File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 94737ms, 87.24% of 108599ms total Dropped 1124 nodes (cum <= 543ms) flat flat% sum% cum cum% 0 0% 0% 108236ms 99.67% __libc_start_call_main 0 0% 0% 108236ms 99.67% __libc_start_main_impl 0 0% 0% 108236ms 99.67% _start 0 0% 0% 108212ms 99.64% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 108212ms 99.64% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 108212ms 99.64% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 108212ms 99.64% main 0 0% 0% 108173ms 99.61% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 108173ms 99.61% CxxTest::TestRunner::runTest (inline) 0 0% 0% 108173ms 99.61% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0018% 0.0018% 108165ms 99.60% AbstractCellBasedSimulation::Solve 18ms 0.017% 0.018% 56277ms 51.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 14ms 0.013% 0.031% 53068ms 48.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 119ms 0.11% 0.14% 51955ms 47.84% AbstractNumericalMethod::ComputeForcesIncludingDamping 345ms 0.32% 0.46% 39952ms 36.79% NagaiHondaForce::AddForceContribution 1ms 0.00092% 0.46% 38641ms 35.58% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0018% 0.46% 23656ms 21.78% VertexBasedCellPopulation::Update 14868ms 13.69% 14.15% 23536ms 21.67% Cylindrical2dVertexMesh::GetVectorFromAtoB 1ms 0.00092% 14.15% 23507ms 21.65% MutableVertexMesh::ReMesh 77ms 0.071% 14.22% 18014ms 16.59% Cell::ReadyToDivide 49ms 0.045% 14.27% 16698ms 15.38% AbstractPhaseBasedCellCycleModel::ReadyToDivide 174ms 0.16% 14.43% 14330ms 13.20% SimpleWntCellCycleModel::UpdateCellCyclePhase 119ms 0.11% 14.54% 14030ms 12.92% CellPropertyCollection::GetPropertiesType (inline) 343ms 0.32% 14.85% 13964ms 12.86% NagaiHondaForce::GetAdhesionParameter 461ms 0.42% 15.28% 13862ms 12.76% boost::numeric::ublas::c_vector::c_vector (partial-inline) 301ms 0.28% 15.56% 12393ms 11.41% boost::numeric::ublas::vector_assign (inline) 3365ms 3.10% 18.65% 12198ms 11.23% __dynamic_cast 74ms 0.068% 18.72% 12114ms 11.15% AbstractCellProperty::IsSubType (inline) 153ms 0.14% 18.86% 11845ms 10.91% MutableVertexMesh::CheckForIntersections 93ms 0.086% 18.95% 11451ms 10.54% VertexBasedCellPopulation::GetDampingConstant 73ms 0.067% 19.02% 10790ms 9.94% AbstractTargetAreaModifier::UpdateTargetAreas 48ms 0.044% 19.06% 10702ms 9.85% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 29ms 0.027% 19.09% 10378ms 9.56% AbstractCellBasedSimulation::DoCellBirth 1239ms 1.14% 20.23% 9865ms 9.08% std::__new_allocator::allocate (inline) 447ms 0.41% 20.64% 9608ms 8.85% VertexMesh::GetNextEdgeGradientOfElementAtNode 2814ms 2.59% 23.23% 9291ms 8.56% boost::numeric::ublas::indexing_vector_assign 0 0% 23.23% 9235ms 8.50% std::allocator_traits::allocate (inline) 0 0% 23.23% 9128ms 8.41% std::_Rb_tree::_M_create_node (inline) 69ms 0.064% 23.29% 8876ms 8.17% Cell::GetMutationState 1203ms 1.11% 24.40% 8745ms 8.05% std::_Rb_tree::_M_erase 27ms 0.025% 24.43% 8708ms 8.02% VertexBasedCellPopulation::GetLocationOfCellCentre 787ms 0.72% 25.15% 8676ms 7.99% operator new 861ms 0.79% 25.94% 8662ms 7.98% VertexMesh::ElementIncludesPoint 0 0% 25.94% 8513ms 7.84% std::_Rb_tree::_M_get_node (inline) 480ms 0.44% 26.39% 8358ms 7.70% VertexMesh::GetCentroidOfElement 281ms 0.26% 26.65% 8019ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.65% 8016ms 7.38% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.65% 7952ms 7.32% std::_Rb_tree::_M_drop_node (inline) 220ms 0.2% 26.85% 7730ms 7.12% std::__new_allocator::deallocate (inline) 0 0% 26.85% 7708ms 7.10% std::allocator_traits::deallocate (inline) 2926ms 2.69% 29.54% 7656ms 7.05% __GI___libc_malloc 0 0% 29.54% 7649ms 7.04% std::_Rb_tree::_M_put_node (inline) 1554ms 1.43% 30.97% 7605ms 7.00% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 0 0% 30.97% 7595ms 6.99% std::set::~set (inline) 17ms 0.016% 30.99% 7468ms 6.88% MutableVertexMesh::RemoveDeletedNodesAndElements 7334ms 6.75% 37.74% 7334ms 6.75% __strcmp_avx2 2509ms 2.31% 40.05% 7306ms 6.73% __GI___libc_free 451ms 0.42% 40.47% 7235ms 6.66% std::map::operator[] (partial-inline) 237ms 0.22% 40.69% 6993ms 6.44% std::_Rb_tree::_Rb_tree (partial-inline) 744ms 0.69% 41.37% 6509ms 5.99% std::_Rb_tree::_M_copy (inline) 15ms 0.014% 41.39% 6491ms 5.98% std::set::set (inline) 129ms 0.12% 41.50% 6327ms 5.83% SimpleWntCellCycleModel::GetWntLevel 2884ms 2.66% 44.16% 6218ms 5.73% __cxxabiv1::__si_class_type_info::__do_dyncast 6134ms 5.65% 49.81% 6134ms 5.65% boost::numeric::ublas::c_vector::operator() 164ms 0.15% 49.96% 6123ms 5.64% WntConcentration::GetWntLevel 2400ms 2.21% 52.17% 5632ms 5.19% std::_Rb_tree::_M_lower_bound (inline) 741ms 0.68% 52.85% 5496ms 5.06% std::_Rb_tree::_M_clone_node (inline) 2026ms 1.87% 54.72% 5380ms 4.95% boost::numeric::ublas::c_vector::operator[] (inline) 22ms 0.02% 54.74% 5104ms 4.70% MutableVertexMesh::RemoveDeletedNodes 0 0% 54.74% 5044ms 4.64% std::set::insert (inline) 25ms 0.023% 54.76% 4893ms 4.51% EdgeHelper::RemoveDeletedEdges 4335ms 3.99% 58.75% 4781ms 4.40% _int_free 0 0% 58.75% 4625ms 4.26% std::_Rb_tree::lower_bound (inline) 0 0% 58.75% 4625ms 4.26% std::map::lower_bound (inline) 194ms 0.18% 58.93% 4620ms 4.25% MutableElement::ResetIndex 40ms 0.037% 58.97% 4608ms 4.24% EdgeHelper::UpdateEdgesMapKey 0 0% 58.97% 4602ms 4.24% AbstractCellBasedSimulation::DoCellRemoval (inline) 137ms 0.13% 59.09% 4280ms 3.94% AbstractCellPopulation::GetCellUsingLocationIndex 444ms 0.41% 59.50% 4222ms 3.89% std::_Rb_tree::_M_insert_ (inline) 113ms 0.1% 59.61% 4143ms 3.81% std::set_intersection (inline) 220ms 0.2% 59.81% 4030ms 3.71% std::__set_intersection 44ms 0.041% 59.85% 4019ms 3.70% Cell::GetCellProliferativeType 46ms 0.042% 59.89% 3951ms 3.64% AbstractCellProperty::IsType (inline) 3713ms 3.42% 63.31% 3713ms 3.42% boost::numeric::ublas::same_impl_ex 16ms 0.015% 63.33% 3458ms 3.18% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 73ms 0.067% 63.39% 3254ms 3.00% Cell::SetCellProliferativeType 2204ms 2.03% 65.42% 3176ms 2.92% _int_malloc 0 0% 65.42% 3110ms 2.86% std::insert_iterator::operator= (inline) 968ms 0.89% 66.31% 3060ms 2.82% AbstractElement::GetNodeLocation 41ms 0.038% 66.35% 2889ms 2.66% CellPropertyCollection::HasProperty 63ms 0.058% 66.41% 2887ms 2.66% std::_Rb_tree::erase 691ms 0.64% 67.05% 2848ms 2.62% AbstractCellProperty::IsSame 0 0% 67.05% 2782ms 2.56% Cell::HasCellProperty (inline) 8ms 0.0074% 67.05% 2719ms 2.50% std::_Rb_tree::_M_insert_unique_ (inline) 2696ms 2.48% 69.54% 2696ms 2.48% std::_Rb_tree::_S_right (inline) 0 0% 69.54% 2620ms 2.41% boost::numeric::ublas::c_vector::operator-= (inline) 206ms 0.19% 69.73% 2564ms 2.36% VertexMesh::GetAreaGradientOfElementAtNode 614ms 0.57% 70.29% 2550ms 2.35% boost::numeric::ublas::vector_binary::size (inline) 0 0% 70.29% 2533ms 2.33% boost::numeric::ublas::c_vector::assign (inline) 25ms 0.023% 70.31% 2513ms 2.31% Cell::GetCellData 0 0% 70.31% 2428ms 2.24% AbstractCellPopulation::WriteResultsToFiles 236ms 0.22% 70.53% 2369ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 87ms 0.08% 70.61% 2364ms 2.18% VertexMesh::GetVolumeOfElement 1ms 0.00092% 70.61% 2325ms 2.14% std::_Rb_tree::_M_insert_unique 42ms 0.039% 70.65% 2301ms 2.12% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 478ms 0.44% 71.09% 2157ms 1.99% std::type_info::operator== (inline) 31ms 0.029% 71.12% 2114ms 1.95% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0046% 71.12% 2025ms 1.86% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.12% 2025ms 1.86% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 5ms 0.0046% 71.13% 2019ms 1.86% AbstractCellPopulation::Iterator::operator++ (inline) 155ms 0.14% 71.27% 2007ms 1.85% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 71.27% 1985ms 1.83% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.00092% 71.27% 1965ms 1.81% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1910ms 1.76% 73.03% 1910ms 1.76% std::_Rb_tree_increment 70ms 0.064% 73.10% 1879ms 1.73% MutableVertexMesh::CheckForSwapsFromShortEdges 1246ms 1.15% 74.24% 1856ms 1.71% std::_Rb_tree::equal_range (inline) 0 0% 74.24% 1752ms 1.61% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.03% 74.27% 1635ms 1.51% VertexMesh::GetSurfaceAreaOfElement 22ms 0.02% 74.29% 1572ms 1.45% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 60ms 0.055% 74.35% 1517ms 1.40% Node::RemoveElement 7ms 0.0064% 74.36% 1461ms 1.35% std::set::erase (inline) 57ms 0.052% 74.41% 1418ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 74.41% 1408ms 1.30% boost::numeric::ublas::vector_binary::operator() (inline) 33ms 0.03% 74.44% 1400ms 1.29% AbstractCellPopulation::GetLocationIndexUsingCell 81ms 0.075% 74.51% 1386ms 1.28% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 0 0% 74.51% 1364ms 1.26% tcache_get (inline) 1364ms 1.26% 75.77% 1364ms 1.26% tcache_get_n (inline) 1305ms 1.20% 76.97% 1305ms 1.20% [libchaste_cell_based.so] 151ms 0.14% 77.11% 1294ms 1.19% CellPropertyCollection::AddProperty 0 0% 77.11% 1276ms 1.17% boost::numeric::ublas::norm_2 (inline) 558ms 0.51% 77.62% 1265ms 1.16% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 2ms 0.0018% 77.63% 1241ms 1.14% OffLatticeSimulation::ApplyBoundaries 68ms 0.063% 77.69% 1198ms 1.10% std::_Rb_tree::_M_erase_aux (partial-inline) 40ms 0.037% 77.72% 1191ms 1.10% CellPropertyRegistry::Get 96ms 0.088% 77.81% 1177ms 1.08% std::less::operator() (inline) 0 0% 77.81% 1114ms 1.03% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.0092% 77.82% 1114ms 1.03% boost::numeric::ublas::c_vector::swap (inline) 0 0% 77.82% 1112ms 1.02% std::_Rb_tree::_Auto_node::_Auto_node (inline) 79ms 0.073% 77.89% 1104ms 1.02% std::swap_ranges (inline) 5ms 0.0046% 77.90% 1103ms 1.02% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 1099ms 1.01% 78.91% 1099ms 1.01% std::_Rb_tree_insert_and_rebalance 877ms 0.81% 79.72% 1081ms 1% std::operator< (inline) 17ms 0.016% 79.73% 1055ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 23ms 0.021% 79.76% 1035ms 0.95% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 211ms 0.19% 79.95% 1030ms 0.95% boost::numeric::ublas::detail::equals 107ms 0.099% 80.05% 1027ms 0.95% std::_Rb_tree::find (inline) 0 0% 80.05% 1025ms 0.94% std::iter_swap (inline) 1025ms 0.94% 80.99% 1025ms 0.94% std::swap (inline) 1ms 0.00092% 80.99% 1011ms 0.93% std::_Rb_tree::clear (inline) 0 0% 80.99% 996ms 0.92% std::map::clear (inline) 137ms 0.13% 81.12% 989ms 0.91% boost::detail::shared_count::~shared_count (inline) 0 0% 81.12% 989ms 0.91% boost::shared_ptr::~shared_ptr (inline) 955ms 0.88% 82.00% 955ms 0.88% Node::rGetLocation 1ms 0.00092% 82.00% 861ms 0.79% std::map::find (inline) 853ms 0.79% 82.79% 853ms 0.79% std::vector::size (inline) 1ms 0.00092% 82.79% 849ms 0.78% VertexMeshWriter::MakeVtkMesh 101ms 0.093% 82.88% 823ms 0.76% boost::numeric::ublas::c_vector::operator= (inline) 21ms 0.019% 82.90% 814ms 0.75% MutableElement::RegisterWithEdges (inline) 793ms 0.73% 83.63% 810ms 0.75% boost::detail::sp_counted_base::release 32ms 0.029% 83.66% 796ms 0.73% Edge::AddElement 761ms 0.7% 84.36% 761ms 0.7% [libchaste_mesh.so] 0 0% 84.36% 749ms 0.69% boost::numeric::ublas::norm_inf (inline) 347ms 0.32% 84.68% 749ms 0.69% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 84.68% 739ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 166ms 0.15% 84.83% 735ms 0.68% MutableElement::GetNodeLocalIndex 404ms 0.37% 85.20% 730ms 0.67% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 1ms 0.00092% 85.20% 713ms 0.66% std::_Vector_base::_M_allocate (inline) 695ms 0.64% 85.84% 695ms 0.64% [libstdc++.so.6.0.33] 335ms 0.31% 86.15% 681ms 0.63% Edge::GetMapIndex 0 0% 86.15% 678ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 221ms 0.2% 86.36% 666ms 0.61% std::__new_allocator::construct (inline) 0 0% 86.36% 666ms 0.61% std::allocator_traits::construct (inline) 0 0% 86.36% 662ms 0.61% std::_Rb_tree::_Auto_node::_M_insert (inline) 23ms 0.021% 86.38% 662ms 0.61% std::_Rb_tree::_M_insert_node (inline) 180ms 0.17% 86.54% 658ms 0.61% boost::shared_ptr::shared_ptr (inline) 24ms 0.022% 86.57% 654ms 0.6% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.57% 654ms 0.6% boost::numeric::ublas::vector::vector (inline) 643ms 0.59% 87.16% 643ms 0.59% Node::GetIndex 0 0% 87.16% 615ms 0.57% std::_Rb_tree::_M_construct_node (inline) 12ms 0.011% 87.17% 604ms 0.56% std::vector::_M_default_append (inline) 1ms 0.00092% 87.17% 604ms 0.56% vtkPolygon::New 0 0% 87.17% 603ms 0.56% vtkPolygon::vtkPolygon 29ms 0.027% 87.20% 595ms 0.55% MutableElement::RegisterWithNodes (inline) 43ms 0.04% 87.24% 557ms 0.51% Node::AddElement