File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 96363ms, 87.43% of 110222ms total Dropped 1079 nodes (cum <= 551.11ms) flat flat% sum% cum cum% 0 0% 0% 109881ms 99.69% __libc_start_call_main 0 0% 0% 109881ms 99.69% __libc_start_main_impl 0 0% 0% 109881ms 99.69% _start 0 0% 0% 109859ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 109859ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 109859ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 109859ms 99.67% main 0 0% 0% 109817ms 99.63% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 109817ms 99.63% CxxTest::TestRunner::runTest (inline) 0 0% 0% 109817ms 99.63% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 4ms 0.0036% 0.0036% 109810ms 99.63% AbstractCellBasedSimulation::Solve 17ms 0.015% 0.019% 57098ms 51.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.018% 0.037% 53756ms 48.77% ForwardEulerNumericalMethod::UpdateAllNodePositions 138ms 0.13% 0.16% 52635ms 47.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 284ms 0.26% 0.42% 40288ms 36.55% NagaiHondaForce::AddForceContribution 0 0% 0.42% 39575ms 35.90% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.00091% 0.42% 24508ms 22.24% VertexBasedCellPopulation::Update 0 0% 0.42% 24355ms 22.10% MutableVertexMesh::ReMesh 14648ms 13.29% 13.71% 23241ms 21.09% Cylindrical2dVertexMesh::GetVectorFromAtoB 102ms 0.093% 13.80% 17731ms 16.09% Cell::ReadyToDivide 66ms 0.06% 13.86% 16434ms 14.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 364ms 0.33% 14.19% 14722ms 13.36% NagaiHondaForce::GetAdhesionParameter 169ms 0.15% 14.35% 14193ms 12.88% SimpleWntCellCycleModel::UpdateCellCyclePhase 505ms 0.46% 14.80% 13833ms 12.55% boost::numeric::ublas::c_vector::c_vector (partial-inline) 115ms 0.1% 14.91% 13636ms 12.37% CellPropertyCollection::GetPropertiesType (inline) 360ms 0.33% 15.24% 12305ms 11.16% boost::numeric::ublas::vector_assign (inline) 146ms 0.13% 15.37% 11846ms 10.75% MutableVertexMesh::CheckForIntersections 83ms 0.075% 15.44% 11725ms 10.64% VertexBasedCellPopulation::GetDampingConstant 3575ms 3.24% 18.69% 11616ms 10.54% __dynamic_cast 75ms 0.068% 18.75% 11504ms 10.44% AbstractCellProperty::IsSubType (inline) 62ms 0.056% 18.81% 10571ms 9.59% AbstractTargetAreaModifier::UpdateTargetAreas 35ms 0.032% 18.84% 10489ms 9.52% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 39ms 0.035% 18.88% 10343ms 9.38% AbstractCellBasedSimulation::DoCellBirth 1525ms 1.38% 20.26% 10267ms 9.31% std::__new_allocator::allocate (inline) 0 0% 20.26% 9745ms 8.84% std::_Rb_tree::_M_create_node (inline) 0 0% 20.26% 9693ms 8.79% std::allocator_traits::allocate (inline) 2760ms 2.50% 22.77% 9243ms 8.39% boost::numeric::ublas::indexing_vector_assign 327ms 0.3% 23.06% 9197ms 8.34% VertexMesh::GetNextEdgeGradientOfElementAtNode 1220ms 1.11% 24.17% 9061ms 8.22% std::_Rb_tree::_M_erase 0 0% 24.17% 9002ms 8.17% std::_Rb_tree::_M_get_node (inline) 39ms 0.035% 24.20% 8984ms 8.15% VertexBasedCellPopulation::GetLocationOfCellCentre 808ms 0.73% 24.94% 8824ms 8.01% operator new 93ms 0.084% 25.02% 8655ms 7.85% Cell::GetMutationState 856ms 0.78% 25.80% 8608ms 7.81% VertexMesh::ElementIncludesPoint 0 0% 25.80% 8557ms 7.76% std::_Rb_tree::_Alloc_node::operator() (inline) 490ms 0.44% 26.24% 8381ms 7.60% VertexMesh::GetCentroidOfElement 0 0% 26.24% 8212ms 7.45% std::_Rb_tree::_M_drop_node (inline) 229ms 0.21% 26.45% 8166ms 7.41% std::_Rb_tree::~_Rb_tree (inline) 504ms 0.46% 26.91% 8092ms 7.34% std::map::operator[] (partial-inline) 16ms 0.015% 26.92% 8048ms 7.30% MutableVertexMesh::RemoveDeletedNodesAndElements 228ms 0.21% 27.13% 7962ms 7.22% std::__new_allocator::deallocate (inline) 0 0% 27.13% 7953ms 7.22% std::allocator_traits::deallocate (inline) 0 0% 27.13% 7889ms 7.16% std::_Rb_tree::_M_put_node (inline) 2786ms 2.53% 29.66% 7804ms 7.08% __GI___libc_malloc 0 0% 29.66% 7752ms 7.03% std::set::~set (inline) 170ms 0.15% 29.81% 7531ms 6.83% std::_Rb_tree::_Rb_tree (partial-inline) 2277ms 2.07% 31.88% 7457ms 6.77% __GI___libc_free 1452ms 1.32% 33.19% 7402ms 6.72% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 785ms 0.71% 33.91% 7115ms 6.46% std::_Rb_tree::_M_copy (inline) 23ms 0.021% 33.93% 7032ms 6.38% std::set::set (inline) 121ms 0.11% 34.04% 6500ms 5.90% SimpleWntCellCycleModel::GetWntLevel 2499ms 2.27% 36.30% 6465ms 5.87% std::_Rb_tree::_M_lower_bound (inline) 6310ms 5.72% 42.03% 6310ms 5.72% __strcmp_avx2 161ms 0.15% 42.18% 6305ms 5.72% WntConcentration::GetWntLevel 916ms 0.83% 43.01% 6103ms 5.54% std::_Rb_tree::_M_clone_node (inline) 5991ms 5.44% 48.44% 5991ms 5.44% boost::numeric::ublas::c_vector::operator() 29ms 0.026% 48.47% 5632ms 5.11% MutableVertexMesh::RemoveDeletedNodes 2854ms 2.59% 51.06% 5465ms 4.96% __cxxabiv1::__si_class_type_info::__do_dyncast 29ms 0.026% 51.08% 5404ms 4.90% EdgeHelper::RemoveDeletedEdges 0 0% 51.08% 5298ms 4.81% std::_Rb_tree::lower_bound (inline) 0 0% 51.08% 5298ms 4.81% std::map::lower_bound (inline) 0 0% 51.08% 5268ms 4.78% std::set::insert (inline) 1972ms 1.79% 52.87% 5236ms 4.75% boost::numeric::ublas::c_vector::operator[] (inline) 4719ms 4.28% 57.15% 5168ms 4.69% _int_free 38ms 0.034% 57.19% 5092ms 4.62% EdgeHelper::UpdateEdgesMapKey 220ms 0.2% 57.39% 4936ms 4.48% MutableElement::ResetIndex 127ms 0.12% 57.50% 4785ms 4.34% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.00091% 57.50% 4712ms 4.28% AbstractCellBasedSimulation::DoCellRemoval (inline) 509ms 0.46% 57.97% 4472ms 4.06% std::_Rb_tree::_M_insert_ (inline) 139ms 0.13% 58.09% 4276ms 3.88% std::set_intersection (inline) 232ms 0.21% 58.30% 4137ms 3.75% std::__set_intersection 39ms 0.035% 58.34% 3876ms 3.52% Cell::GetCellProliferativeType 3732ms 3.39% 61.72% 3732ms 3.39% boost::numeric::ublas::same_impl_ex 60ms 0.054% 61.78% 3726ms 3.38% AbstractCellProperty::IsType (inline) 12ms 0.011% 61.79% 3587ms 3.25% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 2386ms 2.16% 63.95% 3334ms 3.02% _int_malloc 3327ms 3.02% 66.97% 3327ms 3.02% std::_Rb_tree::_S_right (inline) 0 0% 66.97% 3199ms 2.90% std::insert_iterator::operator= (inline) 73ms 0.066% 67.04% 3185ms 2.89% std::_Rb_tree::erase 65ms 0.059% 67.10% 3143ms 2.85% Cell::SetCellProliferativeType 892ms 0.81% 67.91% 3050ms 2.77% AbstractElement::GetNodeLocation 9ms 0.0082% 67.92% 2823ms 2.56% std::_Rb_tree::_M_insert_unique_ (inline) 50ms 0.045% 67.96% 2652ms 2.41% CellPropertyCollection::HasProperty 0 0% 67.96% 2605ms 2.36% boost::numeric::ublas::c_vector::operator-= (inline) 213ms 0.19% 68.15% 2601ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 708ms 0.64% 68.80% 2585ms 2.35% AbstractCellProperty::IsSame 0 0% 68.80% 2570ms 2.33% Cell::HasCellProperty (inline) 581ms 0.53% 69.32% 2566ms 2.33% boost::numeric::ublas::vector_binary::size (inline) 259ms 0.23% 69.56% 2528ms 2.29% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 69.56% 2524ms 2.29% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.56% 2445ms 2.22% std::_Rb_tree::_M_insert_unique (inline) 36ms 0.033% 69.59% 2438ms 2.21% Cell::GetCellData 0 0% 69.59% 2437ms 2.21% boost::numeric::ublas::c_vector::assign (inline) 1ms 0.00091% 69.59% 2311ms 2.10% AbstractCellPopulation::Iterator::operator++ (inline) 93ms 0.084% 69.68% 2309ms 2.09% VertexMesh::GetVolumeOfElement 172ms 0.16% 69.83% 2305ms 2.09% AbstractCellPopulation::Iterator::IsRealCell (inline) 35ms 0.032% 69.86% 2248ms 2.04% std::_Rb_tree::_M_emplace_hint_unique 51ms 0.046% 69.91% 2160ms 1.96% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0018% 69.91% 2126ms 1.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 69.91% 2126ms 1.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1424ms 1.29% 71.20% 2091ms 1.90% std::_Rb_tree::equal_range (inline) 0 0% 71.20% 2059ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 2ms 0.0018% 71.21% 2045ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2003ms 1.82% 73.02% 2003ms 1.82% std::_Rb_tree_increment 478ms 0.43% 73.46% 1877ms 1.70% std::type_info::operator== (inline) 70ms 0.064% 73.52% 1871ms 1.70% MutableVertexMesh::CheckForSwapsFromShortEdges 26ms 0.024% 73.54% 1846ms 1.67% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.00091% 73.55% 1838ms 1.67% VertexMeshWriter::WriteVtkUsingMesh 49ms 0.044% 73.59% 1587ms 1.44% Node::RemoveElement 82ms 0.074% 73.66% 1580ms 1.43% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 44ms 0.04% 73.70% 1580ms 1.43% VertexMesh::GetSurfaceAreaOfElement 36ms 0.033% 73.74% 1565ms 1.42% AbstractCellPopulation::GetLocationIndexUsingCell 9ms 0.0082% 73.74% 1542ms 1.40% std::set::erase (inline) 0 0% 73.74% 1497ms 1.36% tcache_get (inline) 1497ms 1.36% 75.10% 1497ms 1.36% tcache_get_n (inline) 0 0% 75.10% 1367ms 1.24% boost::numeric::ublas::norm_2 (inline) 127ms 0.12% 75.22% 1361ms 1.23% CellPropertyCollection::AddProperty 68ms 0.062% 75.28% 1357ms 1.23% boost::numeric::ublas::vector_reference::operator() (inline) 596ms 0.54% 75.82% 1354ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1ms 0.00091% 75.82% 1346ms 1.22% OffLatticeSimulation::ApplyBoundaries 0 0% 75.82% 1343ms 1.22% boost::numeric::ublas::vector_binary::operator() (inline) 70ms 0.064% 75.89% 1333ms 1.21% std::less::operator() (inline) 1320ms 1.20% 77.08% 1320ms 1.20% [libchaste_cell_based.so] 1060ms 0.96% 78.04% 1263ms 1.15% std::operator< (inline) 79ms 0.072% 78.12% 1222ms 1.11% std::_Rb_tree::_M_erase_aux (partial-inline) 0 0% 78.12% 1188ms 1.08% std::_Rb_tree::_Auto_node::_Auto_node (inline) 1168ms 1.06% 79.18% 1168ms 1.06% std::_Rb_tree_insert_and_rebalance 16ms 0.015% 79.19% 1159ms 1.05% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 84ms 0.076% 79.27% 1151ms 1.04% std::_Rb_tree::find (inline) 26ms 0.024% 79.29% 1144ms 1.04% CellPropertyRegistry::Get 1ms 0.00091% 79.29% 1129ms 1.02% std::_Rb_tree::clear (inline) 0 0% 79.29% 1110ms 1.01% std::map::clear (inline) 5ms 0.0045% 79.30% 1093ms 0.99% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 20ms 0.018% 79.31% 1082ms 0.98% boost::numeric::ublas::detail::expression_type_check (inline) 1081ms 0.98% 80.29% 1081ms 0.98% Node::rGetLocation 0 0% 80.29% 1062ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 17ms 0.015% 80.31% 1062ms 0.96% boost::numeric::ublas::c_vector::swap (inline) 222ms 0.2% 80.51% 1053ms 0.96% boost::numeric::ublas::detail::equals 103ms 0.093% 80.60% 1045ms 0.95% std::swap_ranges (inline) 1ms 0.00091% 80.61% 1008ms 0.91% std::map::find (inline) 99ms 0.09% 80.70% 997ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 80.70% 997ms 0.9% boost::shared_ptr::~shared_ptr (inline) 0 0% 80.70% 942ms 0.85% std::iter_swap (inline) 942ms 0.85% 81.55% 942ms 0.85% std::swap (inline) 0 0% 81.55% 875ms 0.79% VertexMeshWriter::MakeVtkMesh 872ms 0.79% 82.34% 872ms 0.79% std::vector::size (inline) 827ms 0.75% 83.09% 859ms 0.78% boost::detail::sp_counted_base::release 418ms 0.38% 83.47% 816ms 0.74% Edge::GetMapIndex 440ms 0.4% 83.87% 813ms 0.74% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 105ms 0.095% 83.97% 802ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 239ms 0.22% 84.18% 793ms 0.72% std::__new_allocator::construct (inline) 0 0% 84.18% 793ms 0.72% std::allocator_traits::construct (inline) 788ms 0.71% 84.90% 788ms 0.71% [libchaste_mesh.so] 170ms 0.15% 85.05% 761ms 0.69% boost::shared_ptr::shared_ptr (inline) 0 0% 85.05% 759ms 0.69% boost::numeric::ublas::norm_inf (inline) 427ms 0.39% 85.44% 759ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 28ms 0.025% 85.46% 755ms 0.68% MutableElement::RegisterWithEdges (inline) 16ms 0.015% 85.48% 744ms 0.68% Edge::AddElement 0 0% 85.48% 743ms 0.67% std::_Rb_tree::_M_construct_node (inline) 0 0% 85.48% 742ms 0.67% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 85.48% 738ms 0.67% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 133ms 0.12% 85.60% 737ms 0.67% MutableElement::GetNodeLocalIndex 688ms 0.62% 86.22% 688ms 0.62% [libstdc++.so.6.0.33] 0 0% 86.22% 688ms 0.62% std::_Vector_base::_M_allocate (inline) 670ms 0.61% 86.83% 670ms 0.61% Node::GetIndex 0 0% 86.83% 656ms 0.6% vtkPolygon::New 1ms 0.00091% 86.83% 656ms 0.6% vtkPolygon::vtkPolygon 0 0% 86.83% 643ms 0.58% std::_Rb_tree::_Auto_node::_M_insert (inline) 15ms 0.014% 86.85% 643ms 0.58% std::_Rb_tree::_M_insert_node (inline) 38ms 0.034% 86.88% 633ms 0.57% MutableElement::RegisterWithNodes (inline) 26ms 0.024% 86.90% 600ms 0.54% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.90% 600ms 0.54% boost::numeric::ublas::vector::vector (inline) 561ms 0.51% 87.41% 591ms 0.54% boost::detail::shared_count::shared_count (inline) 15ms 0.014% 87.43% 585ms 0.53% Node::AddElement