File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 95921ms, 88.10% of 108875ms total Dropped 1116 nodes (cum <= 544.38ms) flat flat% sum% cum cum% 0 0% 0% 108393ms 99.56% __libc_start_call_main 0 0% 0% 108393ms 99.56% __libc_start_main_impl 0 0% 0% 108393ms 99.56% _start 0 0% 0% 108372ms 99.54% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108372ms 99.54% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108372ms 99.54% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108372ms 99.54% main 0 0% 0% 108333ms 99.50% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108333ms 99.50% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108333ms 99.50% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0046% 0.0046% 108326ms 99.50% AbstractCellBasedSimulation::Solve 9ms 0.0083% 0.013% 56060ms 51.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 22ms 0.02% 0.033% 52830ms 48.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 131ms 0.12% 0.15% 51341ms 47.16% AbstractNumericalMethod::ComputeForcesIncludingDamping 364ms 0.33% 0.49% 39667ms 36.43% NagaiHondaForce::AddForceContribution 2ms 0.0018% 0.49% 39130ms 35.94% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.49% 24324ms 22.34% VertexBasedCellPopulation::Update 1ms 0.00092% 0.49% 24205ms 22.23% MutableVertexMesh::ReMesh 14544ms 13.36% 13.85% 22988ms 21.11% Cylindrical2dVertexMesh::GetVectorFromAtoB 122ms 0.11% 13.96% 17628ms 16.19% Cell::ReadyToDivide 69ms 0.063% 14.03% 16274ms 14.95% AbstractPhaseBasedCellCycleModel::ReadyToDivide 383ms 0.35% 14.38% 14649ms 13.45% NagaiHondaForce::GetAdhesionParameter 387ms 0.36% 14.73% 14196ms 13.04% boost::numeric::ublas::c_vector::c_vector (partial-inline) 134ms 0.12% 14.86% 13933ms 12.80% SimpleWntCellCycleModel::UpdateCellCyclePhase 123ms 0.11% 14.97% 13644ms 12.53% CellPropertyCollection::GetPropertiesType (inline) 382ms 0.35% 15.32% 12709ms 11.67% boost::numeric::ublas::vector_assign (inline) 143ms 0.13% 15.45% 12114ms 11.13% MutableVertexMesh::CheckForIntersections 61ms 0.056% 15.51% 11176ms 10.26% VertexBasedCellPopulation::GetDampingConstant 3120ms 2.87% 18.37% 11128ms 10.22% __dynamic_cast 69ms 0.063% 18.44% 11017ms 10.12% AbstractCellProperty::IsSubType (inline) 78ms 0.072% 18.51% 10632ms 9.77% AbstractTargetAreaModifier::UpdateTargetAreas 60ms 0.055% 18.56% 10536ms 9.68% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 38ms 0.035% 18.60% 10239ms 9.40% AbstractCellBasedSimulation::DoCellBirth 1334ms 1.23% 19.82% 10211ms 9.38% std::__new_allocator::allocate (inline) 0 0% 19.82% 9720ms 8.93% std::_Rb_tree::_M_create_node (inline) 0 0% 19.82% 9692ms 8.90% std::allocator_traits::allocate (inline) 2719ms 2.50% 22.32% 9433ms 8.66% boost::numeric::ublas::indexing_vector_assign 835ms 0.77% 23.09% 9097ms 8.36% VertexMesh::ElementIncludesPoint 800ms 0.73% 23.82% 9033ms 8.30% operator new 0 0% 23.82% 9018ms 8.28% std::_Rb_tree::_M_get_node (inline) 1325ms 1.22% 25.04% 9015ms 8.28% std::_Rb_tree::_M_erase 350ms 0.32% 25.36% 8823ms 8.10% VertexMesh::GetNextEdgeGradientOfElementAtNode 27ms 0.025% 25.39% 8684ms 7.98% VertexBasedCellPopulation::GetLocationOfCellCentre 59ms 0.054% 25.44% 8634ms 7.93% Cell::GetMutationState 0 0% 25.44% 8534ms 7.84% std::_Rb_tree::_Alloc_node::operator() (inline) 476ms 0.44% 25.88% 8233ms 7.56% VertexMesh::GetCentroidOfElement 242ms 0.22% 26.10% 8211ms 7.54% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.10% 8145ms 7.48% std::_Rb_tree::_M_drop_node (inline) 3462ms 3.18% 29.28% 8081ms 7.42% __GI___libc_malloc 265ms 0.24% 29.52% 7981ms 7.33% std::__new_allocator::deallocate (inline) 0 0% 29.52% 7945ms 7.30% std::allocator_traits::deallocate (inline) 0 0% 29.52% 7857ms 7.22% std::_Rb_tree::_M_put_node (inline) 3146ms 2.89% 32.41% 7816ms 7.18% __GI___libc_free 0 0% 32.41% 7762ms 7.13% std::set::~set (inline) 14ms 0.013% 32.43% 7670ms 7.04% MutableVertexMesh::RemoveDeletedNodesAndElements 470ms 0.43% 32.86% 7474ms 6.86% std::map::operator[] (partial-inline) 1395ms 1.28% 34.14% 7068ms 6.49% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 193ms 0.18% 34.32% 6868ms 6.31% std::_Rb_tree::_Rb_tree (partial-inline) 646ms 0.59% 34.91% 6449ms 5.92% std::_Rb_tree::_M_copy (inline) 6430ms 5.91% 40.81% 6430ms 5.91% __strcmp_avx2 10ms 0.0092% 40.82% 6366ms 5.85% std::set::set (inline) 104ms 0.096% 40.92% 6306ms 5.79% SimpleWntCellCycleModel::GetWntLevel 6191ms 5.69% 46.61% 6191ms 5.69% boost::numeric::ublas::c_vector::operator() 134ms 0.12% 46.73% 6121ms 5.62% WntConcentration::GetWntLevel 2513ms 2.31% 49.04% 5862ms 5.38% std::_Rb_tree::_M_lower_bound (inline) 0 0% 49.04% 5595ms 5.14% std::set::insert (inline) 2739ms 2.52% 51.55% 5583ms 5.13% __cxxabiv1::__si_class_type_info::__do_dyncast 697ms 0.64% 52.19% 5521ms 5.07% std::_Rb_tree::_M_clone_node (inline) 32ms 0.029% 52.22% 5497ms 5.05% MutableVertexMesh::RemoveDeletedNodes 39ms 0.036% 52.26% 5335ms 4.90% EdgeHelper::RemoveDeletedEdges 36ms 0.033% 52.29% 5039ms 4.63% EdgeHelper::UpdateEdgesMapKey 1534ms 1.41% 53.70% 4954ms 4.55% boost::numeric::ublas::c_vector::operator[] (inline) 539ms 0.5% 54.20% 4766ms 4.38% std::_Rb_tree::_M_insert_ (inline) 0 0% 54.20% 4739ms 4.35% std::_Rb_tree::lower_bound (inline) 0 0% 54.20% 4739ms 4.35% std::map::lower_bound (inline) 225ms 0.21% 54.40% 4707ms 4.32% MutableElement::ResetIndex 4343ms 3.99% 58.39% 4661ms 4.28% _int_free 0 0% 58.39% 4551ms 4.18% AbstractCellBasedSimulation::DoCellRemoval (inline) 90ms 0.083% 58.47% 4515ms 4.15% std::set_intersection (inline) 286ms 0.26% 58.74% 4425ms 4.06% std::__set_intersection 101ms 0.093% 58.83% 4047ms 3.72% AbstractCellPopulation::GetCellUsingLocationIndex 3913ms 3.59% 62.42% 3913ms 3.59% boost::numeric::ublas::same_impl_ex 46ms 0.042% 62.47% 3908ms 3.59% Cell::GetCellProliferativeType 63ms 0.058% 62.52% 3815ms 3.50% AbstractCellProperty::IsType (inline) 5ms 0.0046% 62.53% 3460ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 39ms 0.036% 62.56% 3176ms 2.92% Cell::SetCellProliferativeType 0 0% 62.56% 3174ms 2.92% std::insert_iterator::operator= (inline) 2201ms 2.02% 64.59% 3158ms 2.90% _int_malloc 879ms 0.81% 65.39% 3127ms 2.87% AbstractElement::GetNodeLocation 36ms 0.033% 65.43% 3057ms 2.81% std::_Rb_tree::erase 623ms 0.57% 66.00% 2847ms 2.61% boost::numeric::ublas::vector_binary::size (inline) 431ms 0.4% 66.39% 2815ms 2.59% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.0055% 66.40% 2813ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0018% 66.40% 2782ms 2.56% std::_Rb_tree::_M_insert_unique 2768ms 2.54% 68.94% 2768ms 2.54% std::_Rb_tree::_S_right (inline) 692ms 0.64% 69.58% 2746ms 2.52% AbstractCellProperty::IsSame 38ms 0.035% 69.61% 2709ms 2.49% CellPropertyCollection::HasProperty 0 0% 69.61% 2609ms 2.40% Cell::HasCellProperty (inline) 0 0% 69.61% 2467ms 2.27% AbstractCellPopulation::WriteResultsToFiles 0 0% 69.61% 2443ms 2.24% boost::numeric::ublas::c_vector::operator-= (inline) 252ms 0.23% 69.85% 2411ms 2.21% VertexMesh::GetAreaGradientOfElementAtNode 25ms 0.023% 69.87% 2389ms 2.19% Cell::GetCellData 0 0% 69.87% 2328ms 2.14% boost::numeric::ublas::c_vector::assign (inline) 98ms 0.09% 69.96% 2289ms 2.10% VertexMesh::GetVolumeOfElement 123ms 0.11% 70.07% 2250ms 2.07% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 2211ms 2.03% 72.10% 2211ms 2.03% std::_Rb_tree_increment 28ms 0.026% 72.13% 2205ms 2.03% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.0018% 72.13% 2154ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 233ms 0.21% 72.34% 2148ms 1.97% AbstractCellPopulation::Iterator::IsRealCell (inline) 475ms 0.44% 72.78% 2054ms 1.89% std::type_info::operator== (inline) 1395ms 1.28% 74.06% 2050ms 1.88% std::_Rb_tree::equal_range (inline) 0 0% 74.06% 2031ms 1.87% VertexBasedCellPopulation::WriteVtkResultsToFile 3ms 0.0028% 74.06% 2021ms 1.86% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0018% 74.07% 1905ms 1.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.07% 1905ms 1.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 59ms 0.054% 74.12% 1805ms 1.66% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 74.12% 1805ms 1.66% VertexMeshWriter::WriteVtkUsingMesh 155ms 0.14% 74.26% 1786ms 1.64% CellPropertyCollection::AddProperty 22ms 0.02% 74.28% 1645ms 1.51% VertexMesh::GetSurfaceAreaOfElement 20ms 0.018% 74.30% 1634ms 1.50% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 51ms 0.047% 74.35% 1583ms 1.45% Node::RemoveElement 15ms 0.014% 74.36% 1543ms 1.42% std::set::erase (inline) 112ms 0.1% 74.46% 1501ms 1.38% boost::numeric::ublas::vector_reference::operator() (inline) 18ms 0.017% 74.48% 1489ms 1.37% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.07% 74.55% 1440ms 1.32% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.55% 1432ms 1.32% boost::numeric::ublas::vector_binary::operator() (inline) 2ms 0.0018% 74.55% 1296ms 1.19% OffLatticeSimulation::ApplyBoundaries 0 0% 74.55% 1293ms 1.19% tcache_get (inline) 1293ms 1.19% 75.74% 1293ms 1.19% tcache_get_n (inline) 66ms 0.061% 75.80% 1255ms 1.15% std::less::operator() (inline) 81ms 0.074% 75.88% 1196ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 941ms 0.86% 76.74% 1189ms 1.09% std::operator< (inline) 0 0% 76.74% 1186ms 1.09% std::_Rb_tree::_Auto_node::_Auto_node (inline) 0 0% 76.74% 1177ms 1.08% boost::numeric::ublas::norm_2 (inline) 522ms 0.48% 77.22% 1172ms 1.08% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 20ms 0.018% 77.24% 1164ms 1.07% CellPropertyRegistry::Get 22ms 0.02% 77.26% 1115ms 1.02% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 1115ms 1.02% 78.28% 1115ms 1.02% Node::rGetLocation 1112ms 1.02% 79.30% 1112ms 1.02% std::_Rb_tree_insert_and_rebalance 101ms 0.093% 79.40% 1097ms 1.01% std::_Rb_tree::find (inline) 1086ms 1% 80.39% 1086ms 1% [libchaste_cell_based.so] 1ms 0.00092% 80.39% 1051ms 0.97% std::_Rb_tree::clear (inline) 8ms 0.0073% 80.40% 1041ms 0.96% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 80.40% 1032ms 0.95% std::map::clear (inline) 23ms 0.021% 80.42% 984ms 0.9% boost::numeric::ublas::detail::expression_type_check (inline) 982ms 0.9% 81.32% 982ms 0.9% std::vector::size (inline) 126ms 0.12% 81.44% 981ms 0.9% boost::detail::shared_count::~shared_count (inline) 0 0% 81.44% 981ms 0.9% boost::shared_ptr::~shared_ptr (inline) 382ms 0.35% 81.79% 967ms 0.89% Edge::GetMapIndex 171ms 0.16% 81.95% 942ms 0.87% boost::numeric::ublas::detail::equals 920ms 0.85% 82.79% 920ms 0.85% [libchaste_mesh.so] 0 0% 82.79% 903ms 0.83% boost::numeric::ublas::c_vector::assign_temporary (inline) 7ms 0.0064% 82.80% 903ms 0.83% boost::numeric::ublas::c_vector::swap 0 0% 82.80% 898ms 0.82% std::map::find (inline) 74ms 0.068% 82.87% 896ms 0.82% std::swap_ranges (inline) 0 0% 82.87% 875ms 0.8% VertexMeshWriter::MakeVtkMesh 820ms 0.75% 83.62% 828ms 0.76% boost::detail::sp_counted_base::release 823ms 0.76% 84.38% 823ms 0.76% std::swap (inline) 0 0% 84.38% 822ms 0.75% std::iter_swap (inline) 92ms 0.085% 84.46% 818ms 0.75% MutableElement::GetNodeLocalIndex 123ms 0.11% 84.57% 811ms 0.74% boost::shared_ptr::shared_ptr (inline) 101ms 0.093% 84.67% 773ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 764ms 0.7% 85.37% 764ms 0.7% Node::GetIndex 110ms 0.1% 85.47% 757ms 0.7% std::__new_allocator::construct (inline) 0 0% 85.47% 757ms 0.7% std::allocator_traits::construct (inline) 16ms 0.015% 85.48% 741ms 0.68% MutableElement::RegisterWithEdges (inline) 0 0% 85.48% 735ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 21ms 0.019% 85.50% 734ms 0.67% Edge::AddElement 420ms 0.39% 85.89% 734ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 85.89% 728ms 0.67% boost::numeric::ublas::norm_inf (inline) 384ms 0.35% 86.24% 728ms 0.67% boost::numeric::ublas::vector_norm_inf::apply (inline) 22ms 0.02% 86.26% 720ms 0.66% AbstractNumericalMethod::DetectStepSizeExceptions 0 0% 86.26% 702ms 0.64% std::_Rb_tree::_M_construct_node (inline) 94ms 0.086% 86.35% 698ms 0.64% VertexBasedCellPopulation::CheckForStepSizeException 660ms 0.61% 86.95% 688ms 0.63% boost::detail::shared_count::shared_count (inline) 2ms 0.0018% 86.96% 675ms 0.62% std::_Vector_base::_M_allocate (inline) 0 0% 86.96% 666ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 21ms 0.019% 86.98% 666ms 0.61% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.98% 623ms 0.57% vtkPolygon::New 2ms 0.0018% 86.98% 622ms 0.57% vtkPolygon::vtkPolygon 583ms 0.54% 87.51% 583ms 0.54% operator delete 8ms 0.0073% 87.52% 577ms 0.53% std::vector::_M_default_append (inline) 575ms 0.53% 88.05% 575ms 0.53% [libstdc++.so.6.0.33] 31ms 0.028% 88.08% 572ms 0.53% MutableElement::RegisterWithNodes (inline) 0 0% 88.08% 566ms 0.52% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 27ms 0.025% 88.10% 547ms 0.5% Node::AddElement