 606ms 0.56% [libstdc++.so.6.0.33] 569ms 0.52% 88.16% 604ms 0.56% boost::detail::shared_count::shared_count (inline) 0 0% 88.16% 559ms 0.51% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 552ms 0.51% 88.67% 552ms 0.51% boost::shared_ptr::operator-> (inline)