File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95417ms, 87.89% of 108560ms total Dropped 1123 nodes (cum <= 542.80ms) flat flat% sum% cum cum% 0 0% 0% 108202ms 99.67% __libc_start_call_main 0 0% 0% 108202ms 99.67% __libc_start_main_impl 0 0% 0% 108202ms 99.67% _start 0 0% 0% 108182ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108182ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108182ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108182ms 99.65% main 0 0% 0% 108140ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108140ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108140ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0028% 0.0028% 108132ms 99.61% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.019% 56111ms 51.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.04% 52833ms 48.67% ForwardEulerNumericalMethod::UpdateAllNodePositions 141ms 0.13% 0.17% 51738ms 47.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 330ms 0.3% 0.47% 40035ms 36.88% NagaiHondaForce::AddForceContribution 0 0% 0.47% 39001ms 35.93% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.0037% 0.48% 24017ms 22.12% VertexBasedCellPopulation::Update 4ms 0.0037% 0.48% 23853ms 21.97% MutableVertexMesh::ReMesh 14845ms 13.67% 14.16% 23498ms 21.65% Cylindrical2dVertexMesh::GetVectorFromAtoB 88ms 0.081% 14.24% 17638ms 16.25% Cell::ReadyToDivide 56ms 0.052% 14.29% 16398ms 15.11% AbstractPhaseBasedCellCycleModel::ReadyToDivide 327ms 0.3% 14.59% 14315ms 13.19% NagaiHondaForce::GetAdhesionParameter 150ms 0.14% 14.73% 14153ms 13.04% SimpleWntCellCycleModel::UpdateCellCyclePhase 403ms 0.37% 15.10% 14083ms 12.97% boost::numeric::ublas::c_vector::c_vector (partial-inline) 125ms 0.12% 15.21% 13246ms 12.20% CellPropertyCollection::GetPropertiesType (inline) 341ms 0.31% 15.53% 12692ms 11.69% boost::numeric::ublas::vector_assign (inline) 157ms 0.14% 15.67% 11869ms 10.93% MutableVertexMesh::CheckForIntersections 3432ms 3.16% 18.83% 11384ms 10.49% __dynamic_cast 77ms 0.071% 18.90% 11255ms 10.37% AbstractCellProperty::IsSubType (inline) 81ms 0.075% 18.98% 11128ms 10.25% VertexBasedCellPopulation::GetDampingConstant 77ms 0.071% 19.05% 10543ms 9.71% AbstractTargetAreaModifier::UpdateTargetAreas 52ms 0.048% 19.10% 10451ms 9.63% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 35ms 0.032% 19.13% 10250ms 9.44% AbstractCellBasedSimulation::DoCellBirth 1326ms 1.22% 20.35% 9625ms 8.87% std::__new_allocator::allocate (inline) 2792ms 2.57% 22.92% 9523ms 8.77% boost::numeric::ublas::indexing_vector_assign 373ms 0.34% 23.27% 9481ms 8.73% VertexMesh::GetNextEdgeGradientOfElementAtNode 1301ms 1.20% 24.47% 9170ms 8.45% std::_Rb_tree::_M_erase 0 0% 24.47% 9044ms 8.33% std::_Rb_tree::_M_create_node (inline) 0 0% 24.47% 9032ms 8.32% std::allocator_traits::allocate (inline) 37ms 0.034% 24.50% 8949ms 8.24% VertexBasedCellPopulation::GetLocationOfCellCentre 856ms 0.79% 25.29% 8737ms 8.05% VertexMesh::ElementIncludesPoint 499ms 0.46% 25.75% 8554ms 7.88% VertexMesh::GetCentroidOfElement 92ms 0.085% 25.83% 8425ms 7.76% Cell::GetMutationState 751ms 0.69% 26.52% 8355ms 7.70% operator new 0 0% 26.52% 8315ms 7.66% std::_Rb_tree::_M_get_node (inline) 239ms 0.22% 26.74% 8305ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.74% 8217ms 7.57% std::_Rb_tree::_M_drop_node (inline) 259ms 0.24% 26.98% 7952ms 7.32% std::__new_allocator::deallocate (inline) 0 0% 26.98% 7943ms 7.32% std::allocator_traits::deallocate (inline) 0 0% 26.98% 7926ms 7.30% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.98% 7883ms 7.26% std::_Rb_tree::_M_put_node (inline) 0 0% 26.98% 7872ms 7.25% std::set::~set (inline) 21ms 0.019% 27.00% 7801ms 7.19% MutableVertexMesh::RemoveDeletedNodesAndElements 1469ms 1.35% 28.36% 7531ms 6.94% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 2219ms 2.04% 30.40% 7501ms 6.91% __GI___libc_free 2878ms 2.65% 33.05% 7425ms 6.84% __GI___libc_malloc 468ms 0.43% 33.48% 7064ms 6.51% std::map::operator[] (partial-inline) 207ms 0.19% 33.67% 6899ms 6.36% std::_Rb_tree::_Rb_tree (partial-inline) 28ms 0.026% 33.70% 6464ms 5.95% std::set::set (inline) 146ms 0.13% 33.83% 6441ms 5.93% SimpleWntCellCycleModel::GetWntLevel 717ms 0.66% 34.49% 6439ms 5.93% std::_Rb_tree::_M_copy (inline) 6281ms 5.79% 40.28% 6281ms 5.79% boost::numeric::ublas::c_vector::operator() 141ms 0.13% 40.41% 6201ms 5.71% WntConcentration::GetWntLevel 6153ms 5.67% 46.08% 6153ms 5.67% __strcmp_avx2 2350ms 2.16% 48.24% 5473ms 5.04% std::_Rb_tree::_M_lower_bound (inline) 737ms 0.68% 48.92% 5440ms 5.01% std::_Rb_tree::_M_clone_node (inline) 2904ms 2.68% 51.60% 5387ms 4.96% __cxxabiv1::__si_class_type_info::__do_dyncast 1977ms 1.82% 53.42% 5382ms 4.96% boost::numeric::ublas::c_vector::operator[] (inline) 4789ms 4.41% 57.83% 5260ms 4.85% _int_free 0 0% 57.83% 5119ms 4.72% std::set::insert (inline) 20ms 0.018% 57.85% 5115ms 4.71% MutableVertexMesh::RemoveDeletedNodes 32ms 0.029% 57.88% 4928ms 4.54% EdgeHelper::RemoveDeletedEdges 200ms 0.18% 58.06% 4889ms 4.50% MutableElement::ResetIndex 2ms 0.0018% 58.06% 4722ms 4.35% AbstractCellBasedSimulation::DoCellRemoval (inline) 32ms 0.029% 58.09% 4618ms 4.25% EdgeHelper::UpdateEdgesMapKey 0 0% 58.09% 4461ms 4.11% std::_Rb_tree::lower_bound (inline) 0 0% 58.09% 4461ms 4.11% std::map::lower_bound (inline) 447ms 0.41% 58.50% 4278ms 3.94% std::_Rb_tree::_M_insert_ (inline) 141ms 0.13% 58.63% 4272ms 3.94% std::set_intersection (inline) 102ms 0.094% 58.73% 4235ms 3.90% AbstractCellPopulation::GetCellUsingLocationIndex 252ms 0.23% 58.96% 4131ms 3.81% std::__set_intersection 37ms 0.034% 58.99% 3911ms 3.60% Cell::GetCellProliferativeType 3804ms 3.50% 62.50% 3804ms 3.50% boost::numeric::ublas::same_impl_ex 56ms 0.052% 62.55% 3757ms 3.46% AbstractCellProperty::IsType (inline) 19ms 0.018% 62.57% 3588ms 3.31% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 84ms 0.077% 62.64% 3240ms 2.98% Cell::SetCellProliferativeType 2161ms 1.99% 64.63% 3099ms 2.85% _int_malloc 889ms 0.82% 65.45% 3080ms 2.84% AbstractElement::GetNodeLocation 0 0% 65.45% 3075ms 2.83% std::insert_iterator::operator= (inline) 58ms 0.053% 65.51% 3000ms 2.76% std::_Rb_tree::erase 269ms 0.25% 65.75% 2720ms 2.51% VertexMesh::GetAreaGradientOfElementAtNode 17ms 0.016% 65.77% 2677ms 2.47% CellPropertyCollection::HasProperty 6ms 0.0055% 65.78% 2672ms 2.46% std::_Rb_tree::_M_insert_unique_ (inline) 2652ms 2.44% 68.22% 2652ms 2.44% std::_Rb_tree::_S_right (inline) 0 0% 68.22% 2617ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 692ms 0.64% 68.86% 2610ms 2.40% boost::numeric::ublas::vector_binary::size (inline) 0 0% 68.86% 2606ms 2.40% Cell::HasCellProperty (inline) 0 0% 68.86% 2605ms 2.40% boost::numeric::ublas::c_vector::assign (inline) 754ms 0.69% 69.55% 2596ms 2.39% AbstractCellProperty::IsSame 258ms 0.24% 69.79% 2576ms 2.37% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.00092% 69.79% 2447ms 2.25% std::_Rb_tree::_M_insert_unique 0 0% 69.79% 2441ms 2.25% AbstractCellPopulation::WriteResultsToFiles 91ms 0.084% 69.87% 2415ms 2.22% VertexMesh::GetVolumeOfElement 15ms 0.014% 69.89% 2353ms 2.17% Cell::GetCellData 65ms 0.06% 69.95% 2177ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.0037% 69.95% 2158ms 1.99% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.95% 2158ms 1.99% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 38ms 0.035% 69.99% 2092ms 1.93% std::_Rb_tree::_M_emplace_hint_unique 2059ms 1.90% 71.88% 2059ms 1.90% std::_Rb_tree_increment 0 0% 71.88% 2020ms 1.86% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 71.88% 2015ms 1.86% AbstractCellPopulation::Iterator::operator++ (inline) 164ms 0.15% 72.04% 2003ms 1.85% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.00092% 72.04% 2002ms 1.84% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1254ms 1.16% 73.19% 1901ms 1.75% std::_Rb_tree::equal_range (inline) 78ms 0.072% 73.26% 1880ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 455ms 0.42% 73.68% 1842ms 1.70% std::type_info::operator== (inline) 1ms 0.00092% 73.68% 1786ms 1.65% VertexMeshWriter::WriteVtkUsingMesh 31ms 0.029% 73.71% 1569ms 1.45% VertexMesh::GetSurfaceAreaOfElement 28ms 0.026% 73.74% 1547ms 1.43% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 63ms 0.058% 73.80% 1483ms 1.37% Node::RemoveElement 65ms 0.06% 73.86% 1443ms 1.33% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.0074% 73.86% 1425ms 1.31% std::set::erase (inline) 29ms 0.027% 73.89% 1419ms 1.31% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.89% 1379ms 1.27% boost::numeric::ublas::norm_2 (inline) 78ms 0.072% 73.96% 1353ms 1.25% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 584ms 0.54% 74.50% 1353ms 1.25% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 0 0% 74.50% 1335ms 1.23% OffLatticeSimulation::ApplyBoundaries 1321ms 1.22% 75.72% 1321ms 1.22% [libchaste_cell_based.so] 71ms 0.065% 75.78% 1289ms 1.19% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 75.78% 1286ms 1.18% boost::numeric::ublas::vector_binary::operator() (inline) 142ms 0.13% 75.91% 1282ms 1.18% CellPropertyCollection::AddProperty 0 0% 75.91% 1269ms 1.17% tcache_get (inline) 1269ms 1.17% 77.08% 1269ms 1.17% tcache_get_n (inline) 61ms 0.056% 77.14% 1162ms 1.07% std::less::operator() (inline) 41ms 0.038% 77.18% 1125ms 1.04% CellPropertyRegistry::Get 0 0% 77.18% 1124ms 1.04% boost::numeric::ublas::c_vector::assign_temporary (inline) 15ms 0.014% 77.19% 1123ms 1.03% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 7ms 0.0064% 77.20% 1123ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 0 0% 77.20% 1118ms 1.03% std::_Rb_tree::_Auto_node::_Auto_node (inline) 107ms 0.099% 77.29% 1116ms 1.03% std::swap_ranges (inline) 0 0% 77.29% 1106ms 1.02% std::_Rb_tree::clear (inline) 900ms 0.83% 78.12% 1101ms 1.01% std::operator< (inline) 6ms 0.0055% 78.13% 1091ms 1.00% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 15ms 0.014% 78.14% 1091ms 1.00% boost::numeric::ublas::detail::expression_type_check (inline) 1080ms 0.99% 79.14% 1080ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 79.14% 1079ms 0.99% std::map::clear (inline) 201ms 0.19% 79.32% 1066ms 0.98% boost::numeric::ublas::detail::equals 1055ms 0.97% 80.29% 1055ms 0.97% Node::rGetLocation 129ms 0.12% 80.41% 1051ms 0.97% boost::detail::shared_count::~shared_count (inline) 0 0% 80.41% 1051ms 0.97% boost::shared_ptr::~shared_ptr (inline) 103ms 0.095% 80.51% 1040ms 0.96% std::_Rb_tree::find (inline) 1010ms 0.93% 81.44% 1010ms 0.93% std::swap (inline) 0 0% 81.44% 1009ms 0.93% std::iter_swap (inline) 0 0% 81.44% 911ms 0.84% std::map::find (inline) 904ms 0.83% 82.27% 904ms 0.83% [libchaste_mesh.so] 846ms 0.78% 83.05% 877ms 0.81% boost::detail::sp_counted_base::release 33ms 0.03% 83.08% 875ms 0.81% MutableElement::RegisterWithEdges (inline) 44ms 0.041% 83.12% 859ms 0.79% Edge::AddElement 0 0% 83.12% 859ms 0.79% VertexMeshWriter::MakeVtkMesh 838ms 0.77% 83.89% 838ms 0.77% std::vector::size (inline) 0 0% 83.89% 829ms 0.76% CellPropertyCollection::~CellPropertyCollection (inline) 246ms 0.23% 84.12% 796ms 0.73% std::__new_allocator::construct (inline) 0 0% 84.12% 796ms 0.73% std::allocator_traits::construct (inline) 90ms 0.083% 84.20% 794ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.20% 779ms 0.72% boost::numeric::ublas::norm_inf (inline) 416ms 0.38% 84.59% 779ms 0.72% boost::numeric::ublas::vector_norm_inf::apply (inline) 167ms 0.15% 84.74% 735ms 0.68% boost::shared_ptr::shared_ptr (inline) 0 0% 84.74% 729ms 0.67% std::_Rb_tree::_M_construct_node (inline) 401ms 0.37% 85.11% 728ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.11% 711ms 0.65% std::_Vector_base::_M_allocate (inline) 378ms 0.35% 85.46% 710ms 0.65% Edge::GetMapIndex 115ms 0.11% 85.56% 705ms 0.65% MutableElement::GetNodeLocalIndex 0 0% 85.56% 684ms 0.63% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 667ms 0.61% 86.18% 667ms 0.61% Node::GetIndex 42ms 0.039% 86.22% 664ms 0.61% MutableElement::RegisterWithNodes (inline) 34ms 0.031% 86.25% 627ms 0.58% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.25% 627ms 0.58% boost::numeric::ublas::vector::vector (inline) 0 0% 86.25% 625ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.018% 86.27% 625ms 0.58% std::_Rb_tree::_M_insert_node (inline) 621ms 0.57% 86.84% 621ms 0.57% [libstdc++.so.6.0.33] 1ms 0.00092% 86.84% 620ms 0.57% vtkPolygon::New 4ms 0.0037% 86.84% 619ms 0.57% vtkPolygon::vtkPolygon 27ms 0.025% 86.87% 592ms 0.55% Node::AddElement 8ms 0.0074% 86.88% 592ms 0.55% std::vector::_M_default_append (inline) 570ms 0.53% 87.40% 570ms 0.53% boost::shared_ptr::operator-> (inline) 535ms 0.49% 87.89% 568ms 0.52% boost::detail::shared_count::shared_count (inline)