File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96423ms, 87.79% of 109834ms total Dropped 1124 nodes (cum <= 549.17ms) flat flat% sum% cum cum% 0 0% 0% 109484ms 99.68% __libc_start_call_main 0 0% 0% 109484ms 99.68% __libc_start_main_impl 0 0% 0% 109484ms 99.68% _start 0 0% 0% 109461ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109461ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109461ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109461ms 99.66% main 0 0% 0% 109422ms 99.62% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109422ms 99.62% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109422ms 99.62% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 109415ms 99.62% AbstractCellBasedSimulation::Solve 17ms 0.015% 0.019% 57041ms 51.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 9ms 0.0082% 0.027% 53595ms 48.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 139ms 0.13% 0.15% 52059ms 47.40% AbstractNumericalMethod::ComputeForcesIncludingDamping 301ms 0.27% 0.43% 40068ms 36.48% NagaiHondaForce::AddForceContribution 1ms 0.00091% 0.43% 39114ms 35.61% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.43% 24150ms 21.99% VertexBasedCellPopulation::Update 2ms 0.0018% 0.43% 24012ms 21.86% MutableVertexMesh::ReMesh 14872ms 13.54% 13.97% 23446ms 21.35% Cylindrical2dVertexMesh::GetVectorFromAtoB 110ms 0.1% 14.07% 17681ms 16.10% Cell::ReadyToDivide 61ms 0.056% 14.13% 16294ms 14.84% AbstractPhaseBasedCellCycleModel::ReadyToDivide 331ms 0.3% 14.43% 14508ms 13.21% NagaiHondaForce::GetAdhesionParameter 136ms 0.12% 14.55% 13911ms 12.67% SimpleWntCellCycleModel::UpdateCellCyclePhase 96ms 0.087% 14.64% 13889ms 12.65% CellPropertyCollection::GetPropertiesType (inline) 481ms 0.44% 15.08% 13812ms 12.58% boost::numeric::ublas::c_vector::c_vector (partial-inline) 300ms 0.27% 15.35% 12321ms 11.22% boost::numeric::ublas::vector_assign (inline) 149ms 0.14% 15.49% 11802ms 10.75% MutableVertexMesh::CheckForIntersections 3425ms 3.12% 18.61% 11760ms 10.71% __dynamic_cast 44ms 0.04% 18.65% 11620ms 10.58% AbstractCellProperty::IsSubType (inline) 79ms 0.072% 18.72% 11397ms 10.38% VertexBasedCellPopulation::GetDampingConstant 77ms 0.07% 18.79% 10773ms 9.81% AbstractTargetAreaModifier::UpdateTargetAreas 45ms 0.041% 18.83% 10667ms 9.71% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 31ms 0.028% 18.86% 10175ms 9.26% AbstractCellBasedSimulation::DoCellBirth 1386ms 1.26% 20.12% 10107ms 9.20% std::__new_allocator::allocate (inline) 0 0% 20.12% 9663ms 8.80% std::_Rb_tree::_M_create_node (inline) 0 0% 20.12% 9593ms 8.73% std::allocator_traits::allocate (inline) 428ms 0.39% 20.51% 9572ms 8.71% VertexMesh::GetNextEdgeGradientOfElementAtNode 2848ms 2.59% 23.10% 9398ms 8.56% boost::numeric::ublas::indexing_vector_assign 1269ms 1.16% 24.26% 8959ms 8.16% std::_Rb_tree::_M_erase 0 0% 24.26% 8853ms 8.06% std::_Rb_tree::_M_get_node (inline) 761ms 0.69% 24.95% 8814ms 8.02% operator new 32ms 0.029% 24.98% 8776ms 7.99% VertexBasedCellPopulation::GetLocationOfCellCentre 849ms 0.77% 25.75% 8728ms 7.95% VertexMesh::ElementIncludesPoint 84ms 0.076% 25.83% 8556ms 7.79% Cell::GetMutationState 0 0% 25.83% 8487ms 7.73% std::_Rb_tree::_Alloc_node::operator() (inline) 452ms 0.41% 26.24% 8239ms 7.50% VertexMesh::GetCentroidOfElement 0 0% 26.24% 8082ms 7.36% std::_Rb_tree::_M_drop_node (inline) 218ms 0.2% 26.44% 8048ms 7.33% std::_Rb_tree::~_Rb_tree (inline) 230ms 0.21% 26.65% 7866ms 7.16% std::__new_allocator::deallocate (inline) 0 0% 26.65% 7864ms 7.16% std::allocator_traits::deallocate (inline) 2945ms 2.68% 29.33% 7836ms 7.13% __GI___libc_malloc 459ms 0.42% 29.75% 7830ms 7.13% std::map::operator[] (partial-inline) 19ms 0.017% 29.76% 7824ms 7.12% MutableVertexMesh::RemoveDeletedNodesAndElements 0 0% 29.76% 7772ms 7.08% std::_Rb_tree::_M_put_node (inline) 0 0% 29.76% 7572ms 6.89% std::set::~set (inline) 1500ms 1.37% 31.13% 7529ms 6.85% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2401ms 2.19% 33.32% 7323ms 6.67% __GI___libc_free 200ms 0.18% 33.50% 7210ms 6.56% std::_Rb_tree::_Rb_tree (partial-inline) 767ms 0.7% 34.20% 6767ms 6.16% std::_Rb_tree::_M_copy (inline) 6762ms 6.16% 40.35% 6762ms 6.16% __strcmp_avx2 31ms 0.028% 40.38% 6696ms 6.10% std::set::set (inline) 111ms 0.1% 40.48% 6249ms 5.69% SimpleWntCellCycleModel::GetWntLevel 2531ms 2.30% 42.79% 6121ms 5.57% std::_Rb_tree::_M_lower_bound (inline) 170ms 0.15% 42.94% 6064ms 5.52% WntConcentration::GetWntLevel 5984ms 5.45% 48.39% 5984ms 5.45% boost::numeric::ublas::c_vector::operator() 842ms 0.77% 49.16% 5735ms 5.22% std::_Rb_tree::_M_clone_node (inline) 2884ms 2.63% 51.78% 5590ms 5.09% __cxxabiv1::__si_class_type_info::__do_dyncast 21ms 0.019% 51.80% 5532ms 5.04% MutableVertexMesh::RemoveDeletedNodes 0 0% 51.80% 5409ms 4.92% std::set::insert (inline) 28ms 0.025% 51.83% 5355ms 4.88% EdgeHelper::RemoveDeletedEdges 1940ms 1.77% 53.59% 5185ms 4.72% boost::numeric::ublas::c_vector::operator[] (inline) 0 0% 53.59% 5073ms 4.62% std::_Rb_tree::lower_bound (inline) 0 0% 53.59% 5073ms 4.62% std::map::lower_bound (inline) 28ms 0.025% 53.62% 5034ms 4.58% EdgeHelper::UpdateEdgesMapKey 4472ms 4.07% 57.69% 4895ms 4.46% _int_free 0 0% 57.69% 4777ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 191ms 0.17% 57.86% 4756ms 4.33% MutableElement::ResetIndex 503ms 0.46% 58.32% 4611ms 4.20% std::_Rb_tree::_M_insert_ (inline) 143ms 0.13% 58.45% 4399ms 4.01% std::set_intersection (inline) 127ms 0.12% 58.57% 4389ms 4.00% AbstractCellPopulation::GetCellUsingLocationIndex 229ms 0.21% 58.78% 4256ms 3.87% std::__set_intersection 41ms 0.037% 58.81% 4159ms 3.79% Cell::GetCellProliferativeType 47ms 0.043% 58.86% 3880ms 3.53% AbstractCellProperty::IsType (inline) 3724ms 3.39% 62.25% 3724ms 3.39% boost::numeric::ublas::same_impl_ex 11ms 0.01% 62.26% 3608ms 3.28% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2267ms 2.06% 64.32% 3291ms 3.00% _int_malloc 0 0% 64.32% 3284ms 2.99% std::insert_iterator::operator= (inline) 46ms 0.042% 64.36% 3142ms 2.86% Cell::SetCellProliferativeType 63ms 0.057% 64.42% 3037ms 2.77% std::_Rb_tree::erase 874ms 0.8% 65.22% 3021ms 2.75% AbstractElement::GetNodeLocation 2948ms 2.68% 67.90% 2948ms 2.68% std::_Rb_tree::_S_right (inline) 11ms 0.01% 67.91% 2832ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 742ms 0.68% 68.59% 2823ms 2.57% AbstractCellProperty::IsSame 27ms 0.025% 68.61% 2780ms 2.53% CellPropertyCollection::HasProperty 0 0% 68.61% 2698ms 2.46% Cell::HasCellProperty (inline) 0 0% 68.61% 2608ms 2.37% boost::numeric::ublas::c_vector::operator-= (inline) 196ms 0.18% 68.79% 2598ms 2.37% VertexMesh::GetAreaGradientOfElementAtNode 261ms 0.24% 69.03% 2597ms 2.36% std::_Rb_tree_const_iterator::operator++ (inline) 623ms 0.57% 69.59% 2577ms 2.35% boost::numeric::ublas::vector_binary::size (inline) 1ms 0.00091% 69.60% 2577ms 2.35% std::_Rb_tree::_M_insert_unique 27ms 0.025% 69.62% 2510ms 2.29% Cell::GetCellData 0 0% 69.62% 2491ms 2.27% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.62% 2445ms 2.23% AbstractCellPopulation::WriteResultsToFiles 44ms 0.04% 69.66% 2309ms 2.10% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 78ms 0.071% 69.73% 2271ms 2.07% VertexMesh::GetVolumeOfElement 39ms 0.036% 69.77% 2228ms 2.03% std::_Rb_tree::_M_emplace_hint_unique 186ms 0.17% 69.94% 2130ms 1.94% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.00091% 69.94% 2121ms 1.93% AbstractCellPopulation::Iterator::operator++ (inline) 485ms 0.44% 70.38% 2081ms 1.89% std::type_info::operator== (inline) 2ms 0.0018% 70.38% 2059ms 1.87% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.38% 2059ms 1.87% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2048ms 1.86% 72.24% 2048ms 1.86% std::_Rb_tree_increment 0 0% 72.24% 1984ms 1.81% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00091% 72.25% 1974ms 1.80% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1332ms 1.21% 73.46% 1974ms 1.80% std::_Rb_tree::equal_range (inline) 58ms 0.053% 73.51% 1860ms 1.69% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 73.51% 1776ms 1.62% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.024% 73.53% 1664ms 1.52% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 29ms 0.026% 73.56% 1595ms 1.45% VertexMesh::GetSurfaceAreaOfElement 49ms 0.045% 73.61% 1497ms 1.36% Node::RemoveElement 132ms 0.12% 73.73% 1491ms 1.36% CellPropertyCollection::AddProperty 44ms 0.04% 73.77% 1473ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 89ms 0.081% 73.85% 1456ms 1.33% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 13ms 0.012% 73.86% 1453ms 1.32% std::set::erase (inline) 0 0% 73.86% 1409ms 1.28% tcache_get (inline) 1409ms 1.28% 75.14% 1409ms 1.28% tcache_get_n (inline) 1382ms 1.26% 76.40% 1382ms 1.26% [libchaste_cell_based.so] 0 0% 76.40% 1377ms 1.25% boost::numeric::ublas::norm_2 (inline) 619ms 0.56% 76.96% 1364ms 1.24% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 69ms 0.063% 77.03% 1362ms 1.24% std::less::operator() (inline) 0 0% 77.03% 1358ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 67ms 0.061% 77.09% 1349ms 1.23% boost::numeric::ublas::vector_reference::operator() (inline) 1ms 0.00091% 77.09% 1338ms 1.22% OffLatticeSimulation::ApplyBoundaries 1044ms 0.95% 78.04% 1293ms 1.18% std::operator< (inline) 79ms 0.072% 78.11% 1208ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 34ms 0.031% 78.14% 1189ms 1.08% CellPropertyRegistry::Get 0 0% 78.14% 1176ms 1.07% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 78.14% 1143ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 13ms 0.012% 78.15% 1143ms 1.04% boost::numeric::ublas::c_vector::swap (inline) 21ms 0.019% 78.17% 1138ms 1.04% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.17% 1131ms 1.03% std::_Rb_tree::clear (inline) 3ms 0.0027% 78.18% 1130ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 90ms 0.082% 78.26% 1130ms 1.03% std::swap_ranges (inline) 1110ms 1.01% 79.27% 1110ms 1.01% std::_Rb_tree_insert_and_rebalance 0 0% 79.27% 1105ms 1.01% std::map::clear (inline) 88ms 0.08% 79.35% 1070ms 0.97% std::_Rb_tree::find (inline) 1051ms 0.96% 80.30% 1051ms 0.96% Node::rGetLocation 0 0% 80.30% 1040ms 0.95% std::iter_swap (inline) 1040ms 0.95% 81.25% 1040ms 0.95% std::swap (inline) 124ms 0.11% 81.36% 1011ms 0.92% boost::detail::shared_count::~shared_count (inline) 0 0% 81.36% 1011ms 0.92% boost::shared_ptr::~shared_ptr (inline) 11ms 0.01% 81.37% 973ms 0.89% boost::numeric::ublas::detail::expression_type_check (inline) 217ms 0.2% 81.57% 954ms 0.87% boost::numeric::ublas::detail::equals 1ms 0.00091% 81.57% 903ms 0.82% std::map::find (inline) 1ms 0.00091% 81.57% 870ms 0.79% VertexMeshWriter::MakeVtkMesh 868ms 0.79% 82.36% 868ms 0.79% std::vector::size (inline) 238ms 0.22% 82.58% 864ms 0.79% std::__new_allocator::construct (inline) 0 0% 82.58% 864ms 0.79% std::allocator_traits::construct (inline) 805ms 0.73% 83.31% 841ms 0.77% boost::detail::sp_counted_base::release 88ms 0.08% 83.39% 816ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.39% 810ms 0.74% std::_Rb_tree::_M_construct_node (inline) 416ms 0.38% 83.77% 793ms 0.72% Edge::GetMapIndex 162ms 0.15% 83.92% 785ms 0.71% boost::shared_ptr::shared_ptr (inline) 22ms 0.02% 83.94% 772ms 0.7% Edge::AddElement 15ms 0.014% 83.95% 772ms 0.7% MutableElement::RegisterWithEdges (inline) 26ms 0.024% 83.98% 751ms 0.68% AbstractNumericalMethod::DetectStepSizeExceptions 751ms 0.68% 84.66% 751ms 0.68% [libchaste_mesh.so] 1ms 0.00091% 84.66% 738ms 0.67% std::_Vector_base::_M_allocate (inline) 0 0% 84.66% 733ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.66% 728ms 0.66% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 130ms 0.12% 84.78% 725ms 0.66% VertexBasedCellPopulation::CheckForStepSizeException 401ms 0.37% 85.15% 725ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 107ms 0.097% 85.24% 698ms 0.64% MutableElement::GetNodeLocalIndex 697ms 0.63% 85.88% 697ms 0.63% [libstdc++.so.6.0.33] 0 0% 85.88% 691ms 0.63% std::_Rb_tree::_Auto_node::_M_insert (inline) 27ms 0.025% 85.90% 691ms 0.63% std::_Rb_tree::_M_insert_node (inline) 0 0% 85.90% 682ms 0.62% boost::numeric::ublas::norm_inf (inline) 371ms 0.34% 86.24% 682ms 0.62% boost::numeric::ublas::vector_norm_inf::apply (inline) 648ms 0.59% 86.83% 648ms 0.59% Node::GetIndex 597ms 0.54% 87.37% 623ms 0.57% boost::detail::shared_count::shared_count (inline) 31ms 0.028% 87.40% 619ms 0.56% MutableElement::RegisterWithNodes (inline) 12ms 0.011% 87.41% 617ms 0.56% std::vector::_M_default_append (inline) 0 0% 87.41% 608ms 0.55% vtkPolygon::New 2ms 0.0018% 87.41% 608ms 0.55% vtkPolygon::vtkPolygon 31ms 0.028% 87.44% 588ms 0.54% Node::AddElement 0 0% 87.44% 555ms 0.51% std::map::map (inline) 381ms 0.35% 87.79% 554ms 0.5% malloc_consolidate