File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 78301ms, 88.08% of 88900ms total Dropped 1000 nodes (cum <= 444.50ms) flat flat% sum% cum cum% 0 0% 0% 88652ms 99.72% __libc_start_call_main 0 0% 0% 88652ms 99.72% __libc_start_main_impl 0 0% 0% 88652ms 99.72% _start 0 0% 0% 88634ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 88634ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 88634ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 88634ms 99.70% main 0 0% 0% 88601ms 99.66% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 88601ms 99.66% CxxTest::TestRunner::runTest (inline) 0 0% 0% 88601ms 99.66% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 3ms 0.0034% 0.0034% 88595ms 99.66% AbstractCellBasedSimulation::Solve 9ms 0.01% 0.013% 47040ms 52.91% OffLatticeSimulation::UpdateCellLocationsAndTopology 17ms 0.019% 0.033% 44028ms 49.53% ForwardEulerNumericalMethod::UpdateAllNodePositions 35ms 0.039% 0.072% 43035ms 48.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 299ms 0.34% 0.41% 33756ms 37.97% NagaiHondaForce::AddForceContribution 0 0% 0.41% 30678ms 34.51% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0011% 0.41% 18199ms 20.47% VertexBasedCellPopulation::Update 0 0% 0.41% 18089ms 20.35% MutableVertexMesh::ReMesh 7950ms 8.94% 9.35% 15202ms 17.10% Cylindrical2dVertexMesh::GetVectorFromAtoB 91ms 0.1% 9.45% 15034ms 16.91% Cell::ReadyToDivide 82ms 0.092% 9.55% 14143ms 15.91% NagaiHondaForce::GetAdhesionParameter 21ms 0.024% 9.57% 14140ms 15.91% AbstractPhaseBasedCellCycleModel::ReadyToDivide 67ms 0.075% 9.65% 12055ms 13.56% SimpleWntCellCycleModel::UpdateCellCyclePhase 352ms 0.4% 10.04% 11689ms 13.15% boost::numeric::ublas::c_vector::c_vector (partial-inline) 542ms 0.61% 10.65% 11448ms 12.88% std::__new_allocator::allocate (inline) 51ms 0.057% 10.71% 11052ms 12.43% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.71% 10976ms 12.35% std::allocator_traits::allocate (inline) 730ms 0.82% 11.53% 10783ms 12.13% operator new 0 0% 11.53% 10711ms 12.05% std::_Rb_tree::_M_create_node (inline) 220ms 0.25% 11.78% 10507ms 11.82% boost::numeric::ublas::vector_assign (inline) 0 0% 11.78% 10438ms 11.74% std::_Rb_tree::_M_get_node (inline) 3474ms 3.91% 15.69% 9758ms 10.98% __GI___libc_malloc 77ms 0.087% 15.77% 9267ms 10.42% AbstractCellProperty::IsSubType (inline) 0 0% 15.77% 9250ms 10.40% std::_Rb_tree::_Alloc_node::operator() (inline) 2156ms 2.43% 18.20% 9191ms 10.34% __dynamic_cast 100ms 0.11% 18.31% 8978ms 10.10% VertexBasedCellPopulation::GetDampingConstant 40ms 0.045% 18.35% 8977ms 10.10% AbstractTargetAreaModifier::UpdateTargetAreas 9ms 0.01% 18.36% 8922ms 10.04% AbstractCellBasedSimulation::DoCellBirth 40ms 0.045% 18.41% 8905ms 10.02% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 115ms 0.13% 18.54% 8410ms 9.46% MutableVertexMesh::CheckForIntersections 882ms 0.99% 19.53% 7918ms 8.91% std::_Rb_tree::_M_erase 0 0% 19.53% 7901ms 8.89% std::_Rb_tree::_M_drop_node (inline) 2184ms 2.46% 21.99% 7607ms 8.56% boost::numeric::ublas::indexing_vector_assign 284ms 0.32% 22.31% 7444ms 8.37% std::_Rb_tree::~_Rb_tree (inline) 79ms 0.089% 22.40% 7206ms 8.11% std::__new_allocator::deallocate (inline) 0 0% 22.40% 7189ms 8.09% std::allocator_traits::deallocate (inline) 0 0% 22.40% 7153ms 8.05% std::_Rb_tree::_M_put_node (inline) 0 0% 22.40% 7096ms 7.98% std::set::~set (inline) 63ms 0.071% 22.47% 6967ms 7.84% Cell::GetMutationState 1872ms 2.11% 24.57% 6924ms 7.79% __GI___libc_free 389ms 0.44% 25.01% 6700ms 7.54% std::map::operator[] (partial-inline) 382ms 0.43% 25.44% 6557ms 7.38% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 25.44% 6550ms 7.37% std::set::insert (inline) 52ms 0.058% 25.50% 6547ms 7.36% VertexBasedCellPopulation::GetLocationOfCellCentre 498ms 0.56% 26.06% 6307ms 7.09% VertexMesh::GetCentroidOfElement 458ms 0.52% 26.57% 6246ms 7.03% VertexMesh::ElementIncludesPoint 6ms 0.0067% 26.58% 6192ms 6.97% MutableVertexMesh::RemoveDeletedNodesAndElements 734ms 0.83% 27.41% 6043ms 6.80% std::_Rb_tree::_M_insert_ (inline) 116ms 0.13% 27.54% 5973ms 6.72% std::_Rb_tree::_Rb_tree (partial-inline) 581ms 0.65% 28.19% 5660ms 6.37% std::_Rb_tree::_M_copy (inline) 5623ms 6.33% 34.52% 5623ms 6.33% __strcmp_evex 13ms 0.015% 34.53% 5605ms 6.30% std::set::set (inline) 5547ms 6.24% 40.77% 5547ms 6.24% boost::numeric::ublas::c_vector::operator() 47ms 0.053% 40.82% 5534ms 6.22% std::set_intersection (inline) 272ms 0.31% 41.13% 5487ms 6.17% std::__set_intersection 822ms 0.92% 42.05% 5240ms 5.89% AbstractMesh::GetDistanceBetweenNodes 127ms 0.14% 42.20% 5026ms 5.65% SimpleWntCellCycleModel::GetWntLevel 4329ms 4.87% 47.07% 5000ms 5.62% _int_free 539ms 0.61% 47.67% 4907ms 5.52% std::_Rb_tree::_M_clone_node (inline) 114ms 0.13% 47.80% 4788ms 5.39% WntConcentration::GetWntLevel 546ms 0.61% 48.41% 4604ms 5.18% boost::numeric::ublas::c_vector::operator[] (inline) 3798ms 4.27% 52.69% 4558ms 5.13% _int_malloc 25ms 0.028% 52.71% 4552ms 5.12% MutableVertexMesh::RemoveDeletedNodes 2081ms 2.34% 55.06% 4511ms 5.07% __cxxabiv1::__si_class_type_info::__do_dyncast 1931ms 2.17% 57.23% 4468ms 5.03% std::_Rb_tree::_M_lower_bound (inline) 36ms 0.04% 57.27% 4441ms 5.00% EdgeHelper::RemoveDeletedEdges 0 0% 57.27% 4279ms 4.81% std::insert_iterator::operator= (inline) 11ms 0.012% 57.28% 4244ms 4.77% EdgeHelper::UpdateEdgesMapKey 0 0% 57.28% 4012ms 4.51% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 57.28% 3900ms 4.39% std::_Rb_tree::lower_bound (inline) 0 0% 57.28% 3900ms 4.39% std::map::lower_bound (inline) 32ms 0.036% 57.32% 3895ms 4.38% Cell::GetCellProliferativeType 94ms 0.11% 57.42% 3671ms 4.13% MutableElement::ResetIndex 3656ms 4.11% 61.53% 3656ms 4.11% boost::numeric::ublas::same_impl_ex 1ms 0.0011% 61.54% 3552ms 4.00% AbstractCellBasedSimulation::DoCellRemoval (inline) 65ms 0.073% 61.61% 3452ms 3.88% AbstractCellPopulation::GetCellUsingLocationIndex 2982ms 3.35% 64.96% 2982ms 3.35% [libchaste_cell_based.so] 157ms 0.18% 65.14% 2921ms 3.29% AbstractCellProperty::IsType (inline) 98ms 0.11% 65.25% 2861ms 3.22% Cell::SetCellProliferativeType 46ms 0.052% 65.30% 2748ms 3.09% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 111ms 0.12% 65.43% 2594ms 2.92% boost::detail::shared_count::~shared_count (inline) 0 0% 65.43% 2594ms 2.92% boost::shared_ptr::~shared_ptr (inline) 1ms 0.0011% 65.43% 2538ms 2.85% std::_Rb_tree::_M_insert_unique 623ms 0.7% 66.13% 2502ms 2.81% AbstractElement::GetNodeLocation 2416ms 2.72% 68.85% 2425ms 2.73% boost::detail::sp_counted_base::release 5ms 0.0056% 68.85% 2375ms 2.67% AbstractCellPopulation::Iterator::operator++ (inline) 183ms 0.21% 69.06% 2366ms 2.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 24ms 0.027% 69.08% 2360ms 2.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 69.08% 2207ms 2.48% boost::numeric::ublas::c_vector::assign (inline) 105ms 0.12% 69.20% 2111ms 2.37% boost::numeric::ublas::vector_binary::size (inline) 56ms 0.063% 69.27% 2090ms 2.35% std::_Rb_tree::erase 57ms 0.064% 69.33% 2041ms 2.30% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.011% 69.34% 2039ms 2.29% Cell::GetCellData 2035ms 2.29% 71.63% 2035ms 2.29% std::_Rb_tree::_S_right (inline) 297ms 0.33% 71.96% 2004ms 2.25% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 71.96% 2000ms 2.25% boost::numeric::ublas::c_vector::operator-= (inline) 230ms 0.26% 72.22% 1884ms 2.12% VertexMesh::GetAreaGradientOfElementAtNode 30ms 0.034% 72.26% 1881ms 2.12% CellPropertyCollection::HasProperty 0 0% 72.26% 1873ms 2.11% AbstractCellPopulation::WriteResultsToFiles 1855ms 2.09% 74.34% 1855ms 2.09% [libchaste_mesh.so] 0 0% 74.34% 1840ms 2.07% Cell::HasCellProperty (inline) 337ms 0.38% 74.72% 1804ms 2.03% AbstractCellProperty::IsSame 26ms 0.029% 74.75% 1751ms 1.97% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 305ms 0.34% 75.09% 1575ms 1.77% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 75ms 0.084% 75.18% 1570ms 1.77% VertexMesh::GetVolumeOfElement 0 0% 75.18% 1550ms 1.74% VertexBasedCellPopulation::WriteVtkResultsToFile 0 0% 75.18% 1545ms 1.74% VertexBasedCellPopulation::WriteCellVtkResultsToFile 2ms 0.0022% 75.18% 1514ms 1.70% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.18% 1514ms 1.70% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 143ms 0.16% 75.34% 1467ms 1.65% std::type_info::operator== (inline) 0 0% 75.34% 1461ms 1.64% std::_Rb_tree::_Auto_node::_Auto_node (inline) 120ms 0.13% 75.48% 1410ms 1.59% CellPropertyCollection::AddProperty 47ms 0.053% 75.53% 1407ms 1.58% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 75.53% 1394ms 1.57% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 75.53% 1385ms 1.56% VertexMeshWriter::WriteVtkUsingMesh 0 0% 75.53% 1352ms 1.52% tcache_get (inline) 1352ms 1.52% 77.05% 1352ms 1.52% tcache_get_n (inline) 64ms 0.072% 77.12% 1318ms 1.48% VertexMesh::GetSurfaceAreaOfElement 0 0% 77.12% 1306ms 1.47% OffLatticeSimulation::ApplyBoundaries 60ms 0.067% 77.19% 1274ms 1.43% std::_Rb_tree::_M_erase_aux (partial-inline) 60ms 0.067% 77.26% 1268ms 1.43% AbstractCellPopulation::GetLocationIndexUsingCell 1148ms 1.29% 78.55% 1148ms 1.29% std::_Rb_tree_increment 63ms 0.071% 78.62% 1131ms 1.27% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 140ms 0.16% 78.78% 1085ms 1.22% boost::numeric::ublas::vector_reference::operator() (inline) 53ms 0.06% 78.84% 1070ms 1.20% CellPropertyRegistry::Get 18ms 0.02% 78.86% 946ms 1.06% MutableElement::RegisterWithEdges (inline) 25ms 0.028% 78.89% 946ms 1.06% Node::RemoveElement 33ms 0.037% 78.92% 938ms 1.06% Edge::AddElement 935ms 1.05% 79.97% 935ms 1.05% [libstdc++.so.6.0.33] 14ms 0.016% 79.99% 933ms 1.05% boost::numeric::ublas::detail::expression_type_check (inline) 0 0% 79.99% 921ms 1.04% std::set::erase (inline) 561ms 0.63% 80.62% 906ms 1.02% std::_Rb_tree::equal_range (inline) 0 0% 80.62% 889ms 1.00% CellPropertyCollection::~CellPropertyCollection (inline) 144ms 0.16% 80.78% 884ms 0.99% boost::numeric::ublas::detail::equals 882ms 0.99% 81.78% 882ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 81.78% 860ms 0.97% boost::numeric::ublas::norm_2 (inline) 336ms 0.38% 82.15% 843ms 0.95% boost::numeric::ublas::vector_norm_2::apply 9ms 0.01% 82.16% 782ms 0.88% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.16% 781ms 0.88% boost::numeric::ublas::c_vector::assign_temporary (inline) 4ms 0.0045% 82.17% 781ms 0.88% boost::numeric::ublas::c_vector::swap (inline) 152ms 0.17% 82.34% 777ms 0.87% std::swap_ranges (inline) 772ms 0.87% 83.21% 772ms 0.87% Node::rGetLocation 2ms 0.0022% 83.21% 766ms 0.86% VertexMeshWriter::MakeVtkMesh 0 0% 83.21% 764ms 0.86% std::_Rb_tree::clear (inline) 573ms 0.64% 83.85% 755ms 0.85% CellPropertyCollection::GetProperty 0 0% 83.85% 750ms 0.84% std::__new_allocator::destroy (inline) 0 0% 83.85% 750ms 0.84% std::allocator_traits::destroy (inline) 0 0% 83.85% 749ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 748ms 0.84% 84.70% 748ms 0.84% tcache_put (inline) 0 0% 84.70% 744ms 0.84% std::map::clear (inline) 44ms 0.049% 84.74% 717ms 0.81% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.74% 659ms 0.74% boost::numeric::ublas::norm_inf (inline) 265ms 0.3% 85.04% 659ms 0.74% boost::numeric::ublas::vector_norm_inf::apply (inline) 51ms 0.057% 85.10% 655ms 0.74% std::less::operator() (inline) 87ms 0.098% 85.20% 646ms 0.73% std::_Rb_tree::find (inline) 0 0% 85.20% 625ms 0.7% std::iter_swap (inline) 625ms 0.7% 85.90% 625ms 0.7% std::swap (inline) 282ms 0.32% 86.22% 604ms 0.68% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 454ms 0.51% 86.73% 604ms 0.68% std::operator< (inline) 0 0% 86.73% 595ms 0.67% std::_Rb_tree::_Auto_node::_M_insert (inline) 17ms 0.019% 86.75% 595ms 0.67% std::_Rb_tree::_M_insert_node (inline) 59ms 0.066% 86.81% 570ms 0.64% MutableElement::GetNodeLocalIndex 0 0% 86.81% 566ms 0.64% vtkPolygon::New 0 0% 86.81% 566ms 0.64% vtkPolygon::vtkPolygon 543ms 0.61% 87.43% 543ms 0.61% std::vector::size (inline) 1ms 0.0011% 87.43% 537ms 0.6% std::_Vector_base::_M_allocate (inline) 0 0% 87.43% 535ms 0.6% std::map::find (inline) 13ms 0.015% 87.44% 485ms 0.55% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 87.44% 485ms 0.55% boost::numeric::ublas::vector::vector (inline) 12ms 0.013% 87.45% 482ms 0.54% MutableElement::RegisterWithNodes (inline) 471ms 0.53% 87.98% 471ms 0.53% Node::GetIndex 38ms 0.043% 88.03% 449ms 0.51% AbstractNumericalMethod::SafeNodePositionUpdate 45ms 0.051% 88.08% 448ms 0.5% Node::AddElement